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Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (pfdhfr-ts) complexed with B12155 inhibitor
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
- 6KPR
- Type
- protein
- Length
- 1,068 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase
- UniProt
- D9N170
- Ligands
- UMP, NDP, DQF
- Pockets
- 16 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 534 | 34% helix, 25% strand | D9N170 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 534 | 33% helix, 24% strand | D9N170 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- DQF · 4-[3-[3-[2,6-bis(azanyl)-5-(3-chlorophenyl)pyrimidin-4-yl]propoxy]phenoxy]butanoic acid · 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
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.73 | 0.82 | 49 | NDP, DQF |
| 2 | 536 | 0.72 | 0.81 | 50 | NDP, DQF |
| 3 | 621 | 0.71 | 0.79 | 54 | UMP, GOL |
| 4 | 600 | 0.70 | 0.79 | 57 | GOL, UMP |
| 5 | 136 | 0.49 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 4158 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 6KPR · 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 6KPR · PDBe 6KPR · UniProt D9N170
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