Research workbench
The structure of oxidized rat cytochrome C (T28A) at 1.362 ångströms resolution.
Analyse The structure of oxidized rat cytochrome C (T28A) at 1.362 ångströms resolution. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C9M
- Type
- protein
- Length
- 416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C, somatic
- UniProt
- P62898
- Ligands
- HEC, FC6
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome C, somatic | protein | 104 | 42% helix, 2% strand | P62898 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, D, B, C
- FC6 · Hexacyanoferrate(3-) · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.83 | 0.86 | 88 | HEC, FC6 |
| 2 | 656 | 0.82 | 0.86 | 91 | HEC, FC6 |
| 3 | 69 | 0.29 | 0.73 | 16 | empty |
| 4 | 51 | 0.26 | 0.74 | 15 | empty |
Interfaces
4 interfaces between chains.
- B–C · 431 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 389 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 223 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 185 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 5C9M · The structure of oxidized rat cytochrome c (T28A) at 1.362 angstroms resolution. · the same entry in another collection · chain D against D, TM-score 1.00
- P62898 · AlphaFold monomer V2.0 prediction for cytochrome C, somatic (P62898) · 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 P62898
- Elsewhere: RCSB PDB 5C9M · PDBe 5C9M · UniProt P62898
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