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 

wwPDB Validation   3D Report Full Report


This is version 1.0 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
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 1A, N514Bos taurusMutation(s): 0 
Gene Names: MT-CO1COICOXIMTCO1
EC: 7.1.1.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 2B, O227Bos taurusMutation(s): 0 
Gene Names: MT-CO2COIICOX2COXIIMTCO2
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
Find proteins for P68530 (Bos taurus)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3C, P261Bos taurusMutation(s): 0 
Gene Names: MT-CO3COIIICOXIIIMTCO3
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1D, Q147Bos taurusMutation(s): 0 
Gene Names: COX4I1COX4
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5AE, R109Bos taurusMutation(s): 0 
Gene Names: COX5A
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5BF, S98Bos taurusMutation(s): 0 
Gene Names: COX5B
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2, mitochondrialG, T85Bos taurusMutation(s): 0 
Gene Names: COX6A2COX6A
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1H, U85Bos taurusMutation(s): 0 
Gene Names: COX6B1COX6B
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6CI, V73Bos taurusMutation(s): 0 
Gene Names: COX6C
Membrane Entity: Yes 
UniProt
Find proteins for P04038 (Bos taurus)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1J, W59Bos taurusMutation(s): 0 
Gene Names: COX7A1COX7ACOX7AH
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7BK, X56Bos taurusMutation(s): 0 
Gene Names: COX7B
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrialL, Y47Bos taurusMutation(s): 0 
Gene Names: COX7CCOX7CP1
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 8BM, Z46Bos taurusMutation(s): 0 
Gene Names: COX8BCOX8H
Membrane Entity: Yes 
UniProt
Find proteins for P10175 (Bos taurus)
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Small Molecules
Ligands 15 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
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
 Ligand Interaction
PEK
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
 Ligand Interaction
PGV
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
 Ligand Interaction
DMU
Query on DMU

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AD [auth N] , AE [auth P] , AF [auth W] , BD [auth N] , BE [auth P] , BF [auth Y] , CD [auth N] , CF [auth Z] , 
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
 Ligand Interaction
CHD
Query on CHD

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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
 Ligand Interaction
LFA
Query on LFA

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AB [auth C] , BB [auth C] , CB [auth C] , DB [auth C] , DC [auth G] , EB [auth C] , EC [auth G] , FB [auth C] , 
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
 Ligand Interaction
CUA
Query on CUA

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

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

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

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AC [auth F] , BC [auth F] , CE [auth P] , DD [auth N] , DE [auth P] , ED [auth N] , EE [auth P] , FD [auth N] , 
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
 Ligand Interaction
PER
Query on PER

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

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

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

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FE [auth P], QB [auth C]UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FME
Query on FME
A, NL-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

View Full Validation Report



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