Research workbench
Monomeric form of bovine heart cytochrome C oxidase in the fully oxidized state
Analyse Monomeric form of bovine heart cytochrome C oxidase in the fully oxidized state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JY3
- Type
- protein
- Length
- 1,729 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase subunit 1; Cytochrome C oxidase subunit 2; Cytochrome C oxidase…
- EC
- 1.9.3.1
- UniProt
- P00396, P68530, P00415, P00423, P00426, P00428, P07471, P00429, P04038, P07470, P13183, P00430, P10175
- Ligands
- CQX, CDL, HEA, PGV, CUA, CHD, PEK, NA, CU, MG, ZN, PER
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 13 distinct chains · 60% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 514 | 72% helix, 2% strand | P00396 |
| B | Cytochrome C oxidase subunit 2 | protein | 227 | 36% helix, 26% strand | P68530 |
| C | Cytochrome C oxidase subunit 3 | protein | 254 | 76% helix, 0% strand | P00415 |
| D | Cytochrome C oxidase subunit 4 isoform 1 | protein | 136 | 53% helix, 3% strand | P00423 |
| E | Cytochrome C oxidase subunit 5A | protein | 102 | 67% helix, 1% strand | P00426 |
| F | Cytochrome C oxidase subunit 5B | protein | 91 | 16% helix, 26% strand | P00428 |
| G | Cytochrome C oxidase subunit 6A2, mitochondrial | protein | 72 | 35% helix, 3% strand | P07471 |
| H | Cytochrome C oxidase subunit 6B1 | protein | 75 | 63% helix, 1% strand | P00429 |
| I | Cytochrome C oxidase subunit 6C | protein | 70 | 73% helix, 1% strand | P04038 |
| J | Cytochrome C oxidase subunit 7A1 | protein | 55 | 71% helix, 0% strand | P07470 |
| K | Cytochrome C oxidase subunit 7B | protein | 49 | 55% helix, 0% strand | P13183 |
| L | Cytochrome C oxidase subunit 7C, mitochondrial | protein | 44 | 61% helix, 0% strand | P00430 |
| M | Cytochrome C oxidase subunit 8B | protein | 40 | 60% helix, 5% strand | P10175 |
Ligands and binding sites
- CQX · (2S,3S,4S,5S,6R)-2-(2-decoxyethoxy)-6-(hydroxymethyl) oxane-3,4,5-triol · ligand · 8 copies · chains A, D, K, B, L, M, I, C, G
- CDL · Cardiolipin · ligand · 3 copies · chains A, L, B, I, C, J
- HEA · Heme-A · ligand · 2 copies · chains A, B
- PGV · (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy) phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl (11E)-octadec-11-enoate · ligand · 2 copies · chains A, C, F
- CUA · Dinuclear copper ion · ligand · chains B
- CHD · Cholic acid · ligand · chains A, C
- PEK · (1S)-2-{[(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(stearoyloxy)methyl]ethyl (5E,8E,11E,14E)-icosa-5,8, 11,14-tetraenoate · ligand · chains A, C, G
- NA · Sodium ion · metal · 2 copies · chains A, C
- CU · Copper (II) ion · metal · chains A
- MG · Magnesium ion · metal · chains A, B
- ZN · Zinc ion · metal · chains F
- PER · Peroxide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.91 | 0.93 | 131 | HEA, PER, CQX |
| 2 | 844 | 0.87 | 0.88 | 90 | PGV |
| 3 | 933 | 0.83 | 0.84 | 95 | empty |
| 4 | 73 | 0.74 | 0.98 | 38 | empty |
| 5 | 919 | 0.73 | 0.77 | 71 | CQX |
Interfaces
34 interfaces between chains.
- A–B · 3557 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 2605 Ų buried · 18 hydrogen bonds · protein-protein
- A–L · 1687 Ų buried · 20 hydrogen bonds · protein-protein
- B–I · 1683 Ų buried · 17 hydrogen bonds · protein-protein
- C–G · 1660 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, formylation).
Compared structures
- 6JY3 · Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Oxidized State · the same entry in another collection · chain K against K, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00396
- Every structure of UniProt P68530
- Every structure of UniProt P00415
- Every structure of UniProt P00423
- Every structure of UniProt P00426
- Every structure of UniProt P00428
- Every structure of UniProt P07471
- Every structure of UniProt P00429
- Every structure of UniProt P04038
- Every structure of UniProt P07470
- Every structure of UniProt P13183
- Every structure of UniProt P00430
- Every structure of UniProt P10175
- Elsewhere: RCSB PDB 6JY3 · PDBe 6JY3 · UniProt P00396 · UniProt P68530 · UniProt P00415 · UniProt P00423 · UniProt P00426 · UniProt P00428 · UniProt P07471 · UniProt P00429 · UniProt P04038 · UniProt P07470 · UniProt P13183 · UniProt P00430 · UniProt P10175
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