Research workbench
Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) complexed with C452 (compound 16) and NADPH
Analyse Quadruple mutant (N51I+C59R+S108N+I164L) 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
- 6LHJ
- Type
- protein
- Length
- 1,088 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Plasmodium falciparum
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase
- UniProt
- D9N170
- Ligands
- EA6, NDP, UMP
- Pockets
- 16 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 547 | 33% helix, 24% strand | D9N170 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 541 | 33% helix, 25% strand | D9N170 |
Ligands and binding sites
- EA6 · 1-[3-(2-chloranyl-4-fluoranyl-phenoxy)propoxy]-6,6-dimethyl-1,3,5-triazine-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
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.75 | 0.83 | 51 | EA6, NDP |
| 2 | 428 | 0.74 | 0.84 | 46 | EA6, NDP |
| 3 | 609 | 0.71 | 0.79 | 62 | GOL, UMP |
| 4 | 632 | 0.70 | 0.78 | 62 | UMP |
| 5 | 468 | 0.60 | 0.75 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 4224 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- 6LHJ · Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate… · 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 D9N170
- Elsewhere: RCSB PDB 6LHJ · PDBe 6LHJ · UniProt D9N170
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