Research workbench
A novel iron centre in the split-Soret cytochrome c from Desulfovibrio desulfuricans ATCC 27774
Analyse A novel iron centre in the split-Soret cytochrome c from Desulfovibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H21
- Type
- protein
- Length
- 960 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.5
- Source
- DESULFOVIBRIO DESULFURICANS
- Molecule
- Split-soret cytochrome C
- UniProt
- P81040
- Ligands
- HEC
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.5 · 1 distinct chain · 55% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Split-soret cytochrome C | protein | 240 | 55% helix, 2% strand | P81040 |
Ligands and binding sites
- HEC · Heme C · ligand · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.81 | 0.84 | 76 | HEC |
| 2 | 836 | 0.81 | 0.83 | 78 | HEC |
| 3 | 133 | 0.62 | 0.86 | 35 | empty |
| 4 | 126 | 0.59 | 0.85 | 37 | empty |
| 5 | 257 | 0.55 | 0.76 | 29 | empty |
Interfaces
3 interfaces between chains.
- C–D · 4138 Ų buried · 51 hydrogen bonds · protein-protein
- A–B · 4129 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 352 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 cofactor (heme c attachment).
Compared structures
- 1H21 · A novel iron centre in the split-soret cytochrome C from desulfovibrio desulfuricans atcc… · the same entry in another collection · chain D against D, TM-score 1.00
- P81040 · AlphaFold monomer V2.0 prediction for split-soret cytochrome C (P81040) · a predicted model of the same protein · chain D against A, TM-score 1.00
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 P81040
- Elsewhere: RCSB PDB 1H21 · PDBe 1H21 · UniProt P81040
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