MolNFT v1 · #10833 · protein
Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (pfdhfr-ts) complexed with WR99210, NADPH, and dump
1J3K · Bifunctional dihydrofolate reductase-thymidylate synthase: “Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase…”. X-ray diffraction, 3 ligands (WRA, NDP, UMP), 15 pockets…
- PDB
- 1J3K
- Type
- protein
- Length
- 1,094 residues
- Chains
- 4
- 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
- P13922
- Ligands
- WRA, NDP, UMP
- Pockets
- 15 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 26% 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 | 221 | 31% helix, 29% strand | P13922 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 221 | 26% helix, 32% strand | P13922 |
| C, D | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 326 | 36% helix, 21% strand | P13922 |
Ligands and binding sites
- WRA · 6,6-dimethyl-1-[3-(2,4,5-trichlorophenoxy)propoxy]-1,6-dihydro-1,3,5-triazine-2,4-diamine · 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 C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.73 | 0.82 | 47 | WRA, NDP |
| 2 | 593 | 0.71 | 0.79 | 55 | UMP |
| 3 | 475 | 0.71 | 0.81 | 49 | WRA, NDP |
| 4 | 537 | 0.68 | 0.78 | 55 | UMP |
| 5 | 271 | 0.54 | 0.76 | 31 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2672 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 966 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 941 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 827 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 815 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1J3K · Quadruple mutant (N51I+C59R+S108N+I164L) Plasmodium falciparum dihydrofolate… · the same entry in another collection · chain D against D, TM-score 1.00
- P13922 · AlphaFold monomer V2.0 prediction for bifunctional dihydrofolate reductase-thymidylate… · 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 P13922
- Elsewhere: RCSB PDB 1J3K · PDBe 1J3K · UniProt P13922
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