Het-PDB Navi2 (PDB: 5X19)

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Ligands
Code	Name	Link
HEA	Heme-a	PoSSuM
CU	Copper (II) ion	PoSSuM
MG	Magnesium ion	PoSSuM
NA	Sodium ion	PoSSuM
CMO	Carbon monoxide	PoSSuM
TGL	Tristearoylglycerol	PoSSuM
PGV	(1r)-2-{[{[(2s)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11e)-octadec-11-enoate	PoSSuM
EDO	1,2-ethanediol	PoSSuM
CUA	Dinuclear copper ion	PoSSuM
CHD	Cholic acid	PoSSuM
PSC	(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	PoSSuM
UNX	Unknown atom or ion	PoSSuM
CDL	Cardiolipin	PoSSuM
PEK	(1s)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(stearoyloxy)methyl]ethyl (5e,8e,11e,14e)-icosa-5,8,11,14-tetraenoate	PoSSuM
ZN	Zinc ion	PoSSuM
DMU	Decyl-beta-D-maltopyranoside	PoSSuM

Non-standard Residues
Code	Name	Show
FME	N-formylmethionine
TPO	Phosphothreonine
SAC	N-acetyl-serine

Glycosylation
Code	Name	Emphasize

Modification
Code	Name	Show

Download interaction data: 5X19

Code :

5X19 PDBj RCSB PDB PDBe

Header :

OXIDOREDUCTASE

Title :

CO bound cytochrome C oxidase at 100 micro sec after pump laser irradiation to release CO from O2 reduction center

Release Data :

2017-08-09

Compound :

mol_id	molecule	chains	synonym
1	Cytochrome c oxidase subunit 1	A,N	Cytochrome c oxidase polypeptide I
	ec: 1.9.3.1

mol_id	molecule	chains	synonym
2	Cytochrome c oxidase subunit 2	B,O	Cytochrome c oxidase polypeptide II

mol_id	molecule	chains	synonym
3	Cytochrome c oxidase subunit 3	C,P	Cytochrome c oxidase polypeptide III

mol_id	molecule	chains	synonym
4	Cytochrome c oxidase subunit 4 isoform 1, mitochondrial	D,Q	Cytochrome c oxidase polypeptide IV,Cytochrome c oxidase subunit IV isoform 1,COX IV-1

mol_id	molecule	chains	synonym
5	Cytochrome c oxidase subunit 5A, mitochondrial	E,R	Cytochrome c oxidase polypeptide Va

mol_id	molecule	chains	synonym
6	Cytochrome c oxidase subunit 5B, mitochondrial	F,S	Cytochrome c oxidase polypeptide VIa,Cytochrome c oxidase polypeptide Vb

mol_id	molecule	chains	synonym
7	Cytochrome c oxidase subunit 6A2, mitochondrial	G,T	Cytochrome c oxidase polypeptide VIa-heart,COXVIAH,Cytochrome c oxidase polypeptide VIb

mol_id	molecule	chains	synonym
8	Cytochrome c oxidase subunit 6B1	H,U	Cytochrome c oxidase polypeptide VII,Cytochrome c oxidase subunit AED,Cytochrome c oxidase subunit VIb isoform 1,COX VIb-1

mol_id	molecule	chains	synonym
9	Cytochrome c oxidase subunit 6C	I,V	Cytochrome c oxidase polypeptide VIc,Cytochrome c oxidase subunit STA

mol_id	molecule	chains	synonym
10	Cytochrome c oxidase subunit 7A1, mitochondrial	J,W	Cytochrome c oxidase subunit VIIIc,VIIIC,Cytochrome c oxidase subunit VIIa-heart,Cytochrome c oxidase subunit VIIa-H,Cytochrome c oxidase subunit VIIa-muscle,Cytochrome c oxidase subunit VIIa-M

mol_id	molecule	chains	synonym
11	Cytochrome c oxidase subunit 7B, mitochondrial	K,X	Cytochrome c oxidase polypeptide VIIb,IHQ

mol_id	molecule	chains	synonym
12	Cytochrome c oxidase subunit 7C, mitochondrial	L,Y	Cytochrome c oxidase polypeptide VIIIA,Cytochrome c oxidase polypeptide VIIc

mol_id	molecule	chains	synonym
13	Cytochrome c oxidase subunit 8B, mitochondrial	M,Z	Cytochrome c oxidase polypeptide VIII-heart,Cytochrome c oxidase subunit 8-1,Cytochrome c oxidase subunit 8H,IX,VIIIb

