Research workbench
Wild-type plasmodium falciparum dihydrofolate reductase-thymidylate synthase (pfdhfr-ts) complexed with methotrexate (mtx), 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
- 7F3Y
- Type
- protein
- Length
- 1,093 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase
- UniProt
- A7UD81
- Ligands
- MTX, NDP, UMP
- Pockets
- 17 · best druggability 0.73
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 | 547 | 33% helix, 25% strand | A7UD81 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 546 | 33% helix, 24% strand | A7UD81 |
Ligands and binding sites
- MTX · Methotrexate · ligand · 3 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
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 457 | 0.73 | 0.82 | 50 | NDP, MTX |
| 2 | 442 | 0.72 | 0.82 | 47 | NDP, MTX |
| 3 | 626 | 0.72 | 0.79 | 54 | GOL, UMP |
| 4 | 664 | 0.72 | 0.79 | 67 | UMP, MTX, GOL |
| 5 | 233 | 0.50 | 0.75 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 4218 Ų buried · 48 hydrogen bonds · protein-protein
Compared structures
- 7F3Y · 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 A7UD81
- Elsewhere: RCSB PDB 7F3Y · PDBe 7F3Y · UniProt A7UD81
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