Research workbench
Crystal structure of cytochrome C' from rhodocyclus gelatinosus at 2.5 angstoms resolution
Analyse Crystal structure of cytochrome C' from rhodocyclus gelatinosus at 2.5 angstoms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JAF
- Type
- protein
- Length
- 256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C'
- UniProt
- P00142
- Ligands
- HEM
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 74% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome C' | protein | 128 | 74% helix, 2% strand | P00142 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.68 | 0.85 | 29 | HEM |
| 2 | 217 | 0.68 | 0.85 | 28 | HEM |
Interfaces
1 interface between chains.
- A–B · 669 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme attachment).
Compared structures
- 1JAF · Crystal structure of cytochrome C' from rhodocyclus gelatinosus at 2.5 angstoms resolution · the same entry in another collection · chain B against B, TM-score 1.00
- P00142 · AlphaFold monomer V2.0 prediction for cytochrome C' (P00142) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P00142
- Elsewhere: RCSB PDB 1JAF · PDBe 1JAF · UniProt P00142
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