Research workbench
The structural characterization of burkholderia pseudomallei oppa.
Analyse The structural characterization of burkholderia pseudomallei oppa. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZS6
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic oligopeptide-binding protein; Oligopeptide dva
- UniProt
- Q63ID0
- Ligands
- CL
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Periplasmic oligopeptide-binding protein | protein | 506 | 35% helix, 22% strand | Q63ID0 |
| B | Oligopeptide dva | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.75 | 0.97 | 32 | empty |
| 2 | 179 | 0.51 | 0.78 | 24 | empty |
| 3 | 105 | 0.36 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 374 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3ZS6 · The Structural characterization of Burkholderia pseudomallei OppA. · 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 Q63ID0
- Elsewhere: RCSB PDB 3ZS6 · PDBe 3ZS6 · UniProt Q63ID0
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