MolNFT v1 · #154864 · protein
Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (pfdhfr-ts) complexed with B12128 and NADPH
6KOT · Bifunctional dihydrofolate reductase-thymidylate synthase: “Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase…”. X-ray diffraction, 3 ligands (DQ0, NDP, UMP), 15 pockets…
- PDB
- 6KOT
- Type
- protein
- Length
- 1,048 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase
- UniProt
- D9N170
- Ligands
- DQ0, NDP, UMP
- Pockets
- 15 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 526 | 34% helix, 25% strand | D9N170 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 522 | 33% helix, 25% strand | D9N170 |
Ligands and binding sites
- DQ0 · 4-[3-[[2,6-bis(azanyl)-5-(3-chlorophenyl)pyrimidin-4-yl]methoxy]phenoxy]butanoic acid · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 554 | 0.74 | 0.82 | 50 | DQ0, NDP |
| 2 | 573 | 0.73 | 0.80 | 50 | DQ0, NDP |
| 3 | 639 | 0.71 | 0.78 | 57 | UMP |
| 4 | 581 | 0.70 | 0.79 | 62 | UMP |
| 5 | 173 | 0.50 | 0.78 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3981 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 6KOT · 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 6KOT · PDBe 6KOT · UniProt D9N170
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