Crystal structure of E.COLI thymidylate synthase with dump and the bgc 945 inhibitor

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).

Ligands and binding sites

• 1JY · N-(4-{[(6S)-2-(hydroxymethyl)-4-oxo-4,6,7,8-tetrahydro-1H-cyclopenta[g]quinazolin-6-yl](prop-2-yn-1-yl)amino}benzoyl)-L-gamma-glutamyl-D-glutamic acid · ligand · 8 copies · chains A, C, B, G, D, E, F, H
• UMC · 2'-deoxy-5'-uridylic acid · ligand · 5 copies · chains B, D, A, E, C, F, G, H
• UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 3 copies · chains A, E, C, F, G, H
• MG · Magnesium ion · metal · 7 copies · chains A, B, C, D, E, 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, 11 with a druggability of 0.5 or more.

Interfaces

13 interfaces between chains.

• C–F · 2284 Ų buried · 37 hydrogen bonds · protein-protein
• G–H · 2238 Ų buried · 36 hydrogen bonds · protein-protein
• A–E · 2225 Ų buried · 32 hydrogen bonds · protein-protein
• B–D · 2223 Ų buried · 37 hydrogen bonds · protein-protein
• B–G · 568 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified, 5 covalent (carboxylation, covalent ligand).

Compared structures

• 4ISK · Crystal structure of E.coli thymidylate synthase with dUMP and the BGC 945 inhibitor · the same entry in another collection · chain H against H, TM-score 1.00
• P0A884 · AlphaFold monomer V2.0 prediction for thymidylate synthase (P0A884) · 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 P0A884
• Elsewhere: RCSB PDB 4ISK · PDBe 4ISK · UniProt P0A884