2FBW

Avian respiratory complex II with carboxin bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 2FBW

Classification: OXIDOREDUCTASE

Total Structure Weight: 254444.63

Macromolecule Entities
Molecule Chains Length Organism Details
Succinate dehydrogenase flavoprotein subunit A, N 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, O 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, P 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, Q 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: mpstruc | 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 13 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FAD
Query on FAD

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

D, Q 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, P 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, O IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
F3S
Query on F3S

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

C, P 2-HEXYLOXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN- 3,4,5-TRIOL
C12 H24 O6
JVAZJLFFSJARQM-YBXAARCKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CBE
Query on CBE

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 (Synonym)
C12 H13 N O2 S
GYSSRZJIHXQEHQ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FES
Query on FES

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

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

B, C, O, P GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AZI
Query on AZI

A AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A, B, N, O POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNL
Query on UNL

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.187
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 118.70 α = 90.00
b = 200.75 β = 90.06
c = 67.63 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-12-10
  • Released Date: 2005-12-20
  • Deposition author(s): Huang, L.S., Sun, G., Cobessi, D., Wang, A.C., Shen, J.T., Tung, E.Y., Anderson, V.E., Berry, E.A.

Revision History

  • Version 1_0: 2005-12-20

    Type: Initial release

  • Version 1_1: 2008-05-01

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Non-polymer description, Version format compliance

  • Version 1_3: 2014-10-29

    Type: Non-polymer description