Research workbench
Crystal structure of HsaD from Mycobacterium tuberculosis at 1.96 A resolution
Analyse Crystal structure of HsaD from Mycobacterium tuberculosis at 1.96 A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZJT
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.96
- Source
- Mycobacterium tuberculosis H37Rv
- Molecule
- 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
- EC
- 3.7.1.17, 3.7.1.8
- UniProt
- P9WNH5
- Ligands
- CL
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.96 · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase (EC 3.7.1.17, 3.7.1.8) | protein | 284 | 44% helix, 18% strand | P9WNH5 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.76 | 0.81 | 78 | CL |
| 2 | 507 | 0.71 | 0.81 | 49 | empty |
| 3 | 467 | 0.69 | 0.80 | 43 | EDO |
| 4 | 66 | 0.51 | 0.85 | 32 | empty |
| 5 | 92 | 0.43 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 550 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- P9WNH5 · AlphaFold monomer V2.0 prediction for 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P9WNH5
- Elsewhere: RCSB PDB 7ZJT · PDBe 7ZJT · UniProt P9WNH5
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