Research workbench
Quadruple mutant (N51I+C59R+S108N+I164L) plasmodium falciparum dihydrofolate reductase-thymidylate synthase (pfdhfr-ts) complexed with RJF670, NADPH, and dump
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
- 3DG8
- Type
- protein
- Length
- 1,094 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional dihydrofolate reductase-thymidylate synthase
- EC
- 1.5.1.3, 2.1.1.45
- UniProt
- Q8I1R6
- Ligands
- RJ6, NDP, UMP
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 221 | 29% helix, 31% strand | Q8I1R6 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 221 | 24% helix, 31% strand | Q8I1R6 |
| C, D | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 326 | 33% helix, 21% strand | Q8I1R6 |
Ligands and binding sites
- RJ6 · N-(3,5-dimethoxyphenyl)imidodicarbonimidic diamide · 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 C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 538 | 0.74 | 0.82 | 47 | RJ6, NDP |
| 2 | 562 | 0.71 | 0.79 | 47 | RJ6, NDP |
| 3 | 659 | 0.69 | 0.77 | 68 | UMP |
| 4 | 493 | 0.66 | 0.78 | 53 | UMP |
| 5 | 279 | 0.55 | 0.76 | 32 | empty |
Interfaces
5 interfaces between chains.
- C–D · 2638 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 971 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 970 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 837 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 825 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3DG8 · 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 Q8I1R6
- Elsewhere: RCSB PDB 3DG8 · PDBe 3DG8 · UniProt Q8I1R6
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