Research workbench
Wild type plasmodium falciparum dihydrofolate reductase-thymidylate synthase (pfdhfr-ts), dhf complex, NADP+, 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
- 4DPD
- Type
- protein
- Length
- 1,073 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
- UniProt
- A7UD81
- Ligands
- UMP, DHF, NAP
- Pockets
- 15 · best druggability 0.75
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 (EC 1.5.1.3) | protein | 530 | 34% helix, 25% strand | A7UD81 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3) | protein | 543 | 32% helix, 25% strand | A7UD81 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- DHF · Dihydrofolic acid · ligand · chains A
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.75 | 0.82 | 50 | DHF, NAP |
| 2 | 377 | 0.73 | 0.84 | 38 | empty |
| 3 | 643 | 0.72 | 0.79 | 67 | UMP |
| 4 | 625 | 0.70 | 0.78 | 64 | UMP |
| 5 | 175 | 0.49 | 0.77 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 4148 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 4DPD · 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 4DPD · PDBe 4DPD · UniProt A7UD81
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