6NDK

Structure of ASLSufA6 A37.5 bound to the 70S A site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.64 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Importance of a tRNA anticodon loop modification and a conserved, noncanonical anticodon stem pairing intRNACGGProfor decoding

Nguyen, H.A., Hoffer, E.D., Dunham, C.M.

(2019) J Biol Chem 294: 5281-5291

  • DOI: https://doi.org/10.1074/jbc.RA119.007410

  • PubMed Abstract: 

    Modification of anticodon nucleotides allows tRNAs to decode multiple codons, expanding the genetic code. Additionally, modifications located in the anticodon loop, outside the anticodon itself, stabilize tRNA–codon interactions, increasing decoding fidelity. Anticodon loop nucleotide 37 is 3′ to the anticodon and, in tRNA CGG Pro , is methylated at the N1 position in its nucleobase (m 1 G37). The m 1 G37 modification in tRNA CGG Pro stabilizes its interaction with the codon and maintains the mRNA frame. However, it is unclear how m 1 G37 affects binding at the decoding center to both cognate and +1 slippery codons. Here, we show that the tRNA CGG Pro m 1 G37 modification is important for the association step during binding to a cognate CCG codon. In contrast, m 1 G37 prevented association with a slippery CCC-U or +1 codon. Similar analyses of frameshift suppressor tRNA SufA6 , a tRNA CGG Pro derivative containing an extra nucleotide in its anticodon loop that undergoes +1 frameshifting, reveal that m 1 G37 destabilizes interactions with both the cognate CCG and slippery codons. One reason for this destabilization is the disruption of a conserved U32·A38 nucleotide pairing in the anticodon stem through insertion of G37.5. Restoring the tRNA SufA6 U32·A37.5 pairing results in a high-affinity association on the slippery CCC-U codon. Further, an X-ray crystal structure of the 70S ribosome bound to tRNA SufA6 U32·A37.5 at 3.6 Å resolution shows a reordering of the anticodon loop consistent with the findings from the high-affinity measurements. Our results reveal how the tRNA modification at nucleotide 37 stabilizes interactions with the mRNA codon to preserve the mRNA frame.

    • Organizational Affiliation: 

    From the Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 and.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth QB],
EB [auth XB]		256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth QC],
FB [auth XC]		239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth QD],
GB [auth XD]		209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth QE],
HB [auth XE]		162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth QF],
IB [auth XF]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth QG],
JB [auth XG]		156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth QH],
KB [auth XH]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth QI],
LB [auth XI]		128Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth QJ],
MB [auth XJ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth QK],
NB [auth XK]		129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth QL],
OB [auth XL]		132Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth QM],
PB [auth XM]		126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14 type ZN [auth QN],
QB [auth XN]		61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth QO],
RB [auth XO]		89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth QP],
SB [auth XP]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth QQ],
