MolNFT v1 · #170150 · protein
Crystal structure of haloalkane dehalogenase dbea-M1 loop variant from bradyrhizobium elkanii
6XY9: “Crystal structure of haloalkane dehalogenase dbea-M1 loop variant from bradyrhizobium elkanii”. X-ray diffraction, 1 ligand (CL), 5 pockets (best druggability 0.61). MolNFT v1 #170150 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6XY9
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase
- EC
- 3.8.1.5
- UniProt
- E2RV62
- Ligands
- CL
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 303 | 46% helix, 19% strand | E2RV62 |
| B | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 301 | 46% helix, 20% strand | E2RV62 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 201 | 0.61 | 0.82 | 33 | CL |
| 2 | 147 | 0.60 | 0.84 | 36 | CL |
| 3 | 95 | 0.38 | 0.76 | 16 | empty |
| 4 | 80 | 0.32 | 0.74 | 17 | empty |
| 5 | 86 | 0.31 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 997 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6XY9 · Crystal structure of haloalkane dehalogenase DbeA-M1 loop variant from Bradyrhizobium… · 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 E2RV62
- Elsewhere: RCSB PDB 6XY9 · PDBe 6XY9 · UniProt E2RV62
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