Research workbench
The complex structure of burkholderia pseudomallei dsba bound to a peptide
Analyse The complex structure of burkholderia pseudomallei dsba bound to a peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VYO
- Type
- protein
- Length
- 781 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein; Disulfide bond formation protein B
- UniProt
- Q63Y08, Q63RY4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | THIOL:DISULFIDE interchange protein | protein | 189 | 55% helix, 14% strand | Q63Y08 |
| C | THIOL:DISULFIDE interchange protein | protein | 191 | 53% helix, 14% strand | Q63Y08 |
| D | THIOL:DISULFIDE interchange protein | protein | 188 | 54% helix, 14% strand | Q63Y08 |
| E, F, G, H | Disulfide bond formation protein B | protein | 6 | 0% helix, 17% strand | Q63RY4 |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 233 | 0.82 | 0.95 | 32 | empty |
| 2 | 617 | 0.73 | 0.80 | 52 | empty |
| 3 | 683 | 0.71 | 0.78 | 72 | empty |
| 4 | 83 | 0.44 | 0.80 | 21 | empty |
| 5 | 77 | 0.36 | 0.76 | 14 | empty |
Interfaces
11 interfaces between chains.
- A–C · 578 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 566 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 462 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 454 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 452 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5VYO · The complex structure of Burkholderia pseudomallei DsbA bound to a peptide · the same entry in another collection · chain H against H, TM-score 1.00
- Q63RY4 · AlphaFold monomer V2.0 prediction for disulfide bond formation protein B (Q63RY4) · a predicted model of the same protein · chain G against A, TM-score 0.48
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 Q63Y08
- Every structure of UniProt Q63RY4
- Elsewhere: RCSB PDB 5VYO · PDBe 5VYO · UniProt Q63Y08 · UniProt Q63RY4
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