MolNFT v1 · #120422 · protein
The complex structure of D-2-haloacid dehalogenase mutant with D-2-cpa
5GZX · (R)-2-haloacid dehalogenase: “The complex structure of D-2-haloacid dehalogenase mutant with D-2-cpa”. X-ray diffraction, 1 ligand (RCI), 14 pockets (best druggability 0.71). MolNFT v1 #120422 on GenesisL1: 3D structure, binding…
- PDB
- 5GZX
- Type
- protein
- Length
- 1,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (R)-2-haloacid dehalogenase
- EC
- 3.8.1.9
- UniProt
- Q52086
- Ligands
- RCI
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | (R)-2-haloacid dehalogenase (EC 3.8.1.9) | protein | 292 | 66% helix, 1% strand | Q52086 |
Ligands and binding sites
- RCI · (R)-2-Chloropropionic acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.71 | 0.98 | 21 | empty |
| 2 | 638 | 0.70 | 0.78 | 62 | empty |
| 3 | 482 | 0.65 | 0.77 | 52 | empty |
| 4 | 255 | 0.59 | 0.79 | 34 | empty |
| 5 | 135 | 0.56 | 0.83 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1125 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 1111 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1100 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1042 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 90 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5GZX · The complex structure of D-2-haloacid dehalogenase mutant with D-2-CPA · the same entry in another collection · chain A against A, TM-score 1.00
- Q52086 · AlphaFold monomer V2.0 prediction for (R)-2-haloacid dehalogenase (Q52086) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q52086
- Elsewhere: RCSB PDB 5GZX · PDBe 5GZX · UniProt Q52086
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