Research workbench
Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Reduced State
Analyse Monomeric Form of Bovine Heart Cytochrome c Oxidase in the Fully Reduced State in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JY4
- Type
- protein
- Length
- 1,729 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.95
- Source
- Bos taurus
- 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
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · resolution 1.95 · 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, 1% 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 | 66% 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 | 32% 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 | 64% helix, 0% strand | P00430 |
| M | Cytochrome c oxidase subunit 8B | protein | 40 | 60% helix, 3% strand | P10175 |
Ligands and binding sites
- CQX · (2S,3S,4S,5S,6R)-2-(2-decoxyethoxy)-6-(hydroxymethyl) oxane-3,4,5-triol · ligand · 7 copies · chains A, B, I, D, K, M, C, G
- CDL · Cardiolipin · ligand · 3 copies · chains A, B, I, C, J, L
- 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.91 | 0.93 | 134 | HEA, CQX |
| 2 | 965 | 0.87 | 0.88 | 103 | PGV, PEK |
| 3 | 926 | 0.83 | 0.84 | 96 | empty |
| 4 | 81 | 0.75 | 0.98 | 37 | empty |
| 5 | 956 | 0.73 | 0.77 | 81 | CQX |
Interfaces
34 interfaces between chains.
- A–B · 3522 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2598 Ų buried · 17 hydrogen bonds · protein-protein
- A–L · 1741 Ų buried · 19 hydrogen bonds · protein-protein
- B–I · 1690 Ų buried · 17 hydrogen bonds · protein-protein
- C–G · 1675 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, formylation).
Compared structures
- 6JY4 · Monomeric form of bovine heart cytochrome C oxidase in the fully reduced 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 6JY4 · PDBe 6JY4 · 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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