ISDA

Deposition Date 2009-12-16

Release Date 2010-03-09

Last Version Date 2023-11-01

Entry Detail

PDB ID:

3ABK

Keywords:

OXIDOREDUCTASE

Title:

Bovine heart cytochrome c oxidase at the NO-bound fully reduced state (50K)

Biological Source:

Source Organism:

Bos taurus (Taxon ID: 9913)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.00 Å

R-Value Free:

0.21

R-Value Work:

0.18

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 1
Gene (Uniprot):MT-CO1
Chain IDs:A, N
Chain Length:514
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P00396 Pfam ID:PF00115 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 2
Gene (Uniprot):MT-CO2
Chain IDs:B, O
Chain Length:227
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P68530 Pfam ID:PF02790, PF00116

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 3
Gene (Uniprot):MT-CO3
Chain IDs:C, P
Chain Length:261
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P00415 Pfam ID:PF00510 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 4 isoform 1
Gene (Uniprot):COX4I1
Chain IDs:D, Q
Chain Length:147
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P00423 Pfam ID:PF02936 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 5A
Gene (Uniprot):COX5A
Chain IDs:E, R
Chain Length:109
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P00426 Pfam ID:PF02284 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 5B
Gene (Uniprot):COX5B
Chain IDs:F, S
Chain Length:98
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P00428 Pfam ID:PF01215 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6A2
Gene (Uniprot):COX6A2
Chain IDs:G, T
Chain Length:85
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P07471 Pfam ID:PF02046 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6B1
Gene (Uniprot):COX6B1
Chain IDs:H, U
Chain Length:85
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P00429 Pfam ID:PF02297 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 6C
Gene (Uniprot):COX6C
Chain IDs:I, V
Chain Length:73
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P04038 Pfam ID:PF02937 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase polypeptide 7A1
Gene (Uniprot):COX7A1
Chain IDs:J, W
Chain Length:59
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P07470 Pfam ID:PF02238 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 7B
Gene (Uniprot):COX7B
Chain IDs:K, X
Chain Length:56
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P13183 Pfam ID:PF05392 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 7C
Gene (Uniprot):COX7C
Chain IDs:L, Y
Chain Length:47
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P00430 Pfam ID:PF02935 EC:7.1.1.9

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Cytochrome c oxidase subunit 8B
Gene (Uniprot):COX8B
Chain IDs:M, Z
Chain Length:46
Number of Molecules:2
Biological Source:Bos taurus

UniProt ID:P10175 Pfam ID:PF02285 EC:7.1.1.9

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details
FME	A	MET	N-FORMYLMETHIONINE
SAC	I	SER	N-ACETYL-SERINE
TPO	G	THR	PHOSPHOTHREONINE

Ligand Molecules

CDL

CHD

CUA

DMU

HEA

PEK

PGV

PSC

TGL

UNX

Primary Citation

X-ray structure of the NO-bound Cu(B) in bovine cytochrome c oxidase

Ohta, K, Muramoto, K, Shinzawa-Itoh, K, Yamashita, E, Yoshikawa, S, Tsukihara, T.Show

Acta Crystallogr.,Sect.F 66 251 253 (2010)

PMID: 20208153 DOI: 10.1107/S1744309109055109

Abstact

The X-ray crystallographic structure of nitric oxide-treated bovine heart cytochrome c oxidase (CcO) in the fully reduced state has been determined at 50 K under light illumination. In this structure, nitric oxide (NO) is bound to the CcO oxygen-reduction site, which consists of haem and a Cu atom (the haem a(3)-Cu(B) site). Electron density for the NO molecule was observed close to Cu(B). The refined structure indicates that NO is bound to Cu(B) in a side-on manner.

Legend

Protein

Chemical

Disease

Primary Citation of related structures