Brand  (β version)

PDB ID: 5X19

Hetero Atom Contents

color scheme of protein:

hetatm:

x
information
centroid:
interaction residue:

chain: Hide other chain(s)

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

Structure summary

Code : 5X19
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

Reaction

Chain : A, N
UniProt : P00396 (COX1_BOVIN)
Reaction : 4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O.
Chain : B, O
UniProt : P68530 (COX2_BOVIN)
Reaction : -
Chain : C, P
UniProt : P00415 (COX3_BOVIN)
Reaction : -
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 : -