MolNFT v1 · #136900 · protein
E. COLI dihydropteroate synthase complexed with an 8-mercaptoguanine derivative: 2-((2-amino-9-methyl-6-oxo-6,9-dihydro-1H-purin-8-yl) thio)-N-phenylacetamide
5V79: “E. COLI dihydropteroate synthase complexed with an 8-mercaptoguanine derivative…”. X-ray diffraction, 2 ligands (8Y4, NO3), 4 pockets (best druggability 0.60). MolNFT v1 #136900 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5V79
- 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
- P0AC14
- Ligands
- 8Y4, NO3
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydropteroate synthase (EC 2.5.1.15) | protein | 266 | 47% helix, 17% strand | P0AC14 |
| B | Dihydropteroate synthase (EC 2.5.1.15) | protein | 259 | 49% helix, 17% strand | P0AC14 |
Ligands and binding sites
- 8Y4 · 2-[(2-amino-9-methyl-6-oxo-6,9-dihydro-1H-purin-8-yl) sulfanyl]-N-phenylacetamide · ligand · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 2 copies · chains A
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 | 279 | 0.60 | 0.79 | 41 | 8Y4, NO3 |
| 2 | 223 | 0.59 | 0.80 | 34 | 8Y4 |
| 3 | 77 | 0.38 | 0.77 | 15 | empty |
| 4 | 63 | 0.34 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1167 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5V79 · E. coli dihydropteroate synthase complexed with an 8-mercaptoguanine derivative… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AC14 · AlphaFold monomer V2.0 prediction for dihydropteroate synthase (P0AC14) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P0AC14
- Elsewhere: RCSB PDB 5V79 · PDBe 5V79 · UniProt P0AC14
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