Research workbench
Crystal structure of the fluoroacetate dehalogenase RPA1163 - ASP110ASN/GLYCOLATE - cocrystallized
Analyse Crystal structure of the fluoroacetate dehalogenase RPA1163… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K3E
- Type
- protein
- Length
- 589 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluoroacetate dehalogenase
- EC
- 3.8.1.3
- UniProt
- Q6NAM1
- Ligands
- GOA, CL
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluoroacetate dehalogenase (EC 3.8.1.3) | protein | 295 | 46% helix, 17% strand | Q6NAM1 |
| B | Fluoroacetate dehalogenase (EC 3.8.1.3) | protein | 294 | 45% helix, 17% strand | Q6NAM1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.54 | 0.82 | 28 | CL |
| 2 | 135 | 0.48 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1160 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5K3E · Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - Asp110Asn/Glycolate… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6NAM1 · AlphaFold monomer V2.0 prediction for fluoroacetate dehalogenase (Q6NAM1) · a predicted model of the same protein · chain B 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 Q6NAM1
- Elsewhere: RCSB PDB 5K3E · PDBe 5K3E · UniProt Q6NAM1
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