Research workbench
Crystal structure of B. anthracis dhps with compound 6: 3-[6- (trifluoromethyl)-1H-benzimidazol-2-YL]PROPAN-1-ol
Analyse Crystal structure of B. anthracis dhps with compound 6: 3-[6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NIR
- Type
- protein
- Length
- 538 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- Q81VW8
- Ligands
- 6DH, SO4
- Pockets
- 4 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 274 | 47% helix, 15% strand | Q81VW8 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 264 | 47% helix, 15% strand | Q81VW8 |
Ligands and binding sites
- 6DH · 3-[6-(trifluoromethyl)-1H-benzimidazol-2-yl]propan-1-ol · ligand · 3 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.49 | 0.78 | 28 | SO4 |
| 2 | 58 | 0.49 | 0.85 | 14 | empty |
| 3 | 68 | 0.38 | 0.79 | 16 | SO4 |
| 4 | 60 | 0.29 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 346 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4NIR · Crystal structure of B. anthracis DHPS with compound 6… · 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 Q81VW8
- Elsewhere: RCSB PDB 4NIR · PDBe 4NIR · UniProt Q81VW8
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