Crystal structure of human thymidylate synthase DELTA(7-29) in complex with dump and 2-amino-4-oxo-4,7-dihydro-PYRROLO[2,3-D]PYRIMIDINE- methyl-phenyl-L-glutamic acid

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 23% strand (DSSP).

Ligands and binding sites

• UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 4 copies · chains B, A, D, C
• 2XB · N-{4-[(2-amino-4-hydroxy-7H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl]benzoyl}-L-glutamic acid · ligand · 4 copies · chains B, A, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Interfaces

4 interfaces between chains.

• A–D · 2165 Ų buried · 31 hydrogen bonds · protein-protein
• B–C · 305 Ų buried · 9 hydrogen bonds · protein-protein
• B–D · 199 Ų buried · 1 hydrogen bond · protein-protein
• B–A · 117 Ų buried · 2 hydrogen bonds · protein-protein

Compared structures

• 6OJV · Crystal structure of human thymidylate synthase delta(7-29) in complex with dUMP and… · the same entry in another collection · chain B against B, TM-score 1.00

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• Every structure of UniProt P04818
• Elsewhere: RCSB PDB 6OJV · PDBe 6OJV · UniProt P04818