Research workbench
Crystal structure of wild-type pfdhfr-ts complexed with NADPH, dump and pyrimethamine
Analyse Crystal structure of wild-type pfdhfr-ts complexed with NADPH, dump and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QGT
- Type
- protein
- Length
- 1,089 residues
- Chains
- 2
- 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
- A7UD81
- Ligands
- CP6, NDP, UMP
- Pockets
- 17 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 31% 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 | 547 | 33% helix, 25% strand | A7UD81 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 542 | 30% helix, 26% strand | A7UD81 |
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 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 529 | 0.75 | 0.82 | 51 | CP6, NDP |
| 2 | 508 | 0.74 | 0.82 | 49 | CP6, NDP |
| 3 | 496 | 0.66 | 0.77 | 49 | UMP |
| 4 | 418 | 0.63 | 0.77 | 39 | UMP |
| 5 | 274 | 0.51 | 0.74 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 4120 Ų buried · 54 hydrogen bonds · protein-protein
Compared structures
- 3QGT · Crystal structure of Wild-type PfDHFR-TS COMPLEXED WITH NADPH, dUMP AND PYRIMETHAMINE · 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 3QGT · PDBe 3QGT · UniProt A7UD81
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