Research workbench
Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (pfdhfr-ts) complexed with P218 and NADPH
Analyse Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DP3
- Type
- protein
- Length
- 1,089 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase
- EC
- 1.5.1.3, 2.1.1.45
- UniProt
- D9N170
- Ligands
- MMV, NDP, PO4
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 545 | 33% helix, 25% strand | D9N170 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 544 | 32% helix, 26% strand | D9N170 |
Ligands and binding sites
- MMV · 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl) oxy]propoxy}phenyl)propanoic acid · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 440 | 0.76 | 0.84 | 49 | MMV, NDP |
| 2 | 435 | 0.74 | 0.84 | 49 | MMV, NDP |
| 3 | 629 | 0.71 | 0.79 | 68 | PO4 |
| 4 | 645 | 0.71 | 0.78 | 67 | PO4 |
| 5 | 265 | 0.53 | 0.75 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 4131 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 4DP3 · Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate… · 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 D9N170
- Elsewhere: RCSB PDB 4DP3 · PDBe 4DP3 · UniProt D9N170
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