MolNFT v1 · #98069 · protein

Crystal structure of non-classical ts inhibitor 2 in complex with toxoplasma gondii ts-DHFR

4KY4 · Bifunctional dihydrofolate reductase-thymidylate synthase: “Crystal structure of non-classical ts inhibitor 2 in complex with toxoplasma gondii ts-DHFR”. X-ray diffraction, 4 ligands (UMP, 04J, NDP), 20 pockets (best druggability…

PDB: 4KY4
Type: protein
Length: 3,920 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, 04J, NDP, 1UE
Pockets: 20 · best druggability 0.81

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	489	29% 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
04J · Aminopterin · 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
1UE · 2-amino-5-(phenylsulfanyl)-3,9-dihydro-4H-pyrimido[4,5-b]indol-4-one · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	552	0.81	0.86	49	UMP, 1UE
2	522	0.80	0.86	47	UMP, 1UE
3	681	0.80	0.84	61	UMP, 1UE
4	542	0.80	0.86	47	UMP, 1UE
5	552	0.79	0.86	50	UMP, 1UE

Interfaces

5 interfaces between chains.

E–F · 3403 Å² buried · 24 hydrogen bonds · protein-protein
G–H · 3400 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 3396 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 3392 Å² buried · 25 hydrogen bonds · protein-protein
B–C · 662 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4KY4 · Crystal structure of non-classical TS inhibitor 2 in complex with Toxoplasma gondii… · the same entry in another collection · chain G against G, TM-score 1.00
Q07422 · AlphaFold monomer V2.0 prediction for bifunctional dihydrofolate reductase-thymidylate… · a predicted model of the same protein · chain G 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 4KY4 · PDBe 4KY4 · UniProt Q07422

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