2Y69

Bovine heart cytochrome c oxidase re-refined with molecular oxygen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 2Y69

Classification: ELECTRON TRANSPORT

Total Structure Weight: 464224.97

Macromolecule Entities
Molecule Chains Length Organism Details
CYTOCHROME C OXIDASE SUBUNIT 1 A, N 514 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): MT-CO1 Gene View COI COXI MTCO1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 2 B, O 227 Bos taurus EC#: 3.1.3.95 IUBMB
Gene Name(s): MT-CO2 Gene View COII COXII MTCO2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 3 C, P 261 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): MT-CO3 Gene View COIII COXIII MTCO3
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 4 ISOFORM 1 D, Q 169 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX4I1 Gene View COX4
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 5A E, R 152 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX5A Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 5B F, S 129 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX5B Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE POLYPEPTIDE 6A2 G, T 97 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX6A2 Gene View COX6A
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT VIB ISOFORM 1 H, U 86 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX6B1 Gene View COX6B
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE POLYPEPTIDE VIC I, V 74 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX6C Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE POLYPEPTIDE 7A1 J, W 80 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX7A1 Gene View COX7A COX7AH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE POLYPEPTIDE 7B K, X 80 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX7B Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE SUBUNIT 7C L, Y 63 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX7C Gene View COX7CP1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CYTOCHROME C OXIDASE POLYPEPTIDE 8H M, Z 70 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX8B COX8H
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Electron Transport Chain Complexes: Complex IV (Cytochrome C Oxidase)

Protein Name: Cytochrome C Oxidase, aa3


Small Molecules
Ligands 10 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEA
Query on HEA

A, N HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEK
Query on PEK

C, P (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}- 1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)- ICOSA-5,8,11,14-TETRAENOATE
PHOSPHATIDYLETHANOLAMINE, 2-ARACHIDONOYL- 1-STEAROYL-SN-GLYCEROL-3-PHOSPHOETHANOLAMINE (Synonym)
C43 H78 N O8 P
ANRKEHNWXKCXDB-BHFWLYLHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGV
Query on PGV

C, P (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}- 1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC- 11-ENOATE
PHOSPHATIDYLGLYCEROL, 2-VACCENOYL-1-PALMITOYL- SN-GLYCEROL-3-PHOSPHOGLYCEROL (Synonym)
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMU
Query on DMU

M, Z DECYL-BETA-D-MALTOPYRANOSIDE
DECYLMALTOSIDE (Synonym)
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CHD
Query on CHD

A, C, G, N, P, T CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CUA
Query on CUA

B, O DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

F, S ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CU
Query on CU

A, N COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OXY
Query on OXY

A, N OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, N MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TPO
Query on TPO
G, T L-PEPTIDE LINKING C4 H10 N O6 P THR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.211
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 183.70 α = 90.00
b = 206.99 β = 90.00
c = 178.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-20
  • Released Date: 2011-02-23
  • Deposition author(s): Kaila, V.R.I., Oksanen, E., Goldman, A., Verkhovsky, M.I., Sundholm, D., Wikstrom, M.

Revision History

  • Version 1_0: 2011-02-23

    Type: Initial release

  • Version 1_1: 2012-04-25

    Type: Database references, Other, Version format compliance

  • Version 1_2: 2015-02-04

    Type: Atomic model, Derived calculations, Other