7EV7 | pdb_00007ev7

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 (Depositor), 0.181 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.160 (Depositor) 

Starting Model: experimental
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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.

Macromolecule Content 

  • Total Structure Weight: 456.03 kDa 
  • Atom Count: 34,489 
  • Modeled Residue Count: 3,550 
  • Deposited Residue Count: 3,614 
  • Unique protein chains: 13

Macromolecules

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|  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)
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UniProt GroupP00396
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Reference Sequence
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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
Find proteins for P68530 (Bos taurus)
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UniProt GroupP68530
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Reference Sequence
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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
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UniProt GroupP00415
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Reference Sequence
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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)
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UniProt GroupP00423
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5A
E, R
109Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrial
F, S
98Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6A2
G, T
85Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6B1
H, U
85Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 6C
I, V
73Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Reference Sequence
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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)
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7B
K, X
56Bos taurusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for P13183 (Bos taurus)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7C, mitochondrial
L, Y
47Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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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)
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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 (Depositor), 0.181 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.160 (Depositor) 
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

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Ligand Structure Quality Assessment 


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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