1KYO

YEAST CYTOCHROME BC1 COMPLEX WITH BOUND SUBSTRATE CYTOCHROME C

Structural Biology Knowledgebase: 1KYO SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.229

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1KYO

Classification: OXIDOREDUCTASE / ELECTRON TRANSPORT

Total Structure Weight: 507205.69

Macromolecule Entities
Molecule Chains Length Organism Details
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX CORE PROTEIN I A, L 430 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 27-457
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, M 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, N 385 Saccharomyces cerevisiae Mutation: D270V
Gene Name(s): COB CYTB Q0105
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C1, HEME PROTEIN D, O 248 Saccharomyces cerevisiae Fragment: RESIDUES 62-309
Gene Name(s): CYT1 CTC1 Gene View YOR065W YOR29-16
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
UBIQUINOL-CYTOCHROME C REDUCTASE IRON-SULFUR SUBUNIT E, P 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 F, Q 74 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 74-147
Mutation: V74D
Gene Name(s): QCR6 UCR6 YFR033C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
UBIQUINOL-CYTOCHROME C REDUCTASE COMPLEX 14 KD PROTEIN G, R 126 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 2-127
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 H, S 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, T 57 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Fragment: RESIDUES 1-57
Mutation: R55K
Gene Name(s): QCR9 UCR9 YGR183C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
HEAVY CHAIN (VH) OF FV-FRAGMENT J, U 127 Mus musculus Fragment: RESIDUES 1-127
LIGHT CHAIN (VL) OF FV-FRAGMENT K, V 107 Mus musculus Fragment: RESIDUES 1-107
CYTOCHROME C, ISO-1 W 108 Saccharomyces cerevisiae Mutation: K77X
Gene Name(s): CYC1 Gene View YJR048W J1653
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

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

Protein Name: Cytochrome bc1


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

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

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

E, P FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
M3L
Query on M3L
W L-PEPTIDE LINKING C9 H21 N2 O2 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.229
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 147.22 α = 90.00
b = 165.53 β = 104.19
c = 195.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-02-05
  • Released Date: 2002-03-06
  • Deposition author(s): Lange, C., Hunte, C.

Revision History

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