1EZV

STRUCTURE OF THE YEAST CYTOCHROME BC1 COMPLEX CO-CRYSTALLIZED WITH AN ANTIBODY FV-FRAGMENT

Structural Biology Knowledgebase: 1EZV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.222

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1EZV

Classification: OXIDOREDUCTASE / ELECTRON TRANSPORT

Total Structure Weight: 247126.69

Macromolecule Entities
Molecule Chains Length Organism Details
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I A 430 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 24-457
Mutation: ΔS45, E152D
Gene Name(s): COR1 QCR1 YBL045C YBL0403
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN 2 B 352 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 17-368
Gene Name(s): QCR2 COR2 UCR2 YPR191W P9677.6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME B C 385 Saccharomyces cerevisiae Gene Name(s): COB CYTB Q0105
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C1 D 245 Saccharomyces cerevisiae Fragment: RESIDUES 62-306
Gene Name(s): CYT1 CTC1 Gene View YOR065W YOR29-16
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT E 185 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 31-215
Gene Name(s): RIP1 YEL024W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 17 KD PROTEIN H 74 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 74-147
Gene Name(s): QCR6 UCR6 YFR033C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN F 125 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 3-127
Gene Name(s): QCR7 CRO1 UCR7 YDR529C D9719.32
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX UBIQUINONE-BINDING PROTEIN QP-C G 93 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 2-94
Gene Name(s): QCR8 YJL166W J0526
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 7.3 KD PROTEIN I 55 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 4-58
Gene Name(s): QCR9 UCR9 YGR183C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HEAVY CHAIN (VH) OF FV-FRAGMENT X 127 Mus musculus Gene Name(s): Ighv3-6 Gm16932
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
LIGHT CHAIN (VL) OF FV-FRAGMENT Y 107 Mus musculus Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex III (Cytochrome bc1)

Protein Name: Cytochrome bc1


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

C, D PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UQ6
Query on UQ6

C 5-(3,7,11,15,19,23-HEXAMETHYL-TETRACOSA-2,6,10,14,18,22- HEXAENYL)-2,3-DIMETHOXY-6-METHYL-BENZENE- 1,4-DIOL
C39 H60 O4
DYOSCPIQEYRQEO-XQCASOQKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SMA
Query on SMA

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

E FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.254
  • R-Value Work: 0.222
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 214.47 α = 90.00
b = 163.92 β = 117.50
c = 147.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-05-12
  • Released Date: 2001-05-16
  • Deposition author(s): Hunte, C., Koepke, J., Lange, C., Rossmanith, T., Michel, H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4