TB [auth XQ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth QR],
UB [auth XR]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth QS],
VB [auth XS]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth QT],
WB [auth XT]		106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein ThxU [auth QU],
XB [auth XU]		27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2AA [auth RD],
DC [auth YD]		276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3BA [auth RE],
EC [auth YE]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4CA [auth RF],
FC [auth YF]		210Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5DA [auth RG],
GC [auth YG]		182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6EA [auth RH],
HC [auth YH]		180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9FA [auth RI],
IC [auth YI]		148Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13GA [auth RN],
JC [auth YN]		140Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14HA [auth RO],
KC [auth YO]		122Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15IA [auth RP],
LC [auth YP]		150Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16JA [auth RQ],
MC [auth YQ]		141Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17KA [auth RR],
NC [auth YR]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18LA [auth RS],
OC [auth YS]		112Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19MA [auth RT],
PC [auth YT]		146Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20NA [auth RU],
QC [auth YU]		118Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21OA [auth RV],
RC [auth YV]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PA [auth RW],
SC [auth YW]		113Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23QA [auth RX],
TC [auth YX]		96Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24RA [auth RY],
UC [auth YY]		110Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25SA [auth RZ],
VC [auth YZ]		206Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27TA [auth R0],
WC [auth Y0]		85Thermus thermophilus HB8Mutation(s): 0 
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UniProt GroupP60493
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28UA [auth R1],
XC [auth Y1]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29VA [auth R2],
YC [auth Y2]		72Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30WA [auth R3],
ZC [auth Y3]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31AD [auth Y4],
XA [auth R4]		71Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SJE1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32BD [auth Y5],
YA [auth R5]		60Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P80339 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33CD [auth Y6],
ZA [auth R6]		54Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P35871 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth R7],
DD [auth Y7]		49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth R8],
ED [auth Y8]		65Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SKU1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth R9],
FD [auth Y9]		37Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SHR2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S rRNAA [auth QA],
DB [auth XA]		1,521Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
P-site tRNAfMetV [auth QV],
YB [auth XV]		77Escherichia coli
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Entity ID: 23
MoleculeChains LengthOrganismImage
mRNAW [auth QX],
