Research workbench
Bovine heart cytochrome C oxidase at the fully oxidized state
Analyse Bovine heart cytochrome C oxidase at 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
- 2OCC
- Type
- protein
- Length
- 3,564 residues
- Chains
- 26
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase
- EC
- 1.9.3.1
- UniProt
- P00396, P00404, P00415, P00423, P00426, P00428, P07471, P00429, P04038, P07470, P13183, P00430, P10175
- Ligands
- HEA, CU, MG, NA, ZN, PER
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 13 distinct chains · 58% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, N | Cytochrome C oxidase (EC 1.9.3.1) | protein | 514 | 71% helix, 2% strand | P00396 |
| B, O | Cytochrome C oxidase (EC 1.9.3.1) | protein | 227 | 33% helix, 26% strand | P00404 |
| C, P | Cytochrome C oxidase (EC 1.9.3.1) | protein | 261 | 75% helix, 0% strand | P00415 |
| D, Q | Cytochrome C oxidase (EC 1.9.3.1) | protein | 144 | 52% helix, 3% strand | P00423 |
| E, R | Cytochrome C oxidase (EC 1.9.3.1) | protein | 105 | 68% helix, 1% strand | P00426 |
| F, S | Cytochrome C oxidase (EC 1.9.3.1) | protein | 98 | 15% helix, 28% strand | P00428 |
| G, T | Cytochrome C oxidase (EC 1.9.3.1) | protein | 84 | 26% helix, 2% strand | P07471 |
| H, U | Cytochrome C oxidase (EC 1.9.3.1) | protein | 79 | 59% helix, 1% strand | P00429 |
| I, V | Cytochrome C oxidase (EC 1.9.3.1) | protein | 73 | 67% helix, 1% strand | P04038 |
| J, W | Cytochrome C oxidase (EC 1.9.3.1) | protein | 58 | 64% helix, 0% strand | P07470 |
| K, X | Cytochrome C oxidase (EC 1.9.3.1) | protein | 49 | 55% helix, 0% strand | P13183 |
| L, Y | Cytochrome C oxidase (EC 1.9.3.1) | protein | 47 | 57% helix, 0% strand | P00430 |
| M, Z | Cytochrome C oxidase (EC 1.9.3.1) | protein | 43 | 67% helix, 5% strand | P10175 |
Ligands and binding sites
- HEA · Heme-A · ligand · 4 copies · chains A, B, N, O
- CU · Copper (II) ion · metal · 6 copies · chains A, B, N, O
- MG · Magnesium ion · metal · 2 copies · chains A, B, N, O
- NA · Sodium ion · metal · 2 copies · chains A, N
- ZN · Zinc ion · metal · 2 copies · chains F, S
- PER · Peroxide ion · ion · 2 copies · chains A, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.91 | 0.93 | 116 | HEA, PER |
| 2 | 1181 | 0.91 | 0.93 | 119 | HEA, PER |
| 3 | 1122 | 0.86 | 0.86 | 103 | empty |
| 4 | 1050 | 0.85 | 0.86 | 83 | empty |
| 5 | 634 | 0.82 | 0.86 | 73 | empty |
Interfaces
80 interfaces between chains.
- N–O · 3571 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 3568 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2652 Ų buried · 14 hydrogen bonds · protein-protein
- N–P · 2650 Ų buried · 14 hydrogen bonds · protein-protein
- N–Y · 1794 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2OCC · Bovine heart cytochrome C oxidase at the fully oxidized state · the same entry in another collection · chain J against J, 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 P00404
- 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 2OCC · PDBe 2OCC · UniProt P00396 · UniProt P00404 · 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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