Research workbench
Cytochrome C oxidase from rhodobacter sphaeroides in the reduced state
Analyse Cytochrome C oxidase from rhodobacter sphaeroides in the reduced state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WEH
- Type
- protein
- Length
- 2,211 residues
- Chains
- 8
- 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
- P33517, Q03736, P84153, Q8KRK5
- Ligands
- 3PE, HEA, LMU, CU1, MG, CA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 6 distinct chains · 58% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Cytochrome C oxidase subunit 1 (EC 1.9.3.1) | protein | 547 | 72% helix, 2% strand | P33517 |
| B | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 254 | 33% helix, 25% strand | Q03736 |
| C, I | Cytochrome C oxidase polypeptide III (cytochrome AA3 subunit 3) (EC 1.9.3.1) | protein | 264 | 72% helix, 1% strand | P84153 |
| D | AA3-type cytochrome C oxidase subunit IV | protein | 40 | 80% helix, 0% strand | Q8KRK5 |
| H | Cytochrome C oxidase subunit 2 (EC 1.9.3.1) | protein | 253 | 33% helix, 26% strand | Q03736 |
| J | AA3-type cytochrome C oxidase subunit IV | protein | 42 | 76% helix, 0% strand | Q8KRK5 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 11 copies · chains A, C, D, G, I, J, B, H
- HEA · Heme-A · ligand · 4 copies · chains A, B, G, H
- LMU · Dodecyl-alpha-D-maltoside · ligand · 3 copies · chains G, C, J
- CU1 · Copper (I) ion · metal · 6 copies · chains A, G, B, H
- MG · Magnesium ion · metal · 2 copies · chains A, B, G, H
- CA · Calcium ion · metal · 2 copies · chains A, G
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 | 1195 | 0.90 | 0.92 | 116 | HEA, CU1 |
| 2 | 1194 | 0.90 | 0.91 | 126 | HEA, MG |
| 3 | 987 | 0.85 | 0.86 | 75 | 3PE |
| 4 | 1184 | 0.83 | 0.83 | 74 | 3PE |
| 5 | 991 | 0.80 | 0.81 | 93 | 3PE |
Interfaces
17 interfaces between chains.
- G–H · 3989 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3893 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 2752 Ų buried · 14 hydrogen bonds · protein-protein
- G–I · 2710 Ų buried · 14 hydrogen bonds · protein-protein
- I–J · 660 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5WEH · Cytochrome c oxidase from Rhodobacter sphaeroides in the reduced state · the same entry in another collection · chain J against J, TM-score 1.00
- P33517 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 1 (P33517) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q03736 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit 2 (Q03736) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P33517
- Every structure of UniProt Q03736
- Every structure of UniProt P84153
- Every structure of UniProt Q8KRK5
- Elsewhere: RCSB PDB 5WEH · PDBe 5WEH · UniProt P33517 · UniProt Q03736 · UniProt P84153 · UniProt Q8KRK5
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