ZB [auth XX]		26Escherichia coli
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Entity ID: 24
MoleculeChains LengthOrganismImage
A-site ASLSufA6 A37.5AC [auth XY],
X [auth QY]		18Salmonella enterica subsp. enterica serovar Typhimurium
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Entity ID: 25
MoleculeChains LengthOrganismImage
23S rRNABC [auth YA],
Y [auth RA]		2,915Thermus thermophilus HB8
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Entity ID: 26
MoleculeChains LengthOrganismImage
5S rRNACC [auth YB],
Z [auth RB]		122Thermus thermophilus HB8
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Entity ID: 56
MoleculeChains LengthOrganismImage
tRNA acceptor end mimicGD [auth ZA],
HD [auth ZB]		3synthetic construct
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
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FI [auth QD],
JFA [auth XD]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
DAA [auth R4],
ECB [auth Y4],
JAA [auth R9],
NI [auth QN],
OFA [auth XN]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AAA [auth R0]
AAB [auth YA]
ABA [auth XA]
ABB [auth YD]
ACA [auth XA]
AAA [auth R0],
AAB [auth YA],
ABA [auth XA],
ABB [auth YD],
ACA [auth XA],
ACB [auth Y1],
ADA [auth XA],
AE [auth QA],
AEA [auth XA],
AF [auth QA],
AFA [auth XA],
AG [auth QA],
AGA [auth YA],
AH [auth QA],
AHA [auth YA],
AI [auth QA],
AIA [auth YA],
AJ [auth RA],
AJA [auth YA],
AK [auth RA],
AKA [auth YA],
AL [auth RA],
ALA [auth YA],
AM [auth RA],
AMA [auth YA],
AN [auth RA],
ANA [auth YA],
AO [auth RA],
AOA [auth YA],
AP [auth RA],
APA [auth YA],
AQ [auth RA],
AQA [auth YA],
AR [auth RA],
ARA [auth YA],
AS [auth RA],
ASA [auth YA],
AT [auth RA],
ATA [auth YA],
AU [auth RA],
AUA [auth YA],
AV [auth RA],
AVA [auth YA],
AW [auth RA],
AWA [auth YA],
AX [auth RA],
AXA [auth YA],
AY [auth RA],
AYA [auth YA],
AZ [auth RD],
AZA [auth YA],
BAA [auth R1],
BAB [auth YA],
BBA [auth XA],
BBB [auth YD],
BCA [auth XA],
BCB [auth Y1],
BDA [auth XA],
BE [auth QA],
BEA [auth XA],
BF [auth QA],
BFA [auth XA],
BG [auth QA],
BGA [auth YA],
BH [auth QA],
BHA [auth YA],
BI [auth QA],
BIA [auth YA],
BJ [auth RA],
BJA [auth YA],
BK [auth RA],
BKA [auth YA],
BL [auth RA],
BLA [auth YA],
BM [auth RA],
BMA [auth YA],
BN [auth RA],
BNA [auth YA],
BO [auth RA],
BOA [auth YA],
BP [auth RA],
BPA [auth YA],
BQ [auth RA],
BQA [auth YA],
BR [auth RA],
BRA [auth YA],
BS [auth RA],
BSA [auth YA],
BT [auth RA],
BTA [auth YA],
BU [auth RA],
BUA [auth YA],
BV [auth RA],
BVA [auth YA],
BW [auth RA],
BWA [auth YA],
BX [auth RA],
BXA [auth YA],
BY [auth RA],
BYA [auth YA],
BZ [auth RD],
BZA [auth YA],
CAA [auth R3],
CAB [auth YA],
CBA [auth XA],
CBB [auth YD],
CCA [auth XA],
CCB [auth Y1],
CDA [auth XA],
CE [auth QA],
CEA [auth XA],
CF [auth QA],
CFA [auth XA],
CG [auth QA],
CGA [auth YA],
CH [auth QA],
CHA [auth YA],
CI [auth QC],
CIA [auth YA],
CJ [auth RA],
CJA [auth YA],
CK [auth RA],
CKA [auth YA],
CL [auth RA],
CLA [auth YA],
CM [auth RA],
CMA [auth YA],
CN [auth RA],
CNA [auth YA],
CO [auth RA],
COA [auth YA],
CP [auth RA],
CPA [auth YA],
CQ [auth RA],
CQA [auth YA],
CR [auth RA],
CRA [auth YA],
CS [auth RA],
CSA [auth YA],
CT [auth RA],
CTA [auth YA],
CU [auth RA],
CUA [auth YA],
CV [auth RA],
CVA [auth YA],
CW [auth RA],
CWA [auth YA],
CX [auth RA],
CXA [auth YA],
CY [auth RA],
CYA [auth YA],
CZ [auth RD],
CZA [auth YA],
DAB [auth YA],
DBA [auth XA],
DBB [auth YD],
DCA [auth XA],
DCB [auth Y3],
DDA [auth XA],
DE [auth QA],
DEA [auth XA],
DF [auth QA],
