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
CU Copper (II) ion PoSSuM
MG Magnesium ion PoSSuM
NA Sodium ion PoSSuM
ZN Zinc ion PoSSuM
CDL Cardiolipin PoSSuM
CHD Cholic acid PoSSuM
CMO Carbon monoxide PoSSuM
CUA Dinuclear copper ion PoSSuM
DMU Decyl-beta-D-maltopyranoside PoSSuM
EDO 1,2-ethanediol PoSSuM
HEA Heme-a 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
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 : -