MolNFT v1 · #159150 · protein
Dihydropteroate synthase from xanthomonas albilineans in complex with 7,8-dihydropteroate
6OFW: “Dihydropteroate synthase from xanthomonas albilineans in complex with 7,8-dihydropteroate”. X-ray diffraction, 2 ligands (22D, SO4), 3 pockets (best druggability 0.48). MolNFT v1 #159150 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6OFW
- Type
- protein
- Length
- 517 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydropteroate synthase
- EC
- 2.5.1.15
- UniProt
- D2UDM3
- Ligands
- 22D, SO4
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 255 | 50% helix, 17% strand | D2UDM3 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 262 | 48% helix, 16% strand | D2UDM3 |
Ligands and binding sites
- 22D · 4-{[(2-amino-4-oxo-3,4-dihydropteridin-6-yl) methyl]amino}benzoic acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.48 | 0.78 | 25 | 22D, SO4 |
| 2 | 140 | 0.44 | 0.76 | 28 | 22D, SO4 |
| 3 | 50 | 0.29 | 0.75 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 1205 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6OFW · Dihydropteroate synthase from Xanthomonas albilineans in complex with 7,8-dihydropteroate · 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 D2UDM3
- Elsewhere: RCSB PDB 6OFW · PDBe 6OFW · UniProt D2UDM3
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