SMTL ID : 6f6z.1

Mouse Thymidylate Synthase Cocrystallized with N(4)OHdCMP and Soaked in Methylenetetrahydrofolate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

2 x NOH: 2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate)(Non-covalent)

NOH.1: 17 residues within 4Å: Chain A: R.44, W.103, L.186, C.189, H.190, Q.208, R.209, S.210, G.211, D.212, G.216, N.220, H.250, Y.252 Chain B: R.169, R.170 Ligands: TGQ.2 12 PLIP interactions: 2 interactions with chain B, 10 interactions with chain A Salt bridges: B:R.169, B:R.170, A:R.44, A:R.209 Hydrogen bonds: A:H.190, A:Q.208, A:S.210, A:S.210, A:D.212, A:N.220, A:H.250 Water bridges: A:C.189 NOH.3: 18 residues within 4Å: Chain A: R.169, R.170 Chain B: R.44, W.103, Y.129, L.186, C.189, H.190, Q.208, R.209, S.210, G.211, D.212, G.216, N.220, H.250, Y.252 Ligands: TGQ.4 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.129, B:H.190, B:Q.208, B:S.210, B:D.212, B:N.220, B:H.250, B:Y.252 Salt bridges: B:R.44, B:R.209, A:R.169, A:R.170 Water bridges: A:R.169

2 x TGQ: (2~{S})-2-[[4-[[(6~{R})-2-azanyl-4-oxidanylidene-5,6,7,8-tetrahydro-1~{H}-pteridin-6-yl]methyl-methyl-amino]phenyl]carbonylamino]pentanedioic acid(Non-covalent)

TGQ.2: 12 residues within 4Å: Chain A: F.74, I.102, W.103, D.212, L.215, G.216, F.219, N.220, Y.252, M.305, A.306 Ligands: NOH.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.74, A:I.102, A:I.102 Hydrogen bonds: A:G.216, A:A.306, A:A.306, A:A.306 Salt bridges: A:D.212 pi-Stacking: A:F.219 TGQ.4: 13 residues within 4Å: Chain B: F.74, I.102, W.103, N.106, D.212, L.215, G.216, F.219, N.220, Y.252, M.305, A.306 Ligands: NOH.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.102, B:I.102 Hydrogen bonds: B:N.106, B:G.216, B:Y.252, B:A.306, B:A.306, B:A.306 Water bridges: B:R.101 Salt bridges: B:K.71, B:D.212 pi-Stacking: B:F.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maj, P. et al., Molecular Mechanism of Thymidylate Synthase Inhibition by N4-Hydroxy-dCMP in View of Spectrophotometric and Crystallographic Studies. Int J Mol Sci (2021)

Release Date

2019-01-30

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate synthase

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