MolNFT v1 · #57498 · protein
Crystal structure of the C-terminal domain of cytochrome cz from chlorobium tepidum
3A9F: “Crystal structure of the C-terminal domain of cytochrome cz from chlorobium tepidum”. X-ray diffraction, 3 ligands (HEC, NA, SO4), 4 pockets (best druggability 0.65). MolNFT v1 #57498 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3A9F
- Type
- protein
- Length
- 155 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C
- UniProt
- O07091
- Ligands
- HEC, NA, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 59% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C | protein | 78 | 60% helix, 0% strand | O07091 |
| B | Cytochrome C | protein | 77 | 58% helix, 0% strand | O07091 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal
- SO4 · Sulfate ion · ion · chains A, B
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · chains A, B
- PGE · Triethylene glycol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.65 | 0.87 | 21 | HEC |
| 2 | 122 | 0.64 | 0.87 | 23 | HEC |
| 3 | 132 | 0.42 | 0.75 | 19 | empty |
| 4 | 86 | 0.36 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 343 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 3A9F · Crystal structure of the C-terminal domain of cytochrome cz from Chlorobium tepidum · the same entry in another collection · chain A against A, TM-score 1.00
- O07091 · AlphaFold monomer V2.0 prediction for cytochrome C (O07091) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O07091
- Elsewhere: RCSB PDB 3A9F · PDBe 3A9F · UniProt O07091
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