Research workbench
Wild-type plasmodium falciparum dihydrofolate reductase-thymidylate synthase (pfdhfr-ts) complexed with RJF01302, NADPH, and dump
Analyse Wild-type plasmodium falciparum dihydrofolate reductase-thymidylate synthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DGA
- 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
- Q8I1R6
- Ligands
- RJ1, NDP, UMP
- Pockets
- 19 · 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 | 219 | 29% helix, 31% strand | Q8I1R6 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 224 | 27% helix, 30% strand | Q8I1R6 |
| C | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 325 | 34% helix, 21% strand | Q8I1R6 |
| D | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 326 | 36% helix, 21% strand | Q8I1R6 |
Ligands and binding sites
- RJ1 · N-[2-chloro-5-(trifluoromethyl)phenyl]imidodicarbonimidic diamide · 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
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.74 | 0.83 | 50 | RJ1, NDP |
| 2 | 514 | 0.72 | 0.81 | 48 | RJ1, NDP |
| 3 | 614 | 0.71 | 0.79 | 61 | UMP |
| 4 | 530 | 0.67 | 0.78 | 50 | UMP |
| 5 | 259 | 0.53 | 0.76 | 35 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2733 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 1037 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 959 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 847 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 775 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3DGA · Wild-type Plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS)… · 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 Q8I1R6
- Elsewhere: RCSB PDB 3DGA · PDBe 3DGA · UniProt Q8I1R6
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