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The crystal structure of cytochrome C' from rubrivivax gelatinosus at 1.3 a resolution and pH 8.0
Analyse The crystal structure of cytochrome C' from rubrivivax gelatinosus at 1.3 a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J8W
- 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
- HEC
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome C' | protein | 128 | 73% helix, 2% strand | P00142 |
Ligands and binding sites
- HEC · Heme C · 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 | 187 | 0.65 | 0.84 | 25 | HEC |
| 2 | 176 | 0.63 | 0.84 | 24 | HEC |
Interfaces
1 interface between chains.
- A–B · 659 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 2J8W · The crystal structure of cytochrome c' from Rubrivivax gelatinosus at 1.3 A Resolution… · the same entry in another collection · chain A against A, 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 2J8W · PDBe 2J8W · UniProt P00142
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