1YIT

Crystal Structure Of Virginiamycin M and S Bound To The 50S Ribosomal Subunit Of Haloarcula Marismortui


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structures of Mlsbk Antibiotics Bound to Mutated Large Ribosomal Subunits Provide a Structural Explanation for Resistance.

TU, D.Blaha, G.Moore, P.B.Steitz, T.A.

(2005) Cell 121: 257

  • DOI: https://doi.org/10.1016/j.cell.2005.02.005
  • Primary Citation of Related Structures:  
    1YHQ, 1YI2, 1YIJ, 1YIT, 1YJ9, 1YJN, 1YJW

  • PubMed Abstract: 

    Crystal structures of H. marismortui large ribosomal subunits containing the mutation G2099A (A2058 in E. coli) with erythromycin, azithromycin, clindamycin, virginiamycin S, and telithromycin bound explain why eubacterial ribosomes containing the mutation A2058G are resistant to them. Azithromycin binds almost identically to both G2099A and wild-type subunits, but the erythromycin affinity increases by more than 10(4)-fold, implying that desolvation of the N2 of G2099 accounts for the low wild-type affinity for macrolides. All macrolides bind similarly to the H. marismortui subunit, but their binding differs significantly from what has been reported in the D. radioidurans subunit. The synergy in the binding of streptogramins A and B appears to result from a reorientation of the base of A2103 (A2062, E. coli) that stacks between them. The structure of large subunit containing a three residue deletion mutant of L22 shows a change in the L22 structure and exit tunnel shape that illuminates its macrolide resistance phenotype.


  • Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L37EB [auth 1]57Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P32410 
Go to UniProtKB:  P32410
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32410
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L39EC [auth 2]50Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P22452 
Go to UniProtKB:  P22452
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22452
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L44ED [auth 3]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P32411 
Go to UniProtKB:  P32411
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32411
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
VIRGINIAMYCIN S1E [auth 8]7Streptomyces virginiaeMutation(s): 0 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2PG [auth A]240Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P20276 
Go to UniProtKB:  P20276
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20276
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3PH [auth B]338Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P20279 
Go to UniProtKB:  P20279
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20279
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4EI [auth C]246Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12735 
Go to UniProtKB:  P12735
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12735
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5PJ [auth D]177Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14124 
Go to UniProtKB:  P14124
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14124
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6PK [auth E]178Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14135 
Go to UniProtKB:  P14135
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14135
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L7AEL [auth F]120Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12743 
Go to UniProtKB:  P12743
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12743
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOGM [auth G]348Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P15825 
Go to UniProtKB:  P15825
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15825
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10EN [auth H]177Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60617 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P60617 
Go to UniProtKB:  P60617
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60617
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11PO [auth I]162Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14122 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14122 
Go to UniProtKB:  P14122
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14122
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13PP [auth J]145Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P29198 
Go to UniProtKB:  P29198
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29198
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14PQ [auth K]132Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P22450 
Go to UniProtKB:  P22450
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22450
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15PR [auth L]165Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12737 
Go to UniProtKB:  P12737
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12737
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15ES [auth M]195Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P60618 
Go to UniProtKB:  P60618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60618
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18PT [auth N]187Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14123 
Go to UniProtKB:  P14123
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14123
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18EU [auth O]116Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12733 
Go to UniProtKB:  P12733
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12733
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19EV [auth P]149Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14119 
Go to UniProtKB:  P14119
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14119
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21EW [auth Q]96Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12734 
Go to UniProtKB:  P12734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12734
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22PX [auth R]155Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P10970 
Go to UniProtKB:  P10970
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10970
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23PY [auth S]85Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12732 
Go to UniProtKB:  P12732
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12732
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24PZ [auth T]120Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P10972 
Go to UniProtKB:  P10972
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10972
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24EAA [auth U]66Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14116 
Go to UniProtKB:  P14116
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14116
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29PBA [auth V]71Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P10971 
Go to UniProtKB:  P10971
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10971
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30PCA [auth W]154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P14121 
Go to UniProtKB:  P14121
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14121
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31EDA [auth X]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P18138 
Go to UniProtKB:  P18138
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18138
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32EEA [auth Y]241Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12736 
Go to UniProtKB:  P12736
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12736
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L37AEFA [auth Z]83Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P60619 
Go to UniProtKB:  P60619
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60619
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNAA [auth 0]2,922Haloarcula marismortui
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAF [auth 9]122Haloarcula marismortui
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VIR
Query on VIR

