Research workbench
The crystal structure of bonito (katsuo) ferrocytochrome C at 2.3 ångströms resolution. II. structure and function
Analyse The crystal structure of bonito (katsuo) ferrocytochrome C at 2.3 ångströms… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1CYC
- Type
- protein
- Length
- 206 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferrocytochrome C
- UniProt
- P00025
- Ligands
- HEC
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ferrocytochrome C | protein | 103 | 37% helix, 2% strand | P00025 |
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
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 | 318 | 0.77 | 0.88 | 37 | HEC |
| 2 | 312 | 0.77 | 0.88 | 37 | HEC |
| 3 | 110 | 0.46 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 347 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 1CYC · The crystal structure of bonito (katsuo) ferrocytochrome C at 2.3 ångströms resolution.… · the same entry in another collection · chain B against B, TM-score 1.00
- P00025 · AlphaFold monomer V2.0 prediction for cytochrome C (P00025) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 P00025
- Elsewhere: RCSB PDB 1CYC · PDBe 1CYC · UniProt P00025
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