Research workbench
Crystal structure of the loop truncated toxoplasma gondii ts-DHFR
Analyse Crystal structure of the loop truncated toxoplasma gondii ts-DHFR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EIL
- Type
- protein
- Length
- 4,004 residues
- Chains
- 8
- 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, CB3, FOL, NDP
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 510 | 30% helix, 25% strand | Q07422 |
| B, D, F, H | Bifunctional dihydrofolate reductase-thymidylate synthase (EC 1.5.1.3, 2.1.1.45) | protein | 491 | 29% helix, 25% strand | Q07422 |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CB3 · 10-propargyl-5,8-dideazafolic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- FOL · Folic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.79 | 0.86 | 46 | UMP, CB3 |
| 2 | 442 | 0.79 | 0.87 | 42 | UMP, CB3 |
| 3 | 481 | 0.79 | 0.86 | 42 | UMP, CB3 |
| 4 | 444 | 0.78 | 0.86 | 43 | UMP, CB3 |
| 5 | 443 | 0.78 | 0.86 | 43 | UMP, CB3 |
Interfaces
8 interfaces between chains.
- E–F · 3397 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 3381 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 3373 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 3372 Ų buried · 25 hydrogen bonds · protein-protein
- D–G · 653 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4EIL · Crystal Structure of the loop truncated Toxoplasma gondii TS-DHFR · the same entry in another collection · chain H against H, TM-score 1.00
- Q07422 · AlphaFold monomer V2.0 prediction for bifunctional dihydrofolate reductase-thymidylate… · a predicted model of the same protein · chain E 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 4EIL · PDBe 4EIL · UniProt Q07422
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