Research workbench
Dihydropteroate synthase in complex with ppi and dhp+
Analyse Dihydropteroate synthase in complex with ppi and dhp+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TYD
- Type
- protein
- Length
- 533 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
- POP, XHP, SO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 271 | 48% helix, 16% strand | Q81VW8 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 262 | 49% helix, 15% strand | Q81VW8 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- XHP · 2-amino-6-methylidene-6,7-dihydropteridin-4(3H)-one · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 12 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.58 | 0.78 | 42 | POP, XHP |
| 2 | 165 | 0.54 | 0.80 | 27 | POP, XHP |
| 3 | 69 | 0.31 | 0.75 | 17 | empty |
| 4 | 52 | 0.28 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 354 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3TYD · Dihydropteroate Synthase in complex with PPi 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 3TYD · PDBe 3TYD · UniProt Q81VW8
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