SMTL ID : 4eb4.2 (2 other biounits)

Crystal structure of mouse thymidylate synthase in ternary complex with dUMP and Tomudex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Non-covalent)

UMP.1: 16 residues within 4Å: Chain A: R.44, C.189, H.190, Q.208, R.209, S.210, G.211, D.212, G.216, V.217, N.220, H.250, Y.252 Chain B: R.169, R.170 Ligands: D16.2 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Q.208, A:S.210, A:S.210, A:D.212, A:N.220, A:N.220, A:H.250, A:Y.252 Water bridges: A:H.190 Salt bridges: A:R.44, A:R.209, B:R.169, B:R.170 UMP.4: 15 residues within 4Å: Chain A: R.169, R.170 Chain B: R.44, C.189, H.190, Q.208, R.209, S.210, G.211, D.212, G.216, N.220, H.250, Y.252 Ligands: D16.5 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.208, B:S.210, B:D.212, B:N.220, B:N.220, B:H.250 Salt bridges: B:R.44, B:R.209, A:R.169, A:R.170

2 x D16: TOMUDEX(Non-covalent)

D16.2: 10 residues within 4Å: Chain A: F.74, R.101, I.102, D.212, L.215, G.216, F.219, N.220, Y.252 Ligands: UMP.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.74, A:F.219, A:Y.252 Hydrogen bonds: A:D.212, A:G.216 Water bridges: A:F.74, A:R.101 Salt bridges: A:R.101 pi-Stacking: A:F.219 D16.5: 14 residues within 4Å: Chain B: F.74, I.102, W.103, D.212, L.215, G.216, F.219, N.220, Y.252, I.301, K.302, M.303, E.304 Ligands: UMP.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:I.102, B:I.102, B:L.215, B:Y.252 Hydrogen bonds: B:D.212, B:G.216, B:M.303, B:E.304 Water bridges: B:R.72, B:I.301 pi-Stacking: B:F.219

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.21, H.22, R.58 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.21, A:R.58, A:S.60 Water bridges: A:R.58 GOL.6: 5 residues within 4Å: Chain B: R.36, C.37, G.38, F.39 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.37 GOL.7: 4 residues within 4Å: Chain A: N.199 Chain B: F.39, K.40 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dowiercial, A. et al., Crystal structure of mouse thymidylate synthase in tertiary complex with dUMP and raltitrexed reveals N-terminus architecture and two different active site conformations. Biomed Res Int (2014)

Release Date

2012-05-02

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Thymidylate synthase

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