Research workbench
Crystal structure of the c-type cytochrome SorU from Sinorhizobium meliloti
Analyse Crystal structure of the c-type cytochrome SorU from Sinorhizobium meliloti in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PWA
- Type
- protein
- Length
- 344 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.19
- Source
- Sinorhizobium meliloti
- Molecule
- Putative cytochrome C
- UniProt
- Q92M25
- Ligands
- HEC
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · resolution 2.19 · 3 distinct chains · 57% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative cytochrome C | protein | 86 | 56% helix, 7% strand | Q92M25 |
| C | Putative cytochrome C | protein | 85 | 58% helix, 7% strand | Q92M25 |
| D | Putative cytochrome C | protein | 87 | 56% helix, 7% strand | Q92M25 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.73 | 0.87 | 38 | HEC |
| 2 | 244 | 0.72 | 0.87 | 37 | HEC |
| 3 | 200 | 0.66 | 0.84 | 29 | HEC |
| 4 | 211 | 0.66 | 0.84 | 30 | HEC |
| 5 | 548 | 0.64 | 0.76 | 48 | empty |
Interfaces
4 interfaces between chains.
- B–D · 519 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 511 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 429 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 4PWA · Crystal structure of the C-type cytochrome soru from sinorhizobium meliloti · the same entry in another collection · chain A 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 Q92M25
- Elsewhere: RCSB PDB 4PWA · PDBe 4PWA · UniProt Q92M25
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