7COH

Dimeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 1occ 2occ 1v54 2dyr 5b1a


Literature

The 1.3-A Resolution structure of bovine cytochrome c oxidase suggests a dimerization mechanism

Shinzawa-Itoh, K.Hatanaka, M.Fujita, K.Yano, N.Ogasawara, Y.Iwata, J.Yamashita, E.Tsukihara, T.Yoshikawa, S.Muramoto, K.

(2021) Biochim Biophys Acta 


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1
A, N
514Bos taurusMutation(s): 0 
Gene Names: MT-CO1COICOXIMTCO1
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2
B, O
227Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3
C, P
261Bos taurusMutation(s): 0 
Gene Names: MT-CO3COIIICOXIIIMTCO3
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1
D, Q
147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A
E, R
109Bos taurusMutation(s): 0 
Gene Names: COX5A
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B
F, S
98Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrial
G, T
85Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1
H, U
85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
Gene Names: COX6C
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1
J, W
59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
Membrane Entity: Yes 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B
K, X
56Bos taurusMutation(s): 0 
Gene Names: COX7B
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrial
L, Y
47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8B
M, Z
46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
Membrane Entity: Yes 
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

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FA [auth A]
GA [auth A]
JE [auth P]
TC [auth N]
UB [auth C]
FA [auth A],
GA [auth A],
JE [auth P],
TC [auth N],
UB [auth C],
UC [auth N]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
HEA
Query on HEA

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AA [auth A],
BA [auth A],
OC [auth N],
PC [auth N]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK (Subject of Investigation/LOI)
Query on PEK

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GE [auth P],
RB [auth C]
(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
PGV (Subject of Investigation/LOI)
Query on PGV

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HE [auth P],
IE [auth P],
SB [auth C],
TB [auth C]
(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 (Subject of Investigation/LOI)
Query on DMU

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AD [auth N]
AE [auth P]
AF [auth W]
BD [auth N]
BE [auth P]
AD [auth N],
AE [auth P],
AF [auth W],
BD [auth N],
BE [auth P],
BF [auth Y],
CD [auth N],
CF [auth Z],
FC [auth G],
GB [auth C],
GC [auth G],
HB [auth C],
HC [auth G],
IA [auth A],
ID [auth O],
JB [auth C],
JD [auth O],
KB [auth C],
KC [auth J],
KD [auth O],
LB [auth C],
LC [auth J],
LE [auth P],
MA [auth A],
MB [auth C],
MC [auth L],
NA [auth A],
NC [auth M],
OA [auth A],
TA [auth B],
UA [auth B],
UE [auth T],
VA [auth B],
VD [auth P],
VE [auth T],
WB [auth C],
WC [auth N],
WD [auth P],
WE [auth T],
YD [auth P],
ZD [auth P],
ZE [auth W]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD (Subject of Investigation/LOI)
Query on CHD

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HA [auth A]
JC [auth G]
KE [auth P]
VB [auth C]
VC [auth N]
HA [auth A],
JC [auth G],
KE [auth P],
VB [auth C],
VC [auth N],
YE [auth T]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
LFA (Subject of Investigation/LOI)
Query on LFA

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AB [auth C]
BB [auth C]
CB [auth C]
DB [auth C]
DC [auth G]
AB [auth C],
BB [auth C],
CB [auth C],
DB [auth C],
DC [auth G],
EB [auth C],
EC [auth G],
FB [auth C],
IB [auth C],
KA [auth A],
LA [auth A],
ND [auth P],
OD [auth P],
PD [auth P],
QD [auth P],
RD [auth P],
SD [auth P],
SE [auth T],
TD [auth P],
TE [auth T],
UD [auth P],
XD [auth P],
YA [auth C],
YC [auth N],
ZA [auth C],
ZC [auth N]
EICOSANE
C20 H42
CBFCDTFDPHXCNY-UHFFFAOYSA-N
CUA
Query on CUA

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MD [auth O],
XA [auth B]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
ZN
Query on ZN

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CC [auth F],
RE [auth S]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

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CA [auth A],
QC [auth N]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO

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AC [auth F]
BC [auth F]
CE [auth P]
DD [auth N]
DE [auth P]
AC [auth F],
BC [auth F],
CE [auth P],
DD [auth N],
DE [auth P],
ED [auth N],
EE [auth P],
FD [auth N],
GD [auth N],
HD [auth N],
IC [auth G],
LD [auth O],
ME [auth R],
NB [auth C],
NE [auth R],
OB [auth C],
OE [auth R],
PA [auth A],
PB [auth C],
PE [auth S],
QA [auth A],
QE [auth S],
RA [auth A],
SA [auth A],
WA [auth B],
XB [auth E],
XE [auth T],
YB [auth E],
ZB [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
PER
Query on PER

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JA [auth A],
XC [auth N]
PEROXIDE ION
O2
ANAIPYUSIMHBEL-UHFFFAOYSA-N
MG
Query on MG

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DA [auth A],
RC [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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EA [auth A],
SC [auth N]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
UNX
Query on UNX

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FE [auth P],
QB [auth C]
UNKNOWN ATOM OR ION
X
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
A, N
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.998α = 90
b = 204.193β = 90
c = 177.759γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP17H03646
Japan Society for the Promotion of Science (JSPS)JapanJP22370060
Japan Society for the Promotion of Science (JSPS)JapanJP18K06162

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description