2WQY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Re-refinement Note

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

  • 2FBW - determined by Huang, L.S., Sun, G., Cobessi, D., Wang, A.C., Shen, J.T., Tung, E.Y., Anderson, V.E., Berry, E.A.  

Literature

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

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

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT
A, N
621Gallus gallusMutation(s): 0 
Gene Names: SDHA
EC: 1.3.5.1
Find proteins for Q9YHT1 (Gallus gallus)
Go to Gene View: SDHA
Go to UniProtKB:  Q9YHT1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE IP SUBUNIT
B, O
252Gallus gallusMutation(s): 0 
Gene Names: SDHB
EC: 1.3.5.1
Find proteins for Q9YHT2 (Gallus gallus)
Go to Gene View: SDHB
Go to UniProtKB:  Q9YHT2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT
C, P
141Gallus gallusMutation(s): 0 
EC: 1.3.5.1
Find proteins for D0VWW3 (Gallus gallus)
Go to UniProtKB:  D0VWW3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT
D, Q
103Gallus gallusMutation(s): 0 
Gene Names: SDHD
Find proteins for Q5ZIS0 (Gallus gallus)
Go to Gene View: SDHD
Go to UniProtKB:  Q5ZIS0
Small Molecules
Ligands 12 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A, B, N, O
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

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Download CCD File 
B, O
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

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Download CCD File 
B, O
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A, N
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
B, C, O, P
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BHG
Query on BHG

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C, P
2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,4,5-TRIOL
C12 H24 O6
JVAZJLFFSJARQM-YBXAARCKSA-N
 Ligand Interaction
AZI
Query on AZI

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A
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
B, O
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
OAA
Query on OAA

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A, N
OXALOACETATE ION
C4 H3 O5
KHPXUQMNIQBQEV-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
C, P
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
CBE
Query on CBE

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Download CCD File 
C, P
2-METHYL-N-PHENYL-5,6-DIHYDRO-1,4-OXATHIINE-3-CARBOXAMIDE
5,6-DIHYDRO-2-METHYL-1,4-OXATHIIN-3-CARBOXANILID; CARBOXIN; CBX
C12 H13 N O2 S
GYSSRZJIHXQEHQ-UHFFFAOYSA-N
 Ligand Interaction
PEE
Query on PEE

Download SDF File 
Download CCD File 
D, Q
1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
DOPE
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 118.700α = 90.00
b = 200.753β = 90.06
c = 67.631γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2012-04-25
    Type: Database references, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2015-05-20
    Type: Non-polymer description
  • Version 1.3: 2019-01-30
    Type: Data collection, Experimental preparation
  • Version 1.4: 2019-02-06
    Type: Data collection, Experimental preparation