Research workbench
Structure of acetylated Pig somatic Cytochrome c (Aly39) at 1.5A
Analyse Structure of acetylated Pig somatic Cytochrome c (Aly39) at 1.5A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DVX
- Type
- protein
- Length
- 416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Sus scrofa
- Molecule
- Cytochrome c
- UniProt
- P62895
- Ligands
- FC6, HEC
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.5 · 1 distinct chain · 41% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome c | protein | 104 | 41% helix, 2% strand | P62895 |
Ligands and binding sites
- FC6 · Hexacyanoferrate(3-) · ligand · 7 copies · chains A, D, B, C
- HEC · Heme C · ligand · 4 copies · chains A, D, B, C
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 | 690 | 0.85 | 0.88 | 89 | HEC, FC6 |
| 2 | 689 | 0.83 | 0.86 | 90 | HEC, FC6 |
| 3 | 56 | 0.25 | 0.73 | 19 | empty |
Interfaces
4 interfaces between chains.
- B–C · 442 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 384 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 258 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 249 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 modified (heme c attachment, acetylation).
Compared structures
- P62895 · AlphaFold monomer V2.0 prediction for cytochrome C (P62895) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P62895
- Elsewhere: RCSB PDB 8DVX · PDBe 8DVX · UniProt P62895
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