Source :

mol_id	organism_scientific	organism_common
1	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
2	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
3	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
4	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
5	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
6	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
7	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
8	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
9	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
10	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
11	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
12	Bos taurus (taxid:9913)	Bovine

mol_id	organism_scientific	organism_common
13	Bos taurus (taxid:9913)	Bovine

Authors :

Shimada, A., Kubo, M., Baba, S., Yamashita, K., Hirata, K., Ueno, G., Nomura, T., Kimura, T., Shinzawa-Itoh, K., Baba, J., Hatano, K., Eto, Y., Miyamoto, A., Murakami, H., Kumasaka, T., Owada, S., Tono, K., Yabashi, M., Yamaguchi, Y., Yanagisawa, S., Sakaguchi, M., Ogura, T., Komiya, R., Yan, J., Yamashita, E., Yamamoto, M., Ago, H., Yoshikawa, S., Tsukihara, T.

Keywords :

cytochrome c oxidase, X-ray free electron laser, time-resolved analysis, proton pump, membrane protein, OXIDOREDUCTASE

Exp. method :

X-RAY DIFFRACTION ( 2.2000 Å )

Citation :

A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.

Shimada, A.,Kubo, M.,Baba, S. et al.
(2017) Sci Adv 3 : e1603042 - e1603042

PubMed: 28740863
DOI: 10.1126/sciadv.1603042

Chain :

A, N

UniProt :

P00396 (COX1_BOVIN)

Reaction:	EC:	Evidence:
Reaction:	Physiological Direction:	Evidence:
4 Fe(II)-[cytochrome c] + O2 + 8 H(+)(in) = 4 Fe(III)- [cytochrome c] + 2 H2O + 4 H(+)(out)	7.1.1.9	UniProtKB:P00401
	left-to-right	UniProtKB:P00401
Cofactor:	Evidence:	Note:
heme	ECO:0000269 \| PubMed:20385840 ECO:0000269 \| PubMed:2165784 ECO:0000269 \| PubMed:8638158	Binds 2 heme A groups non-covalently per subunit.
Cu cation	ECO:0000269 \| PubMed:20385840 ECO:0000269 \| PubMed:2165784 ECO:0000269 \| PubMed:8638158	Binds a copper B center.

Chain :

B, O

UniProt :

P68530 (COX2_BOVIN)

Reaction:	EC:	Evidence:
Reaction:	Physiological Direction:	Evidence:
4 Fe(II)-[cytochrome c] + O2 + 8 H(+)(in) = 4 Fe(III)- [cytochrome c] + 2 H2O + 4 H(+)(out)	7.1.1.9	UniProtKB:P00410
	left-to-right	UniProtKB:P00410
Cofactor:	Evidence:	Note:
Cu cation	ECO:0000269 \| PubMed:20385840 ECO:0000269 \| PubMed:8638158	Binds a dinuclear copper A center per subunit.

Chain :

C, P

UniProt :

P00415 (COX3_BOVIN)

Reaction:	EC:	Evidence:
Reaction:	Physiological Direction:	Evidence:
4 Fe(II)-[cytochrome c] + O2 + 8 H(+)(in) = 4 Fe(III)- [cytochrome c] + 2 H2O + 4 H(+)(out)	7.1.1.9	UniProtKB:P00420
	left-to-right	UniProtKB:P00420

Chain :	D, Q
UniProt :	P00423 (COX41_BOVIN)
Reaction :	-

Chain :	E, R
UniProt :	P00426 (COX5A_BOVIN)
Reaction :	-

Chain :	F, S
UniProt :	P00428 (COX5B_BOVIN)
Reaction :	-

Chain :	G, T
UniProt :	P07471 (CX6A2_BOVIN)
Reaction :	-

Chain :	H, U
UniProt :	P00429 (CX6B1_BOVIN)
Reaction :	-

Chain :	I, V
UniProt :	P04038 (COX6C_BOVIN)
Reaction :	-

Chain :	J, W
UniProt :	P07470 (CX7A1_BOVIN)
Reaction :	-

Chain :	K, X
UniProt :	P13183 (COX7B_BOVIN)
Reaction :	-

Chain :	L, Y
UniProt :	P00430 (COX7C_BOVIN)
Reaction :	-

Chain :	M, Z
UniProt :	P10175 (COX8B_BOVIN)
Reaction :	-

PDB ID: 5X19

Hetero Atom Contents

Structure summary

Reaction