MolNFT v1 · #124043 · protein
Crystal structure of the fluoroacetate dehalogenase RPA1163 - WT/5- fluorotryptophan
5K3C: “Crystal structure of the fluoroacetate dehalogenase RPA1163 - WT/5- fluorotryptophan”. X-ray diffraction, 1 ligand (CL), 2 pockets (best druggability 0.68). MolNFT v1 #124043 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5K3C
- Type
- protein
- Length
- 581 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
- CL
- Pockets
- 2 · best druggability 0.68
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 | 292 | 47% helix, 17% strand | Q6NAM1 |
| B | Fluoroacetate dehalogenase (EC 3.8.1.3) | protein | 289 | 46% helix, 17% strand | Q6NAM1 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.68 | 0.84 | 33 | CL |
| 2 | 352 | 0.66 | 0.80 | 40 | CL |
Interfaces
1 interface between chains.
- A–B · 1151 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (nonstandard).
Compared structures
- 5K3C · Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/5-Fluorotryptophan · 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 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 Q6NAM1
- Elsewhere: RCSB PDB 5K3C · PDBe 5K3C · UniProt Q6NAM1
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