DFA [auth XA],
DG [auth QA],
DGA [auth YA],
DH [auth QA],
DHA [auth YA],
DI [auth QD],
DIA [auth YA],
DJ [auth RA],
DJA [auth YA],
DK [auth RA],
DKA [auth YA],
DL [auth RA],
DLA [auth YA],
DM [auth RA],
DMA [auth YA],
DN [auth RA],
DNA [auth YA],
DO [auth RA],
DOA [auth YA],
DP [auth RA],
DPA [auth YA],
DQ [auth RA],
DQA [auth YA],
DR [auth RA],
DRA [auth YA],
DS [auth RA],
DSA [auth YA],
DT [auth RA],
DTA [auth YA],
DU [auth RA],
DUA [auth YA],
DV [auth RA],
DVA [auth YA],
DW [auth RA],
DWA [auth YA],
DX [auth RA],
DXA [auth YA],
DY [auth RA],
DYA [auth YA],
DZ [auth RD],
DZA [auth YA],
EAA [auth R5],
EAB [auth YA],
EBA [auth XA],
EBB [auth YD],
ECA [auth XA],
EDA [auth XA],
EE [auth QA],
EEA [auth XA],
EF [auth QA],
EFA [auth XA],
EG [auth QA],
EGA [auth YA],
EH [auth QA],
EHA [auth YA],
EI [auth QD],
EIA [auth YA],
EJ [auth RA],
EJA [auth YA],
EK [auth RA],
EKA [auth YA],
EL [auth RA],
ELA [auth YA],
EM [auth RA],
EMA [auth YA],
EN [auth RA],
ENA [auth YA],
EO [auth RA],
EOA [auth YA],
EP [auth RA],
EPA [auth YA],
EQ [auth RA],
EQA [auth YA],
ER [auth RA],
ERA [auth YA],
ES [auth RA],
ESA [auth YA],
ET [auth RA],
ETA [auth YA],
EU [auth RA],
EUA [auth YA],
EV [auth RA],
EVA [auth YA],
EW [auth RA],
EWA [auth YA],
EX [auth RA],
EXA [auth YA],
EY [auth RA],
EYA [auth YA],
EZ [auth RE],
EZA [auth YA],
FAA [auth R6],
FAB [auth YA],
FBA [auth XA],
FBB [auth YE],
FCA [auth XA],
FCB [auth Y5],
FDA [auth XA],
FE [auth QA],
FEA [auth XA],
FF [auth QA],
FFA [auth XA],
FG [auth QA],
FGA [auth YA],
FH [auth QA],
FHA [auth YA],
FIA [auth YA],
FJ [auth RA],
FJA [auth YA],
FK [auth RA],
FKA [auth YA],
FL [auth RA],
FLA [auth YA],
FM [auth RA],
FMA [auth YA],
FN [auth RA],
FNA [auth YA],
FO [auth RA],
FOA [auth YA],
FP [auth RA],
FPA [auth YA],
FQ [auth RA],
FQA [auth YA],
FR [auth RA],
FRA [auth YA],
FS [auth RA],
FSA [auth YA],
FT [auth RA],
FTA [auth YA],
FU [auth RA],
FUA [auth YA],
FV [auth RA],
FVA [auth YA],
FW [auth RA],
FWA [auth YA],
FX [auth RA],
FXA [auth YA],
FY [auth RA],
FYA [auth YA],
FZ [auth RE],
FZA [auth YA],
GAA [auth R7],
GAB [auth YA],
GBA [auth XA],
GBB [auth YE],
GCA [auth XA],
GCB [auth Y6],
GDA [auth XA],
GE [auth QA],
GEA [auth XA],
GF [auth QA],
GFA [auth XA],
GG [auth QA],
GGA [auth YA],
GH [auth QA],
GHA [auth YA],
GI [auth QE],
GIA [auth YA],
GJ [auth RA],
GJA [auth YA],
GK [auth RA],
GKA [auth YA],
GL [auth RA],
GLA [auth YA],
GM [auth RA],
GMA [auth YA],
GN [auth RA],
GNA [auth YA],
GO [auth RA],
GOA [auth YA],
GP [auth RA],
GPA [auth YA],
GQ [auth RA],
GQA [auth YA],
GR [auth RA],
GRA [auth YA],
GS [auth RA],
GSA [auth YA],
GT [auth RA],
GTA [auth YA],
GU [auth RA],
GUA [auth YA],
GV [auth RA],
GVA [auth YA],
GW [auth RA],
GWA [auth YA],
GX [auth RA],
GXA [auth YA],
GY [auth RA],
GYA [auth YA],
GZ [auth RE],
GZA [auth YA],
HAA [auth R8],
HAB [auth YA],
HBA [auth XA],
HBB [auth YE],
HCA [auth XA],
HCB [auth Y7],
HDA [auth XA],
HE [auth QA],
HEA [auth XA],
HF [auth QA],
HFA [auth XA],
HG [auth QA],
HGA [auth YA],
HH [auth QA],
HHA [auth YA],
HI [auth QE],
HIA [auth YA],
HJ [auth RA],
HJA [auth YA],
HK [auth RA],
HKA [auth YA],
HL [auth RA],
HLA [auth YA],
HM [auth RA],
HMA [auth YA],
HN [auth RA],
HNA [auth YA],
HO [auth RA],
HOA [auth YA],
HP [auth RA],
HPA [auth YA],
HQ [auth RA],
HQA [auth YA],
HR [auth RA],
HRA [auth YA],
HS [auth RA],
HSA [auth YA],
HT [auth RA],
HTA [auth YA],
HU [auth RA],
HUA [auth YA],
HV [auth RA],
HVA [auth YA],
HW [auth RA],
HWA [auth YA],
HX [auth RA],
HXA [auth YA],
