MolNFT v1 · #67557 · protein
Trypanosoma cruzi dihydrofolate reductase-thymidylate synthase complexed with NADPH, dump and C-448 antifolate
3INV · Bifunctional dihydrofolate reductase-thymidylate synthase: “Trypanosoma cruzi dihydrofolate reductase-thymidylate synthase complexed with NADPH, dump and C-448 antifolate”. X-ray diffraction, 3 ligands (C50, NDP, UMP), 19 pockets…
- PDB
- 3INV
- Type
- protein
- Length
- 1,027 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
- Q27793
- Ligands
- C50, NDP, UMP
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 30% 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 | 514 | 30% helix, 26% strand | Q27793 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 513 | 29% helix, 27% strand | Q27793 |
Ligands and binding sites
- C50 · 1-[3-(2,3-dichlorophenoxy)propoxy]-6,6-dimethyl-1,6-dihydro-1,3,5-triazine-2,4-diamine · 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 A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 382 | 0.73 | 0.84 | 37 | C50, NDP |
| 2 | 386 | 0.70 | 0.82 | 47 | C50, NDP |
| 3 | 510 | 0.68 | 0.79 | 44 | UMP, GOL |
| 4 | 423 | 0.64 | 0.78 | 35 | UMP, GOL |
| 5 | 238 | 0.60 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2122 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 3INV · Trypanosoma cruzi Dihydrofolate Reductase-Thymidylate Synthase COMPLEXED WITH NADPH, dUMP… · the same entry in another collection · chain A against A, TM-score 1.00
- Q27793 · AlphaFold monomer V2.0 prediction for bifunctional dihydrofolate reductase-thymidylate… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q27793
- Elsewhere: RCSB PDB 3INV · PDBe 3INV · UniProt Q27793
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