Research workbench
Structure of L-2-haloacid dehalogenase from xanthobacter autotrophicus
Analyse Structure of L-2-haloacid dehalogenase from xanthobacter autotrophicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QQ5
- Type
- protein
- Length
- 490 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (L-2-haloacid dehalogenase)
- EC
- 3.8.1.2
- UniProt
- Q60099
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (L-2-haloacid dehalogenase) (EC 3.8.1.2) | protein | 245 | 54% helix, 12% strand | Q60099 |
Ligands and binding sites
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.57 | 0.86 | 20 | empty |
| 2 | 97 | 0.55 | 0.85 | 22 | empty |
| 3 | 71 | 0.33 | 0.75 | 15 | empty |
| 4 | 72 | 0.32 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2228 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 1QQ5 · Structure of L-2-haloacid dehalogenase from xanthobacter autotrophicus · the same entry in another collection · chain A against A, TM-score 1.00
- Q60099 · AlphaFold monomer V2.0 prediction for (S)-2-haloacid dehalogenase (Q60099) · a predicted model of the same protein · 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 Q60099
- Elsewhere: RCSB PDB 1QQ5 · PDBe 1QQ5 · UniProt Q60099
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