Download Ideal Coordinates CCD File 
RH [auth 0]VIRGINIAMYCIN M1
C28 H35 N3 O7
DAIKHDNSXMZDCU-FQTGFAPKSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
AJ [auth U],
DJ [auth Z],
SH [auth 1],
SI [auth O],
VH [auth 3]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
LE [auth 0]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CI [auth A]
CJ [auth Y]
FI [auth B]
HH [auth 0]
IH [auth 0]
CI [auth A],
CJ [auth Y],
FI [auth B],
HH [auth 0],
IH [auth 0],
JH [auth 0],
JI [auth J],
KH [auth 0],
KI [auth J],
LH [auth 0],
LI [auth J],
MH [auth 0],
NH [auth 0],
OH [auth 0],
OI [auth L],
PH [auth 0],
QH [auth 0],
QI [auth M],
RI [auth N],
TI [auth O],
WH [auth 3],
XI [auth R]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 0]
AC [auth 0]
AD [auth 0]
AE [auth 0]
AI [auth A]
AB [auth 0],
AC [auth 0],
AD [auth 0],
AE [auth 0],
AI [auth A],
BB [auth 0],
BC [auth 0],
BD [auth 0],
BE [auth 0],
BJ [auth Y],
CB [auth 0],
CC [auth 0],
CD [auth 0],
CE [auth 0],
DB [auth 0],
DC [auth 0],
DD [auth 0],
DE [auth 0],
DI [auth B],
EB [auth 0],
EC [auth 0],
ED [auth 0],
EE [auth 0],
EI [auth B],
FB [auth 0],
FC [auth 0],
FD [auth 0],
FE [auth 0],
GA [auth 0],
GB [auth 0],
GC [auth 0],
GD [auth 0],
GE [auth 0],
HA [auth 0],
HB [auth 0],
HC [auth 0],
HD [auth 0],
HE [auth 0],
IA [auth 0],
IB [auth 0],
IC [auth 0],
ID [auth 0],
IE [auth 0],
JA [auth 0],
JB [auth 0],
JC [auth 0],
JD [auth 0],
JE [auth 0],
KA [auth 0],
KB [auth 0],
KC [auth 0],
KD [auth 0],
KE [auth 0],
LA [auth 0],
LB [auth 0],
LC [auth 0],
LD [auth 0],
MA [auth 0],
MB [auth 0],
MC [auth 0],
MD [auth 0],
MI [auth K],
NA [auth 0],
NB [auth 0],
NC [auth 0],
ND [auth 0],
OA [auth 0],
OB [auth 0],
OC [auth 0],
OD [auth 0],
PA [auth 0],
PB [auth 0],
PC [auth 0],
PD [auth 0],
QA [auth 0],
QB [auth 0],
QC [auth 0],
QD [auth 0],
RA [auth 0],
RB [auth 0],
RC [auth 0],
RD [auth 0],
SA [auth 0],
SB [auth 0],
SC [auth 0],
SD [auth 0],
TA [auth 0],
TB [auth 0],
TC [auth 0],
TD [auth 0],
TH [auth 2],
UA [auth 0],
UB [auth 0],
UC [auth 0],
UD [auth 0],
UH [auth 3],
VA [auth 0],
VB [auth 0],
VC [auth 0],
VD [auth 0],
WA [auth 0],
WB [auth 0],
WC [auth 0],
WD [auth 0],
XA [auth 0],
XB [auth 0],
XC [auth 0],
XD [auth 0],
XH [auth 9],
YA [auth 0],
YB [auth 0],
YC [auth 0],
YD [auth 0],
ZA [auth 0],
ZB [auth 0],
ZC [auth 0],
ZD [auth 0],
ZI [auth T]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
AF [auth 0]
AG [auth 0]
AH [auth 0]
BF [auth 0]
BG [auth 0]
AF [auth 0],
AG [auth 0],
AH [auth 0],
BF [auth 0],
BG [auth 0],
BH [auth 0],
BI [auth A],
CF [auth 0],
CG [auth 0],
CH [auth 0],
DF [auth 0],
DG [auth 0],
DH [auth 0],
EF [auth 0],
EG [auth 0],
EH [auth 0],
FF [auth 0],
FG [auth 0],
FH [auth 0],
GF [auth 0],
GG [auth 0],
GH [auth 0],
GI [auth C],
HF [auth 0],
HG [auth 0],
HI [auth H],
IF [auth 0],
IG [auth 0],
II [auth J],
JF [auth 0],
JG [auth 0],
KF [auth 0],
KG [auth 0],
LF [auth 0],
LG [auth 0],
ME [auth 0],
MF [auth 0],
MG [auth 0],
NE [auth 0],
NF [auth 0],
NG [auth 0],
NI [auth L],
OE [auth 0],
OF [auth 0],
OG [auth 0],
PE [auth 0],
PF [auth 0],
PG [auth 0],
PI [auth M],
QE [auth 0],
QF [auth 0],
QG [auth 0],
RE [auth 0],
RF [auth 0],
RG [auth 0],
SE [auth 0],
SF [auth 0],
SG [auth 0],
TE [auth 0],
TF [auth 0],
TG [auth 0],
UE [auth 0],
UF [auth 0],
UG [auth 0],
UI [auth Q],
VE [auth 0],
VF [auth 0],
VG [auth 0],
VI [auth R],
WE [auth 0],
WF [auth 0],
WG [auth 0],
WI [auth R],
XE [auth 0],
XF [auth 0],
XG [auth 0],
YE [auth 0],
YF [auth 0],
YG [auth 0],
YH [auth 9],
YI [auth S],
ZE [auth 0],
ZF [auth 0],
ZG [auth 0],
ZH [auth 9]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MEA
Query on MEA
E [auth 8]L-PEPTIDE LINKINGC10 H13 N O2PHE
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.583α = 90
b = 299.758β = 90
c = 573.56γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-26
    Type: Initial release
  • Version 1.1: 2011-06-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Changes: Other