Research workbench
Quadruple mutant plasmodium falciparum dihydrofolate reductase complexed with B10042
Analyse Quadruple mutant plasmodium falciparum dihydrofolate reductase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KP2
- Type
- protein
- Length
- 1,052 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, DQ3, PO4
- Pockets
- 18 · best druggability 0.75
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 | 532 | 33% helix, 25% strand | D9N170 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- DQ3 · 5-(3-chlorophenyl)-6-(3-phenoxypropyl)pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 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
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 564 | 0.75 | 0.82 | 51 | NDP, DQ3 |
| 2 | 513 | 0.73 | 0.81 | 49 | NDP, DQ3 |
| 3 | 611 | 0.70 | 0.78 | 53 | GOL, PO4 |
| 4 | 464 | 0.64 | 0.77 | 46 | PO4 |
| 5 | 138 | 0.53 | 0.81 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 4045 Ų buried · 51 hydrogen bonds · protein-protein
Compared structures
- 6KP2 · Quadruple mutant plasmodium falciparum dihydrofolate reductase complexed with B10042 · 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 6KP2 · PDBe 6KP2 · UniProt D9N170
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