Research workbench
Crystal structure of cytochrome C' from thermochromatium tepidum
Analyse Crystal structure of cytochrome C' from thermochromatium tepidum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VRC
- Type
- protein
- Length
- 261 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C'
- UniProt
- C7G528
- Ligands
- HEC, CD, CL
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C' | protein | 130 | 74% helix, 3% strand | C7G528 |
| B | Cytochrome C' | protein | 131 | 73% helix, 3% strand | C7G528 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 9 copies · chains A, B
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.67 | 0.82 | 35 | HEC |
| 2 | 349 | 0.65 | 0.80 | 45 | HEC |
| 3 | 61 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 675 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 3VRC · Crystal structure of cytochrome c' from Thermochromatium tepidum · 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 C7G528
- Elsewhere: RCSB PDB 3VRC · PDBe 3VRC · UniProt C7G528
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