SMTL ID : 4ez8.1

Crystal structure of mouse thymidylate sythase in ternary complex with N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate and the cofactor product, dihydrofolate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

homo-dimer

Ligands

2 x NOH: 2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate)(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: DHF.2 13 PLIP interactions: 3 interactions with chain B, 10 interactions with chain A Water bridges: B:R.169 Salt bridges: B:R.169, B:R.170, A:R.44, A:R.209 Hydrophobic interactions: A:L.186 Hydrogen bonds: A:Q.208, A:S.210, A:D.212, A:N.220, A:N.220, A:H.250, A:Y.252 NOH.5: 17 residues within 4Å: Chain A: R.169, R.170 Chain B: 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 Ligands: DHF.6 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.186 Hydrogen bonds: B:Q.208, B:S.210, B:D.212, B:N.220, B:N.220, B:H.250 Water bridges: B:Y.129, B:Y.129, A:R.169 Salt bridges: B:R.44, B:R.209, A:R.169, A:R.170

2 x DHF: DIHYDROFOLIC ACID(Non-covalent)

DHF.2: 12 residues within 4Å: Chain A: F.74, I.102, W.103, L.186, D.212, L.215, G.216, F.219, Y.252, M.305, A.306 Ligands: NOH.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.74, A:I.102, A:I.102, A:L.215 Hydrogen bonds: A:R.101, A:D.212, A:Y.252, A:A.306, A:A.306, A:A.306 Water bridges: A:N.220, A:N.220 Salt bridges: A:K.71, A:D.212 pi-Stacking: A:F.219 DHF.6: 12 residues within 4Å: Chain B: F.74, I.102, W.103, L.186, D.212, L.215, G.216, F.219, Y.252, M.305, A.306 Ligands: NOH.5 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.74, B:I.102, B:I.102, B:L.215 Hydrogen bonds: B:R.101, B:A.306, B:A.306, B:A.306 Water bridges: B:N.220, B:N.220 Salt bridges: B:K.71, B:D.212 pi-Stacking: B:F.219

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: D.167, V.198, N.199 Chain B: K.40, K.41, E.42 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.167, A:N.199, B:E.42 Water bridges: A:D.167, A:D.167, A:G.200 GOL.4: 3 residues within 4Å: Chain A: W.75, I.292, Y.295 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.72, A:Y.295 Water bridges: A:K.76, A:K.76, A:I.292 GOL.7: 6 residues within 4Å: Chain A: K.40, K.41, E.42 Chain B: D.167, V.198, N.199 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.167, B:N.199, A:E.42 Water bridges: B:G.200 GOL.8: 3 residues within 4Å: Chain B: W.75, I.292, Y.295 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.72, B:Y.295 Water bridges: B:K.76, B:K.76, B:I.292

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dowiercial, A. et al., Crystal structures of complexes of mouse thymidylate synthase crystallized with N4-OH-dCMP alone or in the presence of N5,10-methylenetetrahydrofolate. Pteridines (2013)

Release Date

2013-05-08

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thymidylate synthase

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