Research workbench
Double mutant (C59R+S108N) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (pfdhfr-ts) complexed with pyrimethamine, NADPH, and dump
Analyse Double mutant (C59R+S108N) 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
- 1J3J
- Type
- protein
- Length
- 1,089 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
- CP6, NDP, UMP
- Pockets
- 17 · best druggability 0.75
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 | 28% helix, 29% strand | P13922 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 216 | 28% helix, 31% strand | P13922 |
| C, D | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 326 | 37% helix, 21% strand | P13922 |
Ligands and binding sites
- CP6 · 5-(4-chloro-phenyl)-6-ethyl-pyrimidine-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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 498 | 0.75 | 0.83 | 51 | CP6, NDP |
| 2 | 478 | 0.73 | 0.82 | 51 | CP6, NDP |
| 3 | 506 | 0.65 | 0.77 | 53 | UMP |
| 4 | 443 | 0.63 | 0.77 | 38 | UMP |
| 5 | 260 | 0.51 | 0.75 | 33 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2639 Ų buried · 31 hydrogen bonds · protein-protein
- B–D · 970 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 957 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 823 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 795 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1J3J · Double mutant (C59R+S108N) Plasmodium falciparum dihydrofolate reductase-thymidylate… · 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 1J3J · PDBe 1J3J · UniProt P13922
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