SMTL ID : 6gko.1

Mouse thymidylate synthase cocrystallized with dUMP and soaked in phenolphthalein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.84 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, N.220, H.250, Y.252 Chain B: R.169, R.170 Ligands: FGT.2, DMS.3 12 PLIP interactions: 8 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.208, A:S.210, A:D.212, A:N.220, A:N.220, A:H.250 Salt bridges: A:R.44, A:R.209, B:R.169, B:R.170 Water bridges: B:R.170, B:R.170 UMP.4: 16 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: FGT.5, DMS.6 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:D.212 Hydrogen bonds: B:Q.208, B:S.210, B:D.212, B:N.220, 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.170, A:R.170

2 x FGT: 3,3-bis(4-hydroxyphenyl)-2-benzofuran-1-one(Non-covalent)

FGT.2: 10 residues within 4Å: Chain A: E.81, I.102, D.212, L.215, G.216, F.219, N.220, M.305 Ligands: UMP.1, DMS.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.102, A:I.102, A:L.215, A:F.219, A:F.219, A:F.219 Hydrogen bonds: A:N.220 Water bridges: A:H.190, A:S.223, A:Y.252, A:A.306 FGT.5: 10 residues within 4Å: Chain B: E.81, I.102, D.212, L.215, G.216, F.219, N.220, M.305 Ligands: UMP.4, DMS.6 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:I.102, B:I.102, B:L.215, B:F.219, B:F.219, B:F.219 Hydrogen bonds: B:H.190, B:N.220 Water bridges: B:S.223, B:A.306

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 6 residues within 4Å: Chain A: I.102, W.103, N.106, L.186 Ligands: UMP.1, FGT.2 2 PLIP interactions: 2 interactions with chain A pi-Cation interactions: A:W.103, A:W.103 DMS.6: 6 residues within 4Å: Chain B: I.102, W.103, N.106, L.186 Ligands: UMP.4, FGT.5 2 PLIP interactions: 2 interactions with chain B pi-Cation interactions: B:W.103, B:W.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maj, P. et al., Thymidylate synthase fragment screening. To Be Published

Release Date

2019-06-05

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate synthase

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