MolNFT v1 · #101156 · protein
Crystal structure of B. anthracis dhps with compound 5: 4- [(TRIFLUOROMETHYL)SULFANYL]BENZAMIDE
4NIL · Dihydropteroate synthase: “Crystal structure of B. anthracis dhps with compound 5: 4- [(TRIFLUOROMETHYL)SULFANYL]BENZAMIDE”. X-ray diffraction, 2 ligands (2O8, SO4), 5 pockets (best druggability 0.45). MolNFT v1 #101156 on…
- PDB
- 4NIL
- Type
- protein
- Length
- 537 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
- 2O8, SO4
- Pockets
- 5 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 48% 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 | 263 | 49% helix, 15% strand | Q81VW8 |
Ligands and binding sites
- 2O8 · 4-[(trifluoromethyl)sulfanyl]benzamide · ligand · 2 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
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.45 | 0.76 | 32 | SO4 |
| 2 | 63 | 0.36 | 0.78 | 14 | SO4 |
| 3 | 53 | 0.32 | 0.76 | 12 | empty |
| 4 | 64 | 0.29 | 0.74 | 17 | empty |
| 5 | 57 | 0.27 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 350 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4NIL · Crystal structure of B. anthracis DHPS with compound 5… · 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 4NIL · PDBe 4NIL · UniProt Q81VW8
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