MolNFT v1 · #10831 · protein
Wild-type plasmodium falciparum dihydrofolate reductase- thymidylate synthase (pfdhfr-ts) complexed with WR99210, NADPH, and dump
1J3I · Bifunctional dihydrofolate reductase-thymidylate synthase: “Wild-type plasmodium falciparum dihydrofolate reductase- thymidylate synthase (pfdhfr-ts) complexed with…”. X-ray diffraction, 3 ligands (WRA, NDP, UMP), 17 pockets (best…
- PDB
- 1J3I
- Type
- protein
- Length
- 1,104 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
- 17 · best druggability 0.74
Structure
x-ray diffraction · 4 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 | 223 | 29% helix, 29% strand | P13922 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 226 | 28% helix, 31% strand | P13922 |
| C | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 327 | 36% helix, 21% strand | P13922 |
| D | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 328 | 34% 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
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.74 | 0.83 | 48 | WRA, NDP |
| 2 | 463 | 0.73 | 0.82 | 47 | WRA, NDP |
| 3 | 717 | 0.72 | 0.78 | 72 | UMP |
| 4 | 681 | 0.71 | 0.78 | 70 | UMP |
| 5 | 295 | 0.54 | 0.75 | 34 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2662 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 971 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 947 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 854 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 775 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1J3I · Wild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS)… · 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 C against A, TM-score 0.98
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 1J3I · PDBe 1J3I · UniProt P13922
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