2WQY

Remodelling of carboxin binding to the Q-site of avian respiratory complex II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 2FBW


Literature

Remodelling of Carboxin Binding to the Q-Site of Avian Respiratory Complex II

Ruprecht, J.Iwata, S.Cecchini, G.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNITA,
E [auth N]
621Gallus gallusMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9YHT1 (Gallus gallus)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YHT1
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE IP SUBUNITB,
F [auth O]
252Gallus gallusMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q9YHT2 (Gallus gallus)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9YHT2
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNITC,
G [auth P]
141Gallus gallusMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for D0VWW3 (Gallus gallus)
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UniProt GroupD0VWW3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNITD,
H [auth Q]
103Gallus gallusMutation(s): 0 
EC: 1.3.5.1
Membrane Entity: Yes 
UniProt
Find proteins for Q5ZIS0 (Gallus gallus)
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Entity Groups  
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UniProt GroupQ5ZIS0
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  • Reference Sequence
Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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AC [auth N],
M [auth A]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
PEE
Query on PEE

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PB [auth D],
TD [auth Q]
1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEM
Query on HEM

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ID [auth P],
XA [auth C]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
SF4
Query on SF4

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BD [auth O],
OA [auth B]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S

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CD [auth O],
PA [auth B]
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
BHG
Query on BHG

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KD [auth P],
WA [auth C]
hexyl beta-D-galactopyranoside
C12 H24 O6
JVAZJLFFSJARQM-YBXAARCKSA-N
CBE
Query on CBE

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JD [auth P],
YA [auth C]
2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE
C12 H13 N O2 S
GYSSRZJIHXQEHQ-UHFFFAOYSA-N
FES
Query on FES

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AD [auth O],
NA [auth B]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
OAA
Query on OAA

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BC [auth N],
N [auth A]
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
GOL
Query on GOL

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HD [auth O],
LD [auth P],
OB [auth C],
VA [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
AZI
Query on AZI

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L [auth A]AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
K
Query on K

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HA [auth B],
K [auth A],
XC [auth O],
ZB [auth N]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
UNL
Query on UNL

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AA [auth A]
AB [auth C]
BA [auth A]
BB [auth C]
CA [auth A]
AA [auth A],
AB [auth C],
BA [auth A],
BB [auth C],
CA [auth A],
CB [auth C],
CC [auth N],
DA [auth A],
DB [auth C],
DC [auth N],
DD [auth O],
EA [auth A],
EB [auth C],
EC [auth N],
ED [auth O],
FA [auth A],
FB [auth C],
FC [auth N],
FD [auth O],
GA [auth A],
GB [auth C],
GC [auth N],
GD [auth O],
HB [auth C],
HC [auth N],
I [auth A],
IA [auth B],
IB [auth C],
IC [auth N],
J [auth A],
JA [auth B],
JB [auth C],
JC [auth N],
KA [auth B],
KB [auth C],
KC [auth N],
LA [auth B],
LB [auth C],
LC [auth N],
MA [auth B],
MB [auth C],
MC [auth N],
MD [auth P],
NB [auth C],
NC [auth N],
ND [auth P],
O [auth A],
OC [auth N],
OD [auth P],
P [auth A],
PC [auth N],
PD [auth P],
Q [auth A],
QA [auth B],
QB [auth D],
QC [auth N],
QD [auth P],
R [auth A],
RA [auth B],
RB [auth D],
RC [auth N],
RD [auth P],
S [auth A],
SA [auth B],
SB [auth D],
SC [auth N],
SD [auth P],
T [auth A],
TA [auth B],
TB [auth D],
TC [auth N],
U [auth A],
UA [auth B],
UB [auth D],
UC [auth N],
UD [auth Q],
V [auth A],
VB [auth D],
VC [auth N],
VD [auth Q],
W [auth A],
WB [auth D],
WC [auth N],
WD [auth Q],
X [auth A],
XB [auth D],
XD [auth Q],
Y [auth A],
YB [auth D],
YC [auth O],
YD [auth Q],
Z [auth A],
ZA [auth C],
ZC [auth O],
ZD [auth Q]
Unknown ligand
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.7α = 90
b = 200.753β = 90.06
c = 67.631γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2012-04-25
    Changes: Database references, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2015-05-20
    Changes: Non-polymer description
  • Version 1.3: 2019-01-30
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2019-02-06
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Derived calculations, Other, Structure summary
  • Version 2.0: 2023-12-20
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary