5B3S | pdb_00005b3s

Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.177 (Depositor), 0.185 (DCC) 
  • R-Value Work: 
    0.153 (Depositor) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 

Literature

Bovine heart cytochrome c oxidase in the carbon monoxide-bound mixed-valence state at 1.68 angstrom resolution (50 K)

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

To be published.

Macromolecule Content 

  • Total Structure Weight: 451.59 kDa 
  • Atom Count: 34,917 
  • Modeled Residue Count: 3,550 
  • Deposited Residue Count: 3,550 
  • 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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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 3
C, P
259Bos taurusMutation(s): 0 
EC: 7.1.1.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial
D, Q
144Bos 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, mitochondrial
E, R
105Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P00426 (Bos taurus)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 5B, mitochondrial
F, S
94Bos 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, mitochondrial
G, T
84Bos 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
79Bos 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 
UniProt
Find proteins for P04038 (Bos taurus)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c oxidase subunit 7A1, mitochondrial
J, W
58Bos 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, mitochondrial
K, X
49Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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
46Bos 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, mitochondrial
M, Z
43Bos 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

Query on CDL


Download:Ideal Coordinates CCD File
LB [auth C],
LC [auth G],
XF [auth T],
YE [auth P]		CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
TGL

Query on TGL


Download:Ideal Coordinates CCD File
DD [auth L]
JF [auth Q]
LG [auth Y]
TD [auth N]
WA [auth B]
DD [auth L],
JF [auth Q],
LG [auth Y],
TD [auth N],
WA [auth B],
ZA [auth B]
TRISTEAROYLGLYCEROL
C57 H110 O6
DCXXMTOCNZCJGO-UHFFFAOYSA-N
HEA

Query on HEA


Download:Ideal Coordinates CCD File
AA [auth A],
BA [auth A],
MD [auth N],
ND [auth N]		HEME-A
C49 H56 Fe N4 O6
ZGGYGTCPXNDTRV-PRYGPKJJSA-L
PEK

Query on PEK


Download:Ideal Coordinates CCD File
HB [auth C]
IB [auth C]
UE [auth P]
VE [auth P]
WE [auth P]
HB [auth C],
IB [auth C],
UE [auth P],
VE [auth P],
WE [auth P],
WF [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
NE [auth O],
YA [auth B]		(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
GA [auth A]
HA [auth A]
JB [auth C]
KB [auth C]
OC [auth G]
GA [auth A],
HA [auth A],
JB [auth C],
KB [auth C],
OC [auth G],
SD [auth N],
UD [auth N],
XE [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
AD [auth K]
BD [auth K]
BF [auth P]
CD [auth K]
ED [auth L]
AD [auth K],
BD [auth K],
BF [auth P],
CD [auth K],
ED [auth L],
FG [auth X],
GD [auth M],
GG [auth X],
HG [auth X],
IF [auth P],
IG [auth X],
JG [auth X],
LD [auth M],
MB [auth C],
MC [auth G],
NB [auth C],
NG [auth Z],
OE [auth O],
XC [auth K],
YC [auth K],
YF [auth T],
ZC [auth K],
ZE [auth P]
DECYL-BETA-D-MALTOPYRANOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
CHD

Query on CHD


Download:Ideal Coordinates CCD File
AF [auth P]
EG [auth W]
GB [auth C]
KG [auth Y]
NC [auth G]
AF [auth P],
EG [auth W],
GB [auth C],
KG [auth Y],
NC [auth G],
TC [auth J],
TE [auth P],
UC [auth J],
VF [auth T]
CHOLIC ACID
C24 H40 O5
BHQCQFFYRZLCQQ-OELDTZBJSA-N
CUA

Query on CUA


Download:Ideal Coordinates CCD File
ME [auth O],
XA [auth B]		DINUCLEAR COPPER ION
Cu2
ALKZAGKDWUSJED-UHFFFAOYSA-N
PO4

Query on PO4


Download:Ideal Coordinates CCD File
CG [auth U],
RC [auth H]		PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN

Query on ZN


Download:Ideal Coordinates CCD File
FC [auth F],
PF [auth S]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU

Query on CU


Download:Ideal Coordinates CCD File
CA [auth A],
OD [auth N]		COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO

Query on EDO


Download:Ideal Coordinates CCD File
AB [auth B]
AC [auth D]
AE [auth N]
AG [auth T]
BB [auth B]
AB [auth B],
AC [auth D],
AE [auth N],
AG [auth T],
BB [auth B],
BC [auth D],
BE [auth N],
BG [auth U],
CB [auth B],
CC [auth E],
CE [auth N],
CF [auth P],
DB [auth B],
DC [auth E],
DE [auth N],
DF [auth P],
DG [auth V],
EB [auth B],
EC [auth E],
EE [auth N],
EF [auth P],
FB [auth B],
FD [auth L],
FE [auth N],
FF [auth P],
GC [auth F],
GE [auth N],
GF [auth P],
HC [auth F],
HD [auth M],
HE [auth N],
HF [auth P],
IA [auth A],
IC [auth F],
ID [auth M],
IE [auth N],
JA [auth A],
JC [auth F],
JD [auth M],
JE [auth N],
KA [auth A],
KC [auth F],
KD [auth M],
KE [auth N],
KF [auth Q],
LA [auth A],
LE [auth N],
LF [auth Q],
MA [auth A],
MF [auth Q],
MG [auth Y],
NA [auth A],
NF [auth R],
OA [auth A],
OB [auth C],
OF [auth R],
PA [auth A],
PB [auth C],
PC [auth G],
PE [auth O],
QA [auth A],
QB [auth C],
QC [auth G],
QE [auth O],
QF [auth S],
RA [auth A],
RB [auth C],
RE [auth O],
RF [auth S],
SA [auth A],
SB [auth C],
SC [auth I],
SE [auth O],
SF [auth S],
TA [auth A],
TB [auth C],
TF [auth S],
UA [auth A],
UB [auth C],
UF [auth S],
VA [auth A],
VB [auth C],
VC [auth J],
VD [auth N],
WB [auth C],
WC [auth J],
WD [auth N],
XB [auth D],
XD [auth N],
YB [auth D],
YD [auth N],
ZB [auth D],
ZD [auth N],
ZF [auth T]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CMO

Query on CMO


Download:Ideal Coordinates CCD File
FA [auth A],
RD [auth N]		CARBON MONOXIDE
C O
UGFAIRIUMAVXCW-UHFFFAOYSA-N
MG

Query on MG


Download:Ideal Coordinates CCD File
DA [auth A],
PD [auth N]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA


Download:Ideal Coordinates CCD File
EA [auth A],
QD [auth N]		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: 1.68 Å
  • R-Value Free:  0.177 (Depositor), 0.185 (DCC) 
  • R-Value Work:  0.153 (Depositor) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.491α = 90
b = 203.303β = 90
c = 177.484γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
DENZOdata reduction
REFMACphasing
PDB_EXTRACTdata extraction

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

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection
  • Version 2.0: 2022-03-02
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Refinement description