MolNFT v1 · #77078 · protein
Crystal structure of the fluoroacetate dehalogenase RPA1163 - WT/GLYCOLATE
3R3Z: “Crystal structure of the fluoroacetate dehalogenase RPA1163 - WT/GLYCOLATE”. X-ray diffraction, 2 ligands (GOA, NI), 10 pockets (best druggability 0.76). MolNFT v1 #77078 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3R3Z
- Type
- protein
- Length
- 1,196 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluoroacetate dehalogenase
- EC
- 3.8.1.3
- UniProt
- Q6NAM1
- Ligands
- GOA, NI
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fluoroacetate dehalogenase (EC 3.8.1.3) | protein | 304 | 46% helix, 16% strand | Q6NAM1 |
| B | Fluoroacetate dehalogenase (EC 3.8.1.3) | protein | 295 | 46% helix, 17% strand | Q6NAM1 |
| C | Fluoroacetate dehalogenase (EC 3.8.1.3) | protein | 301 | 45% helix, 16% strand | Q6NAM1 |
| D | Fluoroacetate dehalogenase (EC 3.8.1.3) | protein | 296 | 48% helix, 16% strand | Q6NAM1 |
Ligands and binding sites
- GOA · Glycolic acid · ligand · 4 copies · chains A, B, C, D
- NI · Nickel (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.76 | 0.81 | 90 | empty |
| 2 | 125 | 0.45 | 0.77 | 22 | empty |
| 3 | 96 | 0.42 | 0.78 | 22 | empty |
| 4 | 121 | 0.39 | 0.75 | 25 | empty |
| 5 | 65 | 0.39 | 0.79 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1192 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1186 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 440 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 439 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3R3Z · Crystal Structure of the Fluoroacetate Dehalogenase RPA1163 - WT/Glycolate · the same entry in another collection · chain D against D, TM-score 1.00
- Q6NAM1 · AlphaFold monomer V2.0 prediction for fluoroacetate dehalogenase (Q6NAM1) · a predicted model of the same protein · chain D 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 3R3Z · PDBe 3R3Z · UniProt Q6NAM1
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