6NKN: Time-resolved SFX structure of the PR intermediate of cytochrome c oxidase at room temperature

PDB ID: 6NKNDownload
MMDB ID: 173475
PDB Deposition Date: 2019/1/7
Updated in MMDB: 2019/12
Experimental Method:
x-ray diffraction
Resolution: 2.5  Å
Source Organism:
Similar Structures:
Biological Unit for 6NKN: 26-meric; determined by author
Molecular Components in 6NKN
Label Count Molecule
Proteins (26 molecules)
2
Cytochrome C Oxidase Subunit 1
Molecule annotation
2
Cytochrome C Oxidase Subunit 2
(Gene symbol: COX2)
Molecule annotation
2
Cytochrome C Oxidase Subunit 3
Molecule annotation
2
Cytochrome C Oxidase Subunit 4 Isoform 1, Mitochondrial
(Gene symbol: COX4I1)
Molecule annotation
2
Cytochrome C Oxidase Subunit 5A, Mitochondrial
(Gene symbol: COX5A)
Molecule annotation
2
Cytochrome C Oxidase Subunit 5B, Mitochondrial
(Gene symbol: COX5B)
Molecule annotation
2
Cytochrome C Oxidase Subunit 6a2, Mitochondrial
(Gene symbol: COX6A2)
Molecule annotation
2
Cytochrome C Oxidase Subunit 6B1
(Gene symbol: COX6B1)
Molecule annotation
2
Cytochrome C Oxidase Subunit 6C
(Gene symbol: MGC148714)
Molecule annotation
2
Cytochrome C Oxidase Subunit 7a1, Mitochondrial
(Gene symbol: COX7A1)
Molecule annotation
2
Cytochrome C Oxidase Subunit 7B, Mitochondrial
(Gene symbol: COX7B)
Molecule annotation
2
Cytochrome C Oxidase Subunit 7C, Mitochondrial
(Gene symbol: COX7C)
Molecule annotation
2
Cytochrome C Oxidase Subunit 8B, Mitochondrial
(Gene symbol: COX8B)
Molecule annotation
Chemicals and Non-standard biopolymers (56 molecules)
1
2
COPPER (II) IONCOPPER (II) ION
2
2
MAGNESIUM IONMAGNESIUM ION
3
2
SODIUM IONSODIUM ION
4
4
HEME-AHEME-A
5
8
(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
6
6
TRISTEAROYLGLYCEROLTRISTEAROYLGLYCEROL
7
2
OXYGEN ATOMOXYGEN ATOM
8
2
HYDROXIDE IONHYDROXIDE ION
9
2
DINUCLEAR COPPER IONDINUCLEAR COPPER ION
10
2
(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
11
8
CHOLIC ACIDCHOLIC ACID
12
6
(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
13
4
CARDIOLIPINCARDIOLIPIN
14
2
ZINC IONZINC ION
15
4
DECYL-BETA-D-MALTOPYRANOSIDEDECYL-BETA-D-MALTOPYRANOSIDE
* 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