Research workbench
Crystal Structure of B562RIL with engineered disulfide bond A20C-Q25C
Analyse Crystal Structure of B562RIL with engineered disulfide bond A20C-Q25C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YO5
- Type
- protein
- Length
- 849 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Escherichia coli
- Molecule
- Soluble cytochrome b562
- UniProt
- P0ABE7
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · resolution 2.2 · 3 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Soluble cytochrome b562 | protein | 107 | 80% helix, 0% strand | P0ABE7 |
| B, D, E, F, H | Soluble cytochrome b562 | protein | 106 | 78% helix, 0% strand | P0ABE7 |
| G | Soluble cytochrome b562 | protein | 105 | 74% helix, 0% strand | P0ABE7 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1053 | 0.82 | 0.83 | 106 | empty |
| 2 | 358 | 0.59 | 0.76 | 31 | empty |
| 3 | 284 | 0.57 | 0.77 | 40 | empty |
| 4 | 130 | 0.53 | 0.82 | 21 | empty |
| 5 | 82 | 0.49 | 0.83 | 16 | empty |
Interfaces
16 interfaces between chains.
- B–D · 459 Ų buried · 8 hydrogen bonds · protein-protein
- C–G · 450 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 443 Ų buried · 5 hydrogen bonds · protein-protein
- C–H · 405 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 288 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5YO5 · Crystal structure of B562RIL with engineered disulfide bond A20C-Q25C · the same entry in another collection · chain H against H, TM-score 1.00
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 P0ABE7
- Elsewhere: RCSB PDB 5YO5 · PDBe 5YO5 · UniProt P0ABE7
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