SMTL ID : 1i00.1

CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE SYNTHASE, TERNARY COMPLEX WITH DUMP AND TOMUDEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

UMP.1: 16 residues within 4Å: Chain A: R.27, C.172, H.173, Q.191, R.192, S.193, G.194, D.195, G.199, V.200, N.203, H.233, Y.235 Chain B: R.152, R.153 Ligands: D16.2 12 PLIP interactions: 3 interactions with chain B, 9 interactions with chain A Water bridges: B:R.152 Salt bridges: B:R.152, B:R.153, A:R.27, A:R.192 Hydrophobic interactions: A:D.195 Hydrogen bonds: A:Q.191, A:S.193, A:D.195, A:N.203, A:N.203, A:H.233 UMP.3: 16 residues within 4Å: Chain A: R.152, R.153 Chain B: R.27, C.172, H.173, Q.191, R.192, S.193, G.194, D.195, G.199, V.200, N.203, H.233, Y.235 Ligands: D16.4 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:D.195 Hydrogen bonds: B:Q.191, B:S.193, B:D.195, B:V.200, B:N.203, B:N.203, B:H.233, B:Y.235, A:R.152, A:R.152 Water bridges: B:R.27, B:Y.112, A:R.152 Salt bridges: B:R.27, B:R.192, A:R.152, A:R.153

2 x D16: TOMUDEX(Non-covalent)

D16.2: 9 residues within 4Å: Chain A: F.57, E.64, I.85, D.195, L.198, G.199, F.202, Y.235 Ligands: UMP.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.57, A:Y.235 Hydrogen bonds: A