Research workbench
Crystal structure of dbja (wild type type I)
Analyse Crystal structure of dbja (wild type type I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A2M
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase
- EC
- 3.8.1.5
- UniProt
- P59337
- Ligands
- GLC, FRU, CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 298 | 48% helix, 20% strand | P59337 |
| B | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 300 | 48% helix, 20% strand | P59337 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.67 | 0.85 | 39 | CL |
| 2 | 198 | 0.64 | 0.83 | 29 | CL |
| 3 | 114 | 0.40 | 0.76 | 22 | FRU, GLC |
| 4 | 89 | 0.36 | 0.75 | 20 | FRU |
Interfaces
1 interface between chains.
- A–B · 845 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 P59337
- Elsewhere: RCSB PDB 3A2M · PDBe 3A2M · UniProt P59337
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