1P84

HDBT inhibited Yeast Cytochrome bc1 Complex

Structural Biology Knowledgebase: 1P84 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.228

Literature

Macromolecules
Sequence Display for 1P84

Classification: OXIDOREDUCTASE

Total Structure Weight: 252732.55

Macromolecule Entities
Molecule Chains Length Organism Details
Ubiquinol-cytochrome C reductase complex core protein I A 431 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Mutation: E153D
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
Gene Name(s): QCR2 COR2 UCR2 YPR191W P9677.6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
cytochrome b C 385 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Mutation: I122T
Gene Name(s): COB CYTB Q0105
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c1, heme protein D 246 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
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
Gene Name(s): RIP1 YEL024W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquinol-cytochrome C reductase complex 17 kDa protein F 74 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Gene Name(s): QCR6 UCR6 YFR033C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquinol-cytochrome C reductase complex 14 kDa protein G 125 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
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 93 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Ubiquinol-cytochrome C reductase complex 7.3 kDa protein I 55 Saccharomyces cerevisiae EC#: 1.10.2.2 IUBMB
Gene Name(s): QCR9 UCR9 YGR183C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Heavy Chain (Vh) Of Fv-Fragment J 127 Mus musculus
Light Chain (Vl) Of Fv-Fragment K 107 Mus musculus

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

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

Protein Name: Cytochrome bc1


Small Molecules
Ligands 9 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CDL
Query on CDL

D CARDIOLIPIN
3'-SN-GLYCEROL, (Synonym)
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PC1
Query on PC1

D 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
3-SN-PHOSPHATIDYLCHOLINE (Synonym)
C44 H88 N O8 P
NRJAVPSFFCBXDT-HUESYALOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3PE
Query on 3PE

C 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
3-SN-PHOSPHATIDYLETHANOLAMINE (Synonym)
C41 H82 N O8 P
LVNGJLRDBYCPGB-LDLOPFEMSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
3PH
Query on 3PH

A, D 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
PHOSPHATIDIC ACID (Synonym)
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

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

A UNDECYL-MALTOSIDE
UNDECYL-BETA-D-MALTOPYRANOSIDE (Synonym)
C23 H44 O11
UYEMNFYVTFDKRG-ZNGNCRBCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DBT
Query on DBT

C 5-HEPTYL-6-HYDROXY-1,3-BENZOTHIAZOLE-4,7- DIONE
C14 H17 N O3 S
CAPIRLKYURUNFL-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FES
Query on FES

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.228
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 215.00 α = 90.00
b = 165.09 β = 117.33
c = 147.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-06
  • Released Date: 2003-07-29
  • Deposition author(s): Palsdottir, H., Lojero, C.G., Trumpower, B.L., Hunte, C.

Revision History

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