MolNFT v1 · #14307 · protein
Structure of cytochrome C oxidase from rhodobactor sphaeroides (wild type)
1M56: “Structure of cytochrome C oxidase from rhodobactor sphaeroides (wild type)”. X-ray diffraction, 5 ligands (3PE, HEA, CU), 20 pockets (best druggability 0.90). MolNFT v1 #14307 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1M56
- Type
- protein
- Length
- 2,228 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C oxidase
- EC
- 1.9.3.1
- UniProt
- P33517, Q03736, P84153, Q8KRK5
- Ligands
- 3PE, HEA, CU, MG, CA
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Cytochrome C oxidase (EC 1.9.3.1) | protein | 547 | 71% helix, 2% strand | P33517 |
| B, H | Cytochrome C oxidase (EC 1.9.3.1) | protein | 260 | 38% helix, 24% strand | Q03736 |
| C, I | Cytochrome C oxidase (EC 1.9.3.1) | protein | 265 | 72% helix, 1% strand | P84153 |
| D, J | Cytochrome C oxidase (EC 1.9.3.1) | protein | 42 | 74% helix, 0% strand | Q8KRK5 |
Ligands and binding sites
- 3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 12 copies · chains A, C, D, B, G, I, J, H
- HEA · Heme-A · ligand · 4 copies · chains A, B, G, H
- CU · Copper (II) ion · metal · 6 copies · chains A, B, G, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.90 | 0.92 | 108 | CU, HEA |
| 2 | 1186 | 0.90 | 0.91 | 109 | HEA |
| 3 | 608 | 0.86 | 0.91 | 92 | 3PE |
| 4 | 974 | 0.85 | 0.85 | 81 | 3PE |
| 5 | 814 | 0.77 | 0.80 | 83 | 3PE |
Interfaces
17 interfaces between chains.
- G–H · 3997 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 3989 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 2766 Ų buried · 17 hydrogen bonds · protein-protein
- G–I · 2750 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 621 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1M56 · Structure of cytochrome c oxidase from Rhodobactor sphaeroides (Wild Type) · 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 G 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 1M56 · PDBe 1M56 · UniProt P33517 · UniProt Q03736 · UniProt P84153 · UniProt Q8KRK5
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