1YQ4

Avian respiratory complex ii with 3-nitropropionate and ubiquinone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.202

Literature

Macromolecules
Sequence Display for 1YQ4

Classification: OXIDOREDUCTASE

Total Structure Weight: 128409.16

Macromolecule Entities
Molecule Chains Length Organism Details
Succinate dehydrogenase flavoprotein subunit A 621 Gallus gallus EC#: 1.3.5.1 IUBMB
Gene Name(s): SDHA Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
succinate dehydrogenase Ip subunit B 252 Gallus gallus EC#: 1.3.5.1 IUBMB
Gene Name(s): SDHB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT C 141 Gallus gallus EC#: 1.3.5.1 IUBMB
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
SUCCINATE DEHYDROGENASE CYTOCHROME B, SMALL SUBUNIT D 103 Gallus gallus EC#: 1.3.5.1 IUBMB
Gene Name(s): SDHD Gene View RCJMB04_23p7
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex II

Protein Name: Succinate:ubiquinone oxidoreductase (SQR, Complex II; chicken heart) w. carboxin inhibitor


Small Molecules
Ligands 10 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UQ
Query on UQ

C Coenzyme Q10, (2Z,6E,10Z,14E,18E,22E,26Z)- isomer
C59 H90 O4
ACTIUHUUMQJHFO-RECDIHICSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FAD
Query on FAD

A FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEE
Query on PEE

C, D 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine
DOPE (Synonym)
C41 H83 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

C PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

B IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
F3S
Query on F3S

B FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
JZR
Query on JZR

C hexyl beta-D-glucopyranoside
C12 H24 O6
JVAZJLFFSJARQM-RMPHRYRLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FES
Query on FES

B FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3NP
Query on 3NP

A 3-NITROPROPANOIC ACID
C3 H5 N O4
WBLZUCOIBUDNBV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.202
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 69.59 α = 90.00
b = 83.49 β = 90.00
c = 288.59 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-02-01
  • Released Date: 2005-12-20
  • Deposition author(s): Huang, L., Sun, G., Cobessi, D., Wang, A., Shen, J.T., Tung, E.Y., Anderson, V.E., Berry, E.A.

Revision History

  • 2007-10-16
    Type: Version format compliance
  • 2011-07-13
    Type: Derived calculations, Version format compliance
  • 2014-10-29
    Type: Non-polymer description
  • 2016-02-17
    Type: Non-polymer description