HY [auth RA],
HYA [auth YA],
HZ [auth RE],
HZA [auth YA],
IAA [auth R9],
IAB [auth YA],
IBA [auth XA],
IBB [auth YE],
ICA [auth XA],
ICB [auth Y8],
ID [auth QA],
IDA [auth XA],
IE [auth QA],
IEA [auth XA],
IF [auth QA],
IFA [auth XD],
IG [auth QA],
IGA [auth YA],
IH [auth QA],
IHA [auth YA],
II [auth QL],
IIA [auth YA],
IJ [auth RA],
IJA [auth YA],
IK [auth RA],
IKA [auth YA],
IL [auth RA],
ILA [auth YA],
IM [auth RA],
IMA [auth YA],
IN [auth RA],
INA [auth YA],
IO [auth RA],
IOA [auth YA],
IP [auth RA],
IPA [auth YA],
IQ [auth RA],
IQA [auth YA],
IR [auth RA],
IRA [auth YA],
IS [auth RA],
ISA [auth YA],
IT [auth RA],
ITA [auth YA],
IU [auth RA],
IUA [auth YA],
IV [auth RA],
IVA [auth YA],
IW [auth RA],
IWA [auth YA],
IX [auth RA],
IXA [auth YA],
IY [auth RA],
IYA [auth YA],
IZ [auth RE],
IZA [auth YA],
JAB [auth YA],
JBA [auth XA],
JBB [auth YE],
JCA [auth XA],
JCB [auth Y9],
JD [auth QA],
JDA [auth XA],
JE [auth QA],
JEA [auth XA],
JF [auth QA],
JG [auth QA],
JGA [auth YA],
JH [auth QA],
JHA [auth YA],
JI [auth QL],
JIA [auth YA],
JJ [auth RA],
JJA [auth YA],
JK [auth RA],
JKA [auth YA],
JL [auth RA],
JLA [auth YA],
JM [auth RA],
JMA [auth YA],
JN [auth RA],
JNA [auth YA],
JO [auth RA],
JOA [auth YA],
JP [auth RA],
JPA [auth YA],
JQ [auth RA],
JQA [auth YA],
JR [auth RA],
JRA [auth YA],
JS [auth RA],
JSA [auth YA],
JT [auth RA],
JTA [auth YA],
JU [auth RA],
JUA [auth YA],
JV [auth RA],
JVA [auth YA],
JW [auth RA],
JWA [auth YA],
JX [auth RA],
JXA [auth YA],
JY [auth RA],
JYA [auth YA],
JZ [auth RF],
JZA [auth YA],
KAA [auth XA],
KAB [auth YA],
KBA [auth XA],
KBB [auth YE],
KCA [auth XA],
KD [auth QA],
KDA [auth XA],
KE [auth QA],
KEA [auth XA],
KF [auth QA],
KFA [auth XJ],
KG [auth QA],
KGA [auth YA],
KH [auth QA],
KHA [auth YA],
KI [auth QM],
KIA [auth YA],
KJ [auth RA],
KJA [auth YA],
KK [auth RA],
KKA [auth YA],
KL [auth RA],
KLA [auth YA],
KM [auth RA],
KMA [auth YA],
KN [auth RA],
KNA [auth YA],
KO [auth RA],
KOA [auth YA],
KP [auth RA],
KPA [auth YA],
KQ [auth RA],
KQA [auth YA],
KR [auth RA],
KRA [auth YA],
KS [auth RA],
KSA [auth YA],
KT [auth RA],
KTA [auth YA],
KU [auth RA],
KUA [auth YA],
KV [auth RA],
KVA [auth YA],
KW [auth RA],
KWA [auth YA],
KX [auth RA],
KXA [auth YA],
KY [auth RA],
KYA [auth YA],
KZ [auth RF],
KZA [auth YA],
LAA [auth XA],
LAB [auth YA],
LBA [auth XA],
LBB [auth YE],
LCA [auth XA],
LD [auth QA],
LDA [auth XA],
LE [auth QA],
LEA [auth XA],
LF [auth QA],
LFA [auth XK],
LG [auth QA],
LGA [auth YA],
LH [auth QA],
LHA [auth YA],
LI [auth QM],
LIA [auth YA],
LJ [auth RA],
LJA [auth YA],
LK [auth RA],
LKA [auth YA],
LL [auth RA],
LLA [auth YA],
LM [auth RA],
LMA [auth YA],
LN [auth RA],
LNA [auth YA],
LO [auth RA],
LOA [auth YA],
LP [auth RA],
LPA [auth YA],
LQ [auth RA],
LQA [auth YA],
LR [auth RA],
LRA [auth YA],
LS [auth RA],
LSA [auth YA],
LT [auth RA],
LTA [auth YA],
LU [auth RA],
LUA [auth YA],
LV [auth RA],
LVA [auth YA],
LW [auth RA],
LWA [auth YA],
LX [auth RA],
LXA [auth YA],
LY [auth RA],
LYA [auth YA],
LZ [auth RF],
LZA [auth YA],
MAA [auth XA],
MAB [auth YA],
MBA [auth XA],
MBB [auth YF],
MCA [auth XA],
MD [auth QA],
MDA [auth XA],
ME [auth QA],
MEA [auth XA],
MF [auth QA],
MFA [auth XK],
MG [auth QA],
MGA [auth YA],
MH [auth QA],
MHA [auth YA],
MI [auth QN],
MIA [auth YA],
MJ [auth RA],
MJA [auth YA],
MK [auth RA],
MKA [auth YA],
ML [auth RA],
MLA [auth YA],
MM [auth RA],
MMA [auth YA],
MN [auth RA],
MNA [auth YA],
MO [auth RA],
MOA [auth YA],
MP [auth RA],
MPA [auth YA],
