8GVM: The structure of azide-bound cytochrome C oxidase determined using the crystals exposed to 20 mm azide solution for 4 days

PDB ID: 8GVMDownload
MMDB ID: 221881
PDB Deposition Date: 2022/9/15
Updated in MMDB: 2023/12
Experimental Method:
x-ray diffraction
Resolution: 1.851  Å
Source Organism:
Similar Structures:
Biological Unit for 8GVM: tridecameric; determined by author
Molecular Components in 8GVM
Label Count Molecule
Proteins (13 molecules)
1
Cytochrome C Oxidase Subunit 1
Molecule annotation
1
Cytochrome C Oxidase Subunit 2
Molecule annotation
1
Cytochrome C Oxidase Subunit 3
Molecule annotation
1
Cytochrome C Oxidase Subunit 4 Isoform 1, Mitochondrial
Molecule annotation
1
Cytochrome C Oxidase Subunit 5A
Molecule annotation
1
Cytochrome C Oxidase Subunit 5B, Mitochondrial
Molecule annotation
1
Cytochrome C Oxidase Subunit 6a2, Mitochondrial
Molecule annotation
1
Cytochrome C Oxidase Subunit 6B1
Molecule annotation
1
Cytochrome C Oxidase Subunit 6C
Molecule annotation
1
Cytochrome C Oxidase Subunit 7A1
Molecule annotation
1
Cytochrome C Oxidase Subunit 7B, Mitochondrial
Molecule annotation
1
Cytochrome C Oxidase Subunit 7C, Mitochondrial
Molecule annotation
1
Cytochrome C Oxidase Subunit 8B, Mitochondrial
Molecule annotation
Chemicals and Non-standard biopolymers (75 molecules)
1
2
HEME-AHEME-A
2
1
COPPER (II) IONCOPPER (II) ION
3
1
MAGNESIUM IONMAGNESIUM ION
4
2
SODIUM IONSODIUM ION
5
2
AZIDE IONAZIDE ION
6
5
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
7
37
1,2-ETHANEDIOL1,2-ETHANEDIOL
8
3
TRISTEAROYLGLYCEROLTRISTEAROYLGLYCEROL
9
6
CHOLIC ACIDCHOLIC ACID
10
1
DINUCLEAR COPPER IONDINUCLEAR COPPER ION
11
1
(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(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
12
5
DECYL-BETA-D-MALTOPYRANOSIDEDECYL-BETA-D-MALTOPYRANOSIDE
13
3
CARDIOLIPINCARDIOLIPIN
14
5
(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE
15
1
ZINC IONZINC ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303