1PPJ

Bovine cytochrome bc1 complex with stigmatellin and antimycin

Structural Biology Knowledgebase: 1PPJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.224

Literature

Macromolecules
Sequence Display for 1PPJ

Classification: OXIDOREDUCTASE

Total Structure Weight: 488126.19

Macromolecule Entities
Molecule Chains Length Organism Details
Ubiquinol-cytochrome C reductase complex core protein I, mitochondrial A, N 446 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRC1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquinol-cytochrome C reductase complex core protein 2, mitochondrial B, O 439 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRC2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b C, P 379 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): MT-CYB Gene View COB CYTB MTCYB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c1, heme protein, mitochondrial D, Q 241 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): CYC1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial E, R 196 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRFS1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquinol-cytochrome C reductase complex 14 kDa protein F, S 110 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRB Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquinol-cytochrome C reductase complex ubiquinone-binding protein QP-C G, T 81 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRQ Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquinol-cytochrome C reductase complex 11 kDa protein H, U 78 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRH Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquinol-cytochrome C reductase iron-sulfur subunit, mitochondrial I, V 78 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCRFS1 Gene View
Ubiquinol-cytochrome C reductase complex 7.2 kDa protein J, W 62 Bos taurus EC#: 1.10.2.2 IUBMB
Gene Name(s): UQCR10 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Super Complexes (Respirasome)

Protein Name: Electron Transport Chain (ETC) Super Complex comprised of ETC complexes I, III, and IV, tight respirasome


Small Molecules
Ligands 11 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CDL
Query on CDL

D, G, P, T CARDIOLIPIN
3'-SN-GLYCEROL, (Synonym)
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEE
Query on PEE

C, D, P, 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)
HEC
Query on HEC

D, Q HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
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)
ANY
Query on ANY

C, P 2-METHYL-BUTYRIC ACID 3-(3-FORMYLAMINO-2- HYDROXY-BENZOYLAMINO)-8-HEPTYL-2,6-DIMETHYL- 4,9-DIOXO-[1,5]DIOXONAN-7-YL ESTER
ANTIMYCIN (Synonym)
C29 H42 N2 O9
BSSBWOQOFMLGAF-GMRPKDQWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SMA
Query on SMA

C, P STIGMATELLIN A
C30 H42 O7
UZHDGDDPOPDJGM-WPPYOTIYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BHG
Query on BHG

A, C, D, F, P, R, S 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)
FES
Query on FES

E, R FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, C, F, P, S PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

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

A, C, G, O, P AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
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: 0.260
  • R-Value Work: 0.224
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 128.53 α = 90.00
b = 168.75 β = 90.00
c = 231.53 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-16
  • Released Date: 2004-07-20
  • Deposition author(s): Huang, L.S., Cobessi, D., Tung, E.Y., Berry, E.A.

Revision History

  • 2014-10-29
    Type: Other | Details: Update ligand name
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4