Research workbench
Crystal structure of dl-2-haloacid dehalogenase mutant with 2-bromo-2- methylpropionate
Analyse Crystal structure of dl-2-haloacid dehalogenase mutant with 2-bromo-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WJ8
- Type
- protein
- Length
- 1,788 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dl-2-haloacid dehalogenase
- EC
- 3.8.1.10
- UniProt
- A6BM74
- Ligands
- B2P
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 60% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G | Dl-2-haloacid dehalogenase (EC 3.8.1.10) | protein | 298 | 60% helix, 1% strand | A6BM74 |
Ligands and binding sites
- B2P · 2-bromo-2-methylpropanoic acid · ligand · 6 copies · chains A, B, D, E, F, G
- GOL · Glycerol · additive · 6 copies · chains A, D, B, G, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.83 | 0.95 | 49 | empty |
| 2 | 235 | 0.83 | 0.95 | 53 | empty |
| 3 | 137 | 0.77 | 0.95 | 35 | empty |
| 4 | 459 | 0.68 | 0.80 | 52 | empty |
| 5 | 51 | 0.68 | 0.97 | 15 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1941 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1930 Ų buried · 26 hydrogen bonds · protein-protein
- F–G · 1897 Ų buried · 21 hydrogen bonds · protein-protein
- B–G · 438 Ų buried · 3 hydrogen bonds · protein-protein
- E–G · 418 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3WJ8 · Crystal Structure of DL-2-haloacid dehalogenase mutant with 2-bromo-2-methylpropionate · the same entry in another collection · 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 A6BM74
- Elsewhere: RCSB PDB 3WJ8 · PDBe 3WJ8 · UniProt A6BM74
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.