MolNFT v1 · #80483 · protein
Dihydropteroate synthase in complex with phba and dhp+
3TYB: “Dihydropteroate synthase in complex with phba and dhp+”. X-ray diffraction, 3 ligands (XHP, PHB, SO4), 3 pockets (best druggability 0.56). MolNFT v1 #80483 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3TYB
- Type
- protein
- Length
- 526 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
- XHP, PHB, SO4
- Pockets
- 3 · best druggability 0.56
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 | 265 | 49% helix, 15% strand | Q81VW8 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 261 | 49% helix, 15% strand | Q81VW8 |
Ligands and binding sites
- XHP · 2-amino-6-methylidene-6,7-dihydropteridin-4(3H)-one · ligand · 2 copies · chains A, B
- PHB · P-hydroxybenzoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 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 | 224 | 0.56 | 0.79 | 36 | XHP, PHB, SO4 |
| 2 | 137 | 0.49 | 0.79 | 26 | XHP, SO4 |
| 3 | 55 | 0.31 | 0.76 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 340 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3TYB · Dihydropteroate Synthase in complex with pHBA and DHP+ · 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 3TYB · PDBe 3TYB · UniProt Q81VW8
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