MolNFT v1 · #134322 · protein
Crystal structure of toxoplasma gondii ts-DHFR complexed with NADPH, dump, pddf and 5-(4-(3,4-DICHLOROPHENYL)PIPERAZIN-1-YL)PYRIMIDINE-2, 4-diamine (trc-15)
5T0L · Bifunctional dihydrofolate reductase-thymidylate synthase: “Crystal structure of toxoplasma gondii ts-DHFR complexed with NADPH, dump, pddf and…”. X-ray diffraction, 4 ligands (UMP, NDP, CB3), 12 pockets (best druggability 0.79).…
- PDB
- 5T0L
- Type
- protein
- Length
- 1,018 residues
- Chains
- 2
- 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
- Q07422
- Ligands
- UMP, NDP, CB3, 73X
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 26% 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 | 508 | 28% helix, 26% strand | Q07422 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 510 | 29% helix, 26% strand | Q07422 |
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
- CB3 · 10-propargyl-5,8-dideazafolic acid · ligand · 2 copies · chains A, B
- 73X · 5-[4-(3,4-dichlorophenyl)piperazin-1-yl]pyrimidine-2,4-diamine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.79 | 0.87 | 43 | UMP, CB3 |
| 2 | 463 | 0.78 | 0.86 | 40 | UMP, CB3 |
| 3 | 388 | 0.73 | 0.84 | 42 | NDP, 73X |
| 4 | 410 | 0.73 | 0.83 | 44 | NDP, 73X |
| 5 | 130 | 0.49 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3312 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- Q07422 · AlphaFold monomer V2.0 prediction for bifunctional dihydrofolate reductase-thymidylate… · a predicted model of the same protein · chain B 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 Q07422
- Elsewhere: RCSB PDB 5T0L · PDBe 5T0L · UniProt Q07422
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