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Crystal structure of dbja (his-dbja)
Analyse Crystal structure of dbja (his-dbja) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3AFI
- Type
- protein
- Length
- 1,204 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase
- EC
- 3.8.1.5
- UniProt
- P59337
- Ligands
- CL
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 301 | 46% helix, 19% strand | P59337 |
| A | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 301 | 47% helix, 20% strand | P59337 |
| B | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 302 | 46% helix, 20% strand | P59337 |
| F | Haloalkane dehalogenase (EC 3.8.1.5) | protein | 300 | 47% helix, 19% strand | P59337 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains E, A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.76 | 0.85 | 46 | empty |
| 2 | 220 | 0.64 | 0.83 | 35 | CL |
| 3 | 193 | 0.64 | 0.83 | 29 | CL |
| 4 | 223 | 0.63 | 0.82 | 30 | CL |
| 5 | 191 | 0.62 | 0.83 | 27 | CL |
Interfaces
3 interfaces between chains.
- E–A · 948 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 885 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 695 Ų buried · 4 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 3AFI · PDBe 3AFI · UniProt P59337
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