Research workbench
Crystal structure of haloalkane dehalogenase RV2579 from mycobacterium tuberculosis
Analyse Crystal structure of haloalkane dehalogenase RV2579 from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QVB
- Type
- protein
- Length
- 593 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Haloalkane dehalogenase 3
- EC
- 3.8.1.5
- UniProt
- Q50642
- Ligands
- CL
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Haloalkane dehalogenase 3 (EC 3.8.1.5) | protein | 296 | 45% helix, 20% strand | Q50642 |
| B | Haloalkane dehalogenase 3 (EC 3.8.1.5) | protein | 297 | 45% helix, 19% strand | Q50642 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 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 | 427 | 0.67 | 0.79 | 49 | CL, EDO |
| 2 | 83 | 0.61 | 0.88 | 23 | CL, EDO |
| 3 | 114 | 0.49 | 0.80 | 18 | empty |
| 4 | 121 | 0.49 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 230 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2QVB · Crystal Structure of Haloalkane Dehalogenase Rv2579 from Mycobacterium tuberculosis · 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 Q50642
- Elsewhere: RCSB PDB 2QVB · PDBe 2QVB · UniProt Q50642
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