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Toxoplasma gondii dihydrofolate reductase thymidylate synthase (tgdhfr-ts) complexed with pyrimethamine, NADPH and dump
Analyse Toxoplasma gondii dihydrofolate reductase thymidylate synthase (tgdhfr-ts)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7FGW
- Type
- protein
- Length
- 2,233 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
- Q07422
- Ligands
- NDP, CP6, UMP, BEN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 25% 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 | 558 | 33% helix, 25% strand | Q07422 |
| B | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 560 | 31% helix, 24% strand | Q07422 |
| C | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 556 | 31% helix, 25% strand | Q07422 |
| D | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 559 | 33% helix, 25% strand | Q07422 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- CP6 · 5-(4-chloro-phenyl)-6-ethyl-pyrimidine-2,4-diamine · ligand · 4 copies · chains A, B, C, D
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains A, B, C, D
- BEN · Benzamidine · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 413 | 0.75 | 0.85 | 40 | NDP, CP6 |
| 2 | 461 | 0.75 | 0.84 | 49 | NDP, CP6, BEN |
| 3 | 460 | 0.74 | 0.83 | 46 | NDP, CP6, BEN |
| 4 | 457 | 0.72 | 0.82 | 42 | NDP, CP6 |
| 5 | 470 | 0.72 | 0.82 | 42 | UMP |
Interfaces
3 interfaces between chains.
- C–D · 3838 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 3794 Ų buried · 39 hydrogen bonds · protein-protein
- A–D · 139 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7FGW · Toxoplasma gondii dihydrofolate reductase thymidylate synthase (TgDHFR-TS) complexed with… · the same entry in another collection · chain D against D, TM-score 1.00
- Q07422 · AlphaFold monomer V2.0 prediction for bifunctional dihydrofolate reductase-thymidylate… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 7FGW · PDBe 7FGW · UniProt Q07422
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