MQ [auth RA],
MQA [auth YA],
MR [auth RA],
MRA [auth YA],
MS [auth RA],
MSA [auth YA],
MT [auth RA],
MTA [auth YA],
MU [auth RA],
MUA [auth YA],
MV [auth RA],
MVA [auth YA],
MW [auth RA],
MWA [auth YA],
MX [auth RA],
MXA [auth YA],
MY [auth RA],
MYA [auth YA],
MZ [auth RF],
MZA [auth YA],
NAA [auth XA],
NAB [auth YA],
NBA [auth XA],
NBB [auth YG],
NCA [auth XA],
ND [auth QA],
NDA [auth XA],
NE [auth QA],
NEA [auth XA],
NF [auth QA],
NFA [auth XN],
NG [auth QA],
NGA [auth YA],
NH [auth QA],
NHA [auth YA],
NIA [auth YA],
NJ [auth RA],
NJA [auth YA],
NK [auth RA],
NKA [auth YA],
NL [auth RA],
NLA [auth YA],
NM [auth RA],
NMA [auth YA],
NN [auth RA],
NNA [auth YA],
NO [auth RA],
NOA [auth YA],
NP [auth RA],
NPA [auth YA],
NQ [auth RA],
NQA [auth YA],
NR [auth RA],
NRA [auth YA],
NS [auth RA],
NSA [auth YA],
NT [auth RA],
NTA [auth YA],
NU [auth RA],
NUA [auth YA],
NV [auth RA],
NVA [auth YA],
NW [auth RA],
NWA [auth YA],
NX [auth RA],
NXA [auth YA],
NY [auth RA],
NYA [auth YA],
NZ [auth RF],
NZA [auth YA],
OAA [auth XA],
OAB [auth YA],
OBA [auth XA],
OBB [auth YP],
OCA [auth XA],
OD [auth QA],
ODA [auth XA],
OE [auth QA],
OEA [auth XA],
OF [auth QA],
OG [auth QA],
OGA [auth YA],
OH [auth QA],
OHA [auth YA],
OI [auth QN],
OIA [auth YA],
OJ [auth RA],
OJA [auth YA],
OK [auth RA],
OKA [auth YA],
OL [auth RA],
OLA [auth YA],
OM [auth RA],
OMA [auth YA],
ON [auth RA],
ONA [auth YA],
OO [auth RA],
OOA [auth YA],
OP [auth RA],
OPA [auth YA],
OQ [auth RA],
OQA [auth YA],
OR [auth RA],
ORA [auth YA],
OS [auth RA],
OSA [auth YA],
OT [auth RA],
OTA [auth YA],
OU [auth RA],
OUA [auth YA],
OV [auth RA],
OVA [auth YA],
OW [auth RA],
OWA [auth YA],
OX [auth RA],
OXA [auth YA],
OY [auth RA],
OYA [auth YA],
OZ [auth RN],
OZA [auth YA],
PAA [auth XA],
PAB [auth YB],
PBA [auth XA],
PBB [auth YP],
PCA [auth XA],
PD [auth QA],
PDA [auth XA],
PE [auth QA],
PEA [auth XA],
PF [auth QA],
PFA [auth XV],
PG [auth QA],
PGA [auth YA],
PH [auth QA],
PHA [auth YA],
PI [auth QO],
PIA [auth YA],
PJ [auth RA],
PJA [auth YA],
PK [auth RA],
PKA [auth YA],
PL [auth RA],
PLA [auth YA],
PM [auth RA],
PMA [auth YA],
PN [auth RA],
PNA [auth YA],
PO [auth RA],
POA [auth YA],
PP [auth RA],
PPA [auth YA],
PQ [auth RA],
PQA [auth YA],
PR [auth RA],
PRA [auth YA],
PS [auth RA],
PSA [auth YA],
PT [auth RA],
PTA [auth YA],
PU [auth RA],
PUA [auth YA],
PV [auth RA],
PVA [auth YA],
PW [auth RA],
PWA [auth YA],
PX [auth RA],
PXA [auth YA],
PY [auth RA],
PYA [auth YA],
PZ [auth RN],
PZA [auth YA],
QAA [auth XA],
QAB [auth YB],
QBA [auth XA],
QBB [auth YP],
QCA [auth XA],
QD [auth QA],
QDA [auth XA],
QE [auth QA],
QEA [auth XA],
QF [auth QA],
QFA [auth XX],
QG [auth QA],
QGA [auth YA],
QH [auth QA],
QHA [auth YA],
QI [auth QV],
QIA [auth YA],
QJ [auth RA],
QJA [auth YA],
QK [auth RA],
QKA [auth YA],
QL [auth RA],
QLA [auth YA],
QM [auth RA],
QMA [auth YA],
QN [auth RA],
QNA [auth YA],
QO [auth RA],
QOA [auth YA],
QP [auth RA],
QPA [auth YA],
QQ [auth RA],
QQA [auth YA],
QR [auth RA],
QRA [auth YA],
QS [auth RA],
QSA [auth YA],
QT [auth RA],
QTA [auth YA],
QU [auth RA],
QUA [auth YA],
QV [auth RA],
QVA [auth YA],
QW [auth RA],
QWA [auth YA],
QX [auth RA],
QXA [auth YA],
QY [auth RA],
QYA [auth YA],
QZ [auth RO],
QZA [auth YA],
RAA [auth XA],
RAB [auth YB],
RBA [auth XA],
RBB [auth YQ],
RCA [auth XA],
RD [auth QA],
RDA [auth XA],
RE [auth QA],
REA [auth XA],
RF [auth QA],
RFA [auth YA],
RG [auth QA],
RGA [auth YA],
RH [auth QA],
RHA [auth YA],
RI [auth QV],
RIA [auth YA],
