Research workbench
Crystal structure of the fluoroacetate dehalogenase D104 mutant from burkholderia sp. FA1 in complex with fluoroacetate
Analyse Crystal structure of the fluoroacetate dehalogenase D104 mutant from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B12
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluoroacetate dehalogenase
- EC
- 3.8.1.3
- UniProt
- Q1JU72
- Ligands
- FAH, MG
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fluoroacetate dehalogenase (EC 3.8.1.3) | protein | 294 | 50% helix, 17% strand | Q1JU72 |
Ligands and binding sites
- FAH · fluoroacetic acid · ligand · 3 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.64 | 0.94 | 19 | FAH |
| 2 | 63 | 0.27 | 0.73 | 19 | empty |
| 3 | 53 | 0.24 | 0.71 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1159 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3B12 · Crystal Structure of the Fluoroacetate Dehalogenase D104 mutant from Burkholderia sp. FA1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q1JU72 · AlphaFold monomer V2.0 prediction for fluoroacetate dehalogenase (Q1JU72) · 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 Q1JU72
- Elsewhere: RCSB PDB 3B12 · PDBe 3B12 · UniProt Q1JU72
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