2EIK

Cadmium ion binding structure of bovine heart cytochrome C oxidase in the fully reduced state

Structural Biology Knowledgebase: 2EIK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2EIK

Classification: OXIDOREDUCTASE

Total Structure Weight: 443434.47

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 147 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX4I1 Gene View COX4
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c oxidase polypeptide Va E, R 109 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX5A Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c oxidase polypeptide Vb F, S 98 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX5B Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c oxidase polypeptide VIa-heart G, T 85 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 85 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 73 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX6C Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c oxidase polypeptide VIIa-heart J, W 59 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 VIIb K, X 56 Bos taurus EC#: 1.9.3.1 IUBMB
Gene Name(s): COX7B Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c oxidase polypeptide VIIc L, Y 47 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 VIII-heart M, Z 46 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 14 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CDL
Query on CDL

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

A, L, N, Q, Y TRISTEAROYLGLYCEROL
TRIACYLGLYCEROL (Synonym)
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEA
Query on HEA

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

C, G, P, T (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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PSC
Query on PSC

B, O (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9- OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA- 4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4- OXIDE
PHOSPHATIDYLCHOLINE, 2-LINOLEOYL-1-PALMITOYL- SN-GYCEROL-3-PHOSPHOCHOLINE (Synonym)
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PGV
Query on PGV

A, C, N, 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMU
Query on DMU

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

B, C, J, O, P, W CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CUA
Query on CUA

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

A, C, E, N, P CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

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

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

A, N MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A, N SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 3 Unique
ID Chains Type Formula 2D Diagram Parent
FME
Query on FME
A, B, N, O L-PEPTIDE LINKING C6 H11 N O3 S MET
TPO
Query on TPO
G, T L-PEPTIDE LINKING C4 H10 N O6 P THR
SAC
Query on SAC
I, V L-PEPTIDE LINKING C5 H9 N O4 SER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.199
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 183.32 α = 90.00
b = 206.52 β = 90.00
c = 178.16 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-03-13
  • Released Date: 2007-05-29
  • Deposition author(s): Muramoto, K., Hirata, K., Shinzawa-Itoh, K., Yoko-O, S., Yamashita, E., Aoyama, H., Tsukihara, T., Yoshikawa, S.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4