RJ [auth RA],
RJA [auth YA],
RK [auth RA],
RKA [auth YA],
RL [auth RA],
RLA [auth YA],
RM [auth RA],
RMA [auth YA],
RN [auth RA],
RNA [auth YA],
RO [auth RA],
ROA [auth YA],
RP [auth RA],
RPA [auth YA],
RQ [auth RA],
RQA [auth YA],
RR [auth RA],
RRA [auth YA],
RS [auth RA],
RSA [auth YA],
RT [auth RA],
RTA [auth YA],
RU [auth RA],
RUA [auth YA],
RV [auth RA],
RVA [auth YA],
RW [auth RA],
RWA [auth YA],
RX [auth RA],
RXA [auth YA],
RY [auth RB],
RYA [auth YA],
RZ [auth RP],
RZA [auth YA],
SAA [auth XA],
SAB [auth YB],
SBA [auth XA],
SBB [auth YQ],
SCA [auth XA],
SD [auth QA],
SDA [auth XA],
SE [auth QA],
SEA [auth XA],
SF [auth QA],
SFA [auth YA],
SG [auth QA],
SGA [auth YA],
SH [auth QA],
SHA [auth YA],
SI [auth QV],
SIA [auth YA],
SJ [auth RA],
SJA [auth YA],
SK [auth RA],
SKA [auth YA],
SL [auth RA],
SLA [auth YA],
SM [auth RA],
SMA [auth YA],
SN [auth RA],
SNA [auth YA],
SO [auth RA],
SOA [auth YA],
SP [auth RA],
SPA [auth YA],
SQ [auth RA],
SQA [auth YA],
SR [auth RA],
SRA [auth YA],
SS [auth RA],
SSA [auth YA],
ST [auth RA],
STA [auth YA],
SU [auth RA],
SUA [auth YA],
SV [auth RA],
SVA [auth YA],
SW [auth RA],
SWA [auth YA],
SX [auth RA],
SXA [auth YA],
SY [auth RB],
SYA [auth YA],
SZ [auth RP],
SZA [auth YA],
TAA [auth XA],
TAB [auth YB],
TBA [auth XA],
TBB [auth YR],
TCA [auth XA],
TD [auth QA],
TDA [auth XA],
TE [auth QA],
TEA [auth XA],
TF [auth QA],
TFA [auth YA],
TG [auth QA],
TGA [auth YA],
TH [auth QA],
THA [auth YA],
TI [auth RA],
TIA [auth YA],
TJ [auth RA],
TJA [auth YA],
TK [auth RA],
TKA [auth YA],
TL [auth RA],
TLA [auth YA],
TM [auth RA],
TMA [auth YA],
TN [auth RA],
TNA [auth YA],
TO [auth RA],
TOA [auth YA],
TP [auth RA],
TPA [auth YA],
TQ [auth RA],
TQA [auth YA],
TR [auth RA],
TRA [auth YA],
TS [auth RA],
TSA [auth YA],
TT [auth RA],
TTA [auth YA],
TU [auth RA],
TUA [auth YA],
TV [auth RA],
TVA [auth YA],
TW [auth RA],
TWA [auth YA],
TX [auth RA],
TXA [auth YA],
TY [auth RB],
TYA [auth YA],
TZ [auth RQ],
TZA [auth YA],
UAA [auth XA],
UAB [auth YB],
UBA [auth XA],
UBB [auth YT],
UCA [auth XA],
UD [auth QA],
UDA [auth XA],
UE [auth QA],
UEA [auth XA],
UF [auth QA],
UFA [auth YA],
UG [auth QA],
UGA [auth YA],
UH [auth QA],
UHA [auth YA],
UI [auth RA],
UIA [auth YA],
UJ [auth RA],
UJA [auth YA],
UK [auth RA],
UKA [auth YA],
UL [auth RA],
ULA [auth YA],
UM [auth RA],
UMA [auth YA],
UN [auth RA],
UNA [auth YA],
UO [auth RA],
UOA [auth YA],
UP [auth RA],
UPA [auth YA],
UQ [auth RA],
UQA [auth YA],
UR [auth RA],
URA [auth YA],
US [auth RA],
USA [auth YA],
UT [auth RA],
UTA [auth YA],
UU [auth RA],
UUA [auth YA],
UV [auth RA],
UVA [auth YA],
UW [auth RA],
UWA [auth YA],
UX [auth RA],
UXA [auth YA],
UY [auth RB],
UYA [auth YA],
UZ [auth RR],
UZA [auth YA],
VAA [auth XA],
VAB [auth YB],
VBA [auth XA],
VBB [auth YU],
VCA [auth XA],
VD [auth QA],
VDA [auth XA],
VE [auth QA],
VEA [auth XA],
VF [auth QA],
VFA [auth YA],
VG [auth QA],
VGA [auth YA],
VH [auth QA],
VHA [auth YA],
VI [auth RA],
VIA [auth YA],
VJ [auth RA],
VJA [auth YA],
VK [auth RA],
VKA [auth YA],
VL [auth RA],
VLA [auth YA],
VM [auth RA],
VMA [auth YA],
VN [auth RA],
VNA [auth YA],
VO [auth RA],
VOA [auth YA],
VP [auth RA],
VPA [auth YA],
VQ [auth RA],
VQA [auth YA],
VR [auth RA],
VRA [auth YA],
VS [auth RA],
VSA [auth YA],
VT [auth RA],
VTA [auth YA],
VU [auth RA],
VUA [auth YA],
VV [auth RA],
VVA [auth YA],
VW [auth RA],
VWA [auth YA],
VX [auth RA],
VXA [auth YA],
VY [auth RB],
VYA [auth YA],
VZ [auth RV],
VZA [auth YA],
WAA [auth XA],
WAB [auth YB],
WBA [auth XA],
WBB [auth YV],
WCA [auth XA],
WD [auth QA],
WDA [auth XA],
WE [auth QA],
WEA [auth XA],
WF [auth QA],
WFA [auth YA],
WG [auth QA],
WGA [auth YA],
WH [auth QA],
WHA [auth YA],
WI [auth RA],
WIA [auth YA],
WJ [auth RA],
WJA [auth YA],
WK [auth RA],
WKA [auth YA],
WL [auth RA],
WLA [auth YA],
WM [auth RA],
WMA [auth YA],
WN [auth RA],
WNA [auth YA],
WO [auth RA],
WOA [auth YA],
WP [auth RA],
WPA [auth YA],
WQ [auth RA],
WQA [auth YA],
WR [auth RA],
WRA [auth YA],
WS [auth RA],
WSA [auth YA],
WT [auth RA],
WTA [auth YA],
WU [auth RA],
WUA [auth YA],
WV [auth RA],
WVA [auth YA],
WW [auth RA],
WWA [auth YA],
WX [auth RA],
WXA [auth YA],
WY [auth RB],
WYA [auth YA],
WZ [auth RW],
WZA [auth YA],
XAA [auth XA],
XAB [auth YD],
XBA [auth XA],
XBB [auth YW],
XCA [auth XA],
XD [auth QA],
XDA [auth XA],
XE [auth QA],
XEA [auth XA],
XF [auth QA],
XFA [auth YA],
XG [auth QA],
XGA [auth YA],
XH [auth QA],
XHA [auth YA],
XI [auth RA],
XIA [auth YA],
XJ [auth RA],
XJA [auth YA],
XK [auth RA],
XKA [auth YA],
XL [auth RA],
XLA [auth YA],
XM [auth RA],
XMA [auth YA],
XN [auth RA],
XNA [auth YA],
XO [auth RA],
XOA [auth YA],
XP [auth RA],
XPA [auth YA],
XQ [auth RA],
XQA [auth YA],
XR [auth RA],
XRA [auth YA],
XS [auth RA],
XSA [auth YA],
XT [auth RA],
XTA [auth YA],
XU [auth RA],
XUA [auth YA],
XV [auth RA],
XVA [auth YA],
XW [auth RA],
XWA [auth YA],
XX [auth RA],
XXA [auth YA],
XY [auth RB],
XYA [auth YA],
XZ [auth RX],
XZA [auth YA],
YAA [auth XA],
YAB [auth YD],
YBA [auth XA],
YBB [auth YX],
YCA [auth XA],
YD [auth QA],
YDA [auth XA],
YE [auth QA],
YEA [auth XA],
YF [auth QA],
YFA [auth YA],
YG [auth QA],
YGA [auth YA],
YH [auth QA],
YHA [auth YA],
YI [auth RA],
YIA [auth YA],
YJ [auth RA],
YJA [auth YA],
YK [auth RA],
YKA [auth YA],
YL [auth RA],
YLA [auth YA],
YM [auth RA],
YMA [auth YA],
YN [auth RA],
YNA [auth YA],
YO [auth RA],
YOA [auth YA],
YP [auth RA],
YPA [auth YA],
YQ [auth RA],
YQA [auth YA],
YR [auth RA],
YRA [auth YA],
YS [auth RA],
YSA [auth YA],
YT [auth RA],
YTA [auth YA],
YU [auth RA],
YUA [auth YA],
YV [auth RA],
YVA [auth YA],
YW [auth RA],
YWA [auth YA],
YX [auth RA],
YXA [auth YA],
YY [auth RB],
YYA [auth YA],
YZ [auth RZ],
YZA [auth YA],
ZAA [auth XA],
ZAB [auth YD],
ZBA [auth XA],
ZBB [auth Y0],
ZCA [auth XA],
ZD [auth QA],
ZDA [auth XA],
ZE [auth QA],
ZEA [auth XA],
ZF [auth QA],
ZFA [auth YA],
ZG [auth QA],
ZGA [auth YA],
ZH [auth QA],
ZHA [auth YA],
ZI [auth RA],
ZIA [auth YA],
ZJ [auth RA],
ZJA [auth YA],
ZK [auth RA],
ZKA [auth YA],
ZL [auth RA],
ZLA [auth YA],
ZM [auth RA],
ZMA [auth YA],
ZN [auth RA],
ZNA [auth YA],
ZO [auth RA],
ZOA [auth YA],
ZP [auth RA],
ZPA [auth YA],
ZQ [auth RA],
ZQA [auth YA],
ZR [auth RA],
ZRA [auth YA],
ZS [auth RA],
ZSA [auth YA],
ZT [auth RA],
ZTA [auth YA],
ZU [auth RA],
ZUA [auth YA],
ZV [auth RA],
ZVA [auth YA],
ZW [auth RA],
ZWA [auth YA],
ZX [auth RA],
ZXA [auth YA],
ZY [auth RD],
ZYA [auth YA],
ZZ [auth R0],
ZZA [auth YA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
0TD
Query on 0TD		L [auth QL],
OB [auth XL]		L-PEPTIDE LINKINGC5 H9 N O4 SASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.64 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.91α = 90
b = 445.91β = 90
c = 617.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
Cootmodel building
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM093278
National Science Foundation (NSF, United States)United StatesCHE 1808711

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection