SMTL ID : 4o1u.1

Crystal structure of human thymidylate synthase mutant Y202C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

homo-dimer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: R.62, R.197, L.201 Chain B: R.188 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.197, B:R.188 Water bridges: B:R.188 SO4.2: 6 residues within 4Å: Chain A: R.62, N.195, H.208, R.227, S.228 Chain B: R.187 7 PLIP interactions: 1 interactions with chain B, 6 interactions with chain A Salt bridges: B:R.187, A:R.62, A:H.208, A:R.227 Hydrogen bonds: A:N.195, A:S.228 Water bridges: A:R.227 SO4.6: 3 residues within 4Å: Chain A: E.284, R.286, H.316 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.284 Salt bridges: A:R.286, A:H.316 SO4.7: 4 residues within 4Å: Chain A: R.188 Chain B: R.62, R.197, L.201 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:R.188 Salt bridges: A:R.188, B:R.197 SO4.8: 3 residues within 4Å: Chain B: E.284, R.286, H.316 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.286, B:H.316 SO4.9: 5 residues within 4Å: Chain A: R.187 Chain B: N.195, H.208, R.227, S.228 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain B Salt bridges: A:R.187, B:H.208, B:R.227 Hydrogen bonds: B:N.195, B:S.228 Water bridges: B:R.227

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: Q.48, M.73, Q.74, A.75, V.235, H.262, L.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.48, A:M.73, A:H.262 Water bridges: A:Q.48 EDO.4: 4 residues within 4Å: Chain A: G.229, D.230, G.234, N.238 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.230 Water bridges: A:Q.226, A:G.234 EDO.10: 7 residues within 4Å: Chain B: Q.48, M.73, Q.74, A.75, V.235, H.262, L.264 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.48, B:H.262 EDO.11: 3 residues within 4Å: Chain B: F.154, W.194, L.199 No protein-ligand interaction detected (PLIP)

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 1 residues within 4Å: Chain A: F.92 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: G.229, D.230, G.234 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: F.92 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Costantino, L. et al., Destabilizers of the thymidylate synthase homodimer accelerate its proteasomal degradation and inhibit cancer growth. Elife (2022)

Release Date

2015-01-21

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate synthase