MolNFT v1 · #101789 · protein
Crystal structure of colwellia psychrerythraea cytochrome C
4O1W · Cytochrome C552: “Crystal structure of colwellia psychrerythraea cytochrome C”. X-ray diffraction, 2 ligands (HEC, SO4), 5 pockets (best druggability 0.82). MolNFT v1 #101789 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4O1W
- Type
- protein
- Length
- 471 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C552
- UniProt
- Q48A34
- Ligands
- HEC, SO4
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Cytochrome C552 | protein | 79 | 57% helix, 0% strand | Q48A34 |
| B, D, F | Cytochrome C552 | protein | 78 | 62% helix, 0% strand | Q48A34 |
Ligands and binding sites
- HEC · Heme C · ligand · 6 copies · chains A, B, D, C, E, F
- SO4 · Sulfate ion · ion · chains A, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.82 | 0.87 | 72 | HEC |
| 2 | 491 | 0.82 | 0.88 | 58 | HEC |
| 3 | 514 | 0.81 | 0.87 | 73 | HEC |
| 4 | 235 | 0.50 | 0.75 | 41 | empty |
| 5 | 153 | 0.41 | 0.74 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–D · 756 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 697 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 692 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 441 Ų buried · 2 hydrogen bonds · protein-protein
- A–E · 246 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4O1W · Crystal Structure of Colwellia psychrerythraea cytochrome c · the same entry in another collection · chain A against A, 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 Q48A34
- Elsewhere: RCSB PDB 4O1W · PDBe 4O1W · UniProt Q48A34
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