Research workbench
Structure of bpsb deaceylase domain from bordetella bronchiseptica
Analyse Structure of bpsb deaceylase domain from bordetella bronchiseptica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BU6
- Type
- protein
- Length
- 528 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bpsb (pgab), poly-beta-1,6-N-acetyl-D-glucosamine N- deacetylase
- EC
- 3.5.1.33
- UniProt
- A0A0E1QQI1
- Ligands
- NI, SCN
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Bpsb (pgab), poly-beta-1,6-N-acetyl-D-glucosamine N- deacetylase (EC 3.5.1.33) | protein | 264 | 32% helix, 23% strand | A0A0E1QQI1 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 5 copies · chains A, B
- SCN · Thiocyanate ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
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 | 774 | 0.74 | 0.79 | 90 | NI, SCN |
| 2 | 507 | 0.66 | 0.78 | 59 | SCN |
| 3 | 74 | 0.32 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 627 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5BU6 · Structure of BpsB deaceylase domain from Bordetella bronchiseptica · 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 A0A0E1QQI1
- Elsewhere: RCSB PDB 5BU6 · PDBe 5BU6 · UniProt A0A0E1QQI1
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