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Crystal structure of 2-haloacid dehalogenase from pseudomonas syringae pv. tomato DC3000
Analyse Crystal structure of 2-haloacid dehalogenase from pseudomonas syringae pv.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VAY
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Had-superfamily hydrolase
- UniProt
- Q88B12
- Ligands
- MG, IOD
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Had-superfamily hydrolase | protein | 230 | 53% helix, 13% strand | Q88B12 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.79 | 0.86 | 46 | IOD |
| 2 | 544 | 0.74 | 0.82 | 53 | MG, IOD |
| 3 | 476 | 0.74 | 0.83 | 41 | MG, IOD |
| 4 | 117 | 0.41 | 0.76 | 27 | empty |
| 5 | 50 | 0.39 | 0.82 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 723 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3VAY · Crystal structure of 2-Haloacid Dehalogenase from Pseudomonas syringae pv. Tomato DC3000 · 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 Q88B12
- Elsewhere: RCSB PDB 3VAY · PDBe 3VAY · UniProt Q88B12
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