7EV7

Bovine heart cytochrome c oxidase in the carbon monoxide-bound fully reduced state at a 50 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure of CO-bound fully reduced state of bovine heart cytochrome c oxidase

Shimada, A.Shinzawa-Itoh, K.Muramoto, K.Tsukihara, T.Yoshikawa, S.

To be published.

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: 7.1.1.9
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: 7.1.1.9
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: 7.1.1.9
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 
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 
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, mitochondrial
F, S
98Bos taurusMutation(s): 0 
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 
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 
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 
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 subunit 7A1
J, W
59Bos taurusMutation(s): 0 
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 
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, mitochondrial
L, Y
47Bos taurusMutation(s): 0 
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 
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 16 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL (Subject of Investigation/LOI)
Query on CDL

Download Ideal Coordinates CCD File 
EH [auth T],
TF [auth P],
WB [auth C],
ZC [auth G]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL
Query on TGL

Download Ideal Coordinates CCD File 
BB [auth B]
IC [auth D]
IE [auth N]
KG [auth Q]
PH [auth Y]
BB [auth B],
IC [auth D],
IE [auth N],
KG [auth Q],
PH [auth Y],
QD [auth L]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA (Subject of Investigation/LOI)
Query on HEA

Download Ideal Coordinates CCD File 
BA [auth A],
CA [auth A],
CE [auth N],
DE [auth N]
HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK
Query on PEK

Download Ideal Coordinates CCD File 
OF [auth P]
PF [auth P]
QF [auth P]
RB [auth C]
SB [auth C]
OF [auth P],
PF [auth P],
QF [auth P],
RB [auth C],
SB [auth C],
TB [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
PSC
Query on PSC

Download Ideal Coordinates CCD File 
CB [auth B],
FF [auth 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
C42 H81 N O8 P
JLPULHDHAOZNQI-AUSZDXHESA-O
PGV
Query on PGV

Download Ideal Coordinates CCD File 
AA [auth A]
BE [auth N]
HA [auth A]
JE [auth N]
RF [auth P]
AA [auth A],
BE [auth N],
HA [auth A],
JE [auth N],
RF [auth P],
SF [auth P],
UB [auth C],
VB [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
Query on DMU

Download Ideal Coordinates CCD File 
AE [auth M]
GD [auth G]
HC [auth C]
IG [auth P]
JG [auth P]
AE [auth M],
GD [auth G],
HC [auth C],
IG [auth P],
JG [auth P],
KH [auth V],
TH [auth Z],
UF [auth P],
UH [auth Z],
VD [auth M],
YB [auth C]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD
Query on CHD

Download Ideal Coordinates CCD File 
AD [auth G]
DB [auth B]
LD [auth J]
LH [auth W]
MF [auth P]
AD [auth G],
DB [auth B],
LD [auth J],
LH [auth W],
MF [auth P],
PB [auth C],
SH [auth Y],
VF [auth P],
WF [auth P],
XB [auth C],
ZB [auth C]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA
Query on CUA

Download Ideal Coordinates CCD File 
EB [auth B],
GF [auth O]
DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
IH [auth U],
KD [auth H]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
SC [auth F],
SG [auth S]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU
Query on CU

Download Ideal Coordinates CCD File 
DA [auth A],
EE [auth N]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth C]
AF [auth N]
AG [auth P]
AH [auth S]
AB [auth A],
AC [auth C],
AF [auth N],
AG [auth P],
AH [auth S],
BC [auth C],
BD [auth G],
BF [auth N],
BG [auth P],
BH [auth S],
CC [auth C],
CD [auth G],
CF [auth N],
CG [auth P],
CH [auth S],
DC [auth C],
DD [auth G],
DF [auth N],
DG [auth P],
DH [auth S],
EC [auth C],
ED [auth G],
EF [auth N],
EG [auth P],
FB [auth B],
FC [auth C],
FD [auth G],
FG [auth P],
FH [auth T],
GB [auth B],
GC [auth C],
GG [auth P],
GH [auth T],
HB [auth B],
HD [auth H],
HF [auth O],
HG [auth P],
HH [auth U],
IA [auth A],
IB [auth B],
ID [auth H],
IF [auth O],
JA [auth A],
JB [auth B],
JC [auth D],
JD [auth H],
JF [auth O],
JH [auth V],
KA [auth A],
KB [auth B],
KC [auth D],
KE [auth N],
KF [auth O],
LA [auth A],
LB [auth B],
LC [auth D],
LE [auth N],
LF [auth O],
LG [auth Q],
MA [auth A],
MB [auth B],
MC [auth D],
MD [auth J],
ME [auth N],
MG [auth Q],
MH [auth W],
NA [auth A],
NB [auth B],
NC [auth D],
ND [auth J],
NE [auth N],
NG [auth R],
NH [auth W],
OA [auth A],
OB [auth B],
OC [auth D],
OD [auth K],
OE [auth N],
OG [auth R],
OH [auth W],
PA [auth A],
PC [auth E],
PD [auth K],
PE [auth N],
PG [auth R],
QA [auth A],
QC [auth E],
QE [auth N],
QG [auth R],
QH [auth Y],
RA [auth A],
RC [auth E],
RD [auth L],
RE [auth N],
RG [auth R],
RH [auth Y],
SA [auth A],
SD [auth L],
SE [auth N],
TA [auth A],
TC [auth F],
TD [auth L],
TE [auth N],
TG [auth S],
UA [auth A],
UC [auth F],
UD [auth L],
UE [auth N],
UG [auth S],
VA [auth A],
VC [auth F],
VE [auth N],
VG [auth S],
WA [auth A],
WC [auth F],
WD [auth M],
WE [auth N],
WG [auth S],
XA [auth A],
XC [auth F],
XD [auth M],
XE [auth N],
XF [auth P],
XG [auth S],
YA [auth A],
YC [auth F],
YD [auth M],
YE [auth N],
YF [auth P],
YG [auth S],
ZA [auth A],
ZD [auth M],
ZE [auth N],
ZF [auth P],
ZG [auth S]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CMO
Query on CMO

Download Ideal Coordinates CCD File 
GA [auth A],
HE [auth N]
CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
EA [auth A],
FE [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
FA [auth A],
GE [auth N],
NF [auth P],
QB [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
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: 1.70 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.539α = 90
b = 203.655β = 90
c = 177.569γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18K06092
Japan Society for the Promotion of Science (JSPS)Japan15K18493
Japan Society for the Promotion of Science (JSPS)Japan18K14635
Japan Society for the Promotion of Science (JSPS)Japan26291033
Japan Science and TechnologyJapan12101577

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description