1YQ3

Avian respiratory complex ii with oxaloacetate and ubiquinone

Structural Biology Knowledgebase: 1YQ3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1YQ3

Classification: OXIDOREDUCTASE

Total Structure Weight: 128423.17

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 11 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
UQ
Query on UQ

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

A FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer
 
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
 
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

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

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

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

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

A MALATE LIKE INTERMEDIATE
C4 H4 O5
QFBHYOKSQPPXHZ-UWTATZPHSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

Unknown ligand
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.175
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.01 α = 90.00
b = 84.40 β = 90.00
c = 289.50 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., Cobessi, D., Tung, E.Y., Berry, E.A.

Revision History

  • 2016-02-17
    Type: Non-polymer description | Details: corrected BHG to JZR, corrected SF4 chirality
  • 2014-10-29
    Type: Non-polymer description | Details: Update ligand name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update