MolNFT v1 · #88920 · protein
Crystal structure of B. anthracis dhps with compound 17
4D9P · Dihydropteroate synthase: “Crystal structure of B. anthracis dhps with compound 17”. X-ray diffraction, 2 ligands (Z17, SO4), 3 pockets (best druggability 0.55). MolNFT v1 #88920 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4D9P
- Type
- protein
- Length
- 525 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- C3P9L8
- Ligands
- Z17, SO4
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 264 | 49% helix, 15% strand | C3P9L8 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 261 | 49% helix, 15% strand | C3P9L8 |
Ligands and binding sites
- Z17 · (3R)-3-(7-amino-1-methyl-4,5-dioxo-1,4,5,6-tetrahydropyrimido[4,5-c]pyridazin-3-yl)butanoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.55 | 0.78 | 38 | Z17 |
| 2 | 124 | 0.44 | 0.77 | 28 | Z17 |
| 3 | 58 | 0.28 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 350 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4D9P · Crystal structure of B. anthracis DHPS with compound 17 · 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 C3P9L8
- Elsewhere: RCSB PDB 4D9P · PDBe 4D9P · UniProt C3P9L8
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