MolNFT v1 · #154876 · protein
Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (pfdhfr-ts) complexed with B12154
6KP7 · Bifunctional dihydrofolate reductase-thymidylate synthase: “Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase…”. X-ray diffraction, 3 ligands (NDP, UMP, DQ9), 18 pockets…
- PDB
- 6KP7
- Type
- protein
- Length
- 1,053 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase
- UniProt
- D9N170
- Ligands
- NDP, UMP, DQ9
- Pockets
- 18 · best druggability 0.74
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 | 520 | 35% helix, 25% strand | D9N170 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase | protein | 533 | 32% helix, 25% strand | D9N170 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 2 copies · chains A, B
- DQ9 · 2-[3-[3-[2,6-bis(azanyl)-5-(3-chlorophenyl)pyrimidin-4-yl]propoxy]phenoxy]ethanoic acid · 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
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 543 | 0.74 | 0.82 | 49 | NDP, DQ9 |
| 2 | 533 | 0.73 | 0.81 | 49 | NDP, DQ9 |
| 3 | 586 | 0.70 | 0.79 | 58 | UMP |
| 4 | 487 | 0.68 | 0.79 | 40 | UMP |
| 5 | 135 | 0.49 | 0.79 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 4060 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 6KP7 · 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 6KP7 · PDBe 6KP7 · UniProt D9N170
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