MolNFT v1 · #98075 · protein
Crystal structure of non-classical ts inhibitor 3 in complex with toxoplasma gondii ts-DHFR
4KYA · Bifunctional dihydrofolate reductase-thymidylate synthase: “Crystal structure of non-classical ts inhibitor 3 in complex with toxoplasma gondii ts-DHFR”. X-ray diffraction, 4 ligands (UMP, 1UG, FOL), 20 pockets (best druggability…
- PDB
- 4KYA
- 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, 1UG, FOL, NDP
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 29% 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, 26% 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
- 1UG · 2-Amino-5-(1-naphthylsulfanyl)-3,9-dihydro-4H-pyrimido[4,5-b]indol-4-one · 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 | 552 | 0.80 | 0.86 | 43 | UMP, 1UG |
| 2 | 558 | 0.80 | 0.86 | 40 | UMP, 1UG |
| 3 | 549 | 0.80 | 0.86 | 47 | UMP, 1UG |
| 4 | 526 | 0.80 | 0.86 | 45 | UMP, 1UG |
| 5 | 517 | 0.79 | 0.86 | 45 | UMP, 1UG |
Interfaces
5 interfaces between chains.
- A–B · 3408 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 3407 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 3398 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 3395 Ų buried · 30 hydrogen bonds · protein-protein
- A–F · 609 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4KYA · Crystal structure of non-classical TS inhibitor 3 in complex with Toxoplasma gondii… · 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 C 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 4KYA · PDBe 4KYA · UniProt Q07422
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