Research workbench
Bordetella alcaligenes hdah native
Analyse Bordetella alcaligenes hdah native in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5G1B
- Type
- protein
- Length
- 741 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone deacetylase-like amidohydrolase
- EC
- 3.5.1.4
- UniProt
- Q70I53
- Ligands
- K, ZN
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone deacetylase-like amidohydrolase (EC 3.5.1.4) | protein | 371 | 39% helix, 14% strand | Q70I53 |
| B | Histone deacetylase-like amidohydrolase (EC 3.5.1.4) | protein | 370 | 39% helix, 14% strand | Q70I53 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.63 | 0.88 | 31 | empty |
| 2 | 439 | 0.63 | 0.77 | 39 | empty |
| 3 | 83 | 0.61 | 0.89 | 32 | empty |
| 4 | 217 | 0.48 | 0.75 | 28 | empty |
| 5 | 173 | 0.45 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 399 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 Q70I53
- Elsewhere: RCSB PDB 5G1B · PDBe 5G1B · UniProt Q70I53
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