3ABK

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


Literature

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.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 251-253

  • DOI: https://doi.org/10.1107/S1744309109055109
  • Primary Citation of Related Structures:  
    3ABK

  • PubMed Abstract: 

    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.

    • Organizational Affiliation: 

    Institute for Protein Research, Osaka University, OLABB, 6-2-6 Furuedai, Suita, Osaka 565-0874, Japan.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
A, N
514Bos taurusMutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00396 (Bos taurus)
Explore P00396 
Go to UniProtKB:  P00396
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00396
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2
B, O
227Bos taurusMutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P68530 (Bos taurus)
Explore P68530 
Go to UniProtKB:  P68530
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68530
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3
C, P
261Bos taurusMutation(s): 0 
EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P00415 (Bos taurus)
Explore P00415 
Go to UniProtKB:  P00415
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00415
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1
D, Q
147Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00423 (Bos taurus)
Explore P00423 
Go to UniProtKB:  P00423
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00423
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A
E, R
109Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00426 (Bos taurus)
Explore P00426 
Go to UniProtKB:  P00426
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00426
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B
F, S
98Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00428 (Bos taurus)
Explore P00428 
Go to UniProtKB:  P00428
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00428
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2
G, T
85Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P07471 (Bos taurus)
Explore P07471 
Go to UniProtKB:  P07471
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07471
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1
H, U
85Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00429 (Bos taurus)
Explore P00429 
Go to UniProtKB:  P00429
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00429
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P04038 (Bos taurus)
Explore P04038 
Go to UniProtKB:  P04038
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04038
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase polypeptide 7A1
J, W
59Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P07470 (Bos taurus)
Explore P07470 
Go to UniProtKB:  P07470
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07470
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B
K, X
56Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P13183 (Bos taurus)
Explore P13183 
Go to UniProtKB:  P13183
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13183
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C
L, Y
47Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P00430 (Bos taurus)
Explore P00430 
Go to UniProtKB:  P00430
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00430
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B
M, Z
46Bos taurusMutation(s): 0 
EC: 1.9.3.1
Membrane Entity: Yes 
UniProt
Find proteins for P10175 (Bos taurus)
Explore P10175 
Go to UniProtKB:  P10175
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10175
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL
Download Ideal Coordinates CCD File 
SA [auth C],
TB [auth P],
XA [auth G],
ZB [auth T]		CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL
Download Ideal Coordinates CCD File 
AB [auth L]
CC [auth Y]
IB [auth N]
JA [auth B]
NB [auth O]
AB [auth L],
CC [auth Y],
IB [auth N],
JA [auth B],
NB [auth O],
VA [auth D]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA
Query on HEA
Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
CB [auth N],
DB [auth N]		HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK
Download Ideal Coordinates CCD File 
OA [auth C]
PA [auth C]
RB [auth P]
XB [auth T]
YA [auth G]
OA [auth C],
PA [auth C],
RB [auth P],
XB [auth T],
YA [auth G],
YB [auth T]
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
C43 H78 N O8 P
ANRKEHNWXKCXDB-BHFWLYLHSA-N
PSC
Query on PSC
Download Ideal Coordinates CCD File 
KA [auth B],
VB [auth R]		(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
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O
PGV
Query on PGV
Download Ideal Coordinates CCD File 
AC [auth U]
GA [auth A]
HA [auth A]
JB [auth N]
KB [auth N]
AC [auth U],
GA [auth A],
HA [auth A],
JB [auth N],
KB [auth N],
QA [auth C],
RA [auth C],
SB [auth P]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
DMU
Query on DMU
Download Ideal Coordinates CCD File 
BB [auth M],
DC [auth Z],
PB [auth P],
UA [auth C]		DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD
Download Ideal Coordinates CCD File 
BC [auth W]
LA [auth B]
MB [auth O]
NA [auth C]
QB [auth P]
BC [auth W],
LA [auth B],
MB [auth O],
NA [auth C],
QB [auth P],
TA [auth C],
UB [auth P],
ZA [auth J]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA
Download Ideal Coordinates CCD File 
IA [auth B],
LB [auth O]		DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN
Download Ideal Coordinates CCD File 
WA [auth F],
WB [auth S]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU
Download Ideal Coordinates CCD File 
DA [auth A],
FB [auth N]		COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
NO
Query on NO
Download Ideal Coordinates CCD File 
CA [auth A],
EB [auth N]		NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
EA [auth A],
GB [auth N]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
FA [auth A],
HB [auth N]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX
Query on UNX
Download Ideal Coordinates CCD File 
MA [auth C],
OB [auth P]		UNKNOWN ATOM OR ION
X
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, N
L-PEPTIDE LINKINGC6 H11 N O3 SMET
TPO
Query on TPO
G, T
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
SAC
Query on SAC
I, V
L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 182.247α = 90
b = 207.944β = 90
c = 177.997γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-02
    Changes: Database references
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary