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The structure of a putative haloacid dehalogenase-like family hydrolase from bacteroides thetaiotaomicron vpi-5482
Analyse The structure of a putative haloacid dehalogenase-like family hydrolase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DDH
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative haloacid dehalogenase-like family hydrolase
- UniProt
- Q8A5Q8
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative haloacid dehalogenase-like family hydrolase | protein | 229 | 53% helix, 14% strand | Q8A5Q8 |
| B | Putative haloacid dehalogenase-like family hydrolase | protein | 223 | 54% helix, 14% strand | Q8A5Q8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.66 | 0.95 | 23 | empty |
| 2 | 411 | 0.66 | 0.79 | 37 | CL, GOL |
| 3 | 359 | 0.64 | 0.79 | 40 | CL, GOL |
| 4 | 208 | 0.51 | 0.76 | 30 | MG |
| 5 | 174 | 0.44 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1721 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 3DDH · The structure of a putative haloacid dehalogenase-like family hydrolase from Bacteroides… · 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 Q8A5Q8
- Elsewhere: RCSB PDB 3DDH · PDBe 3DDH · UniProt Q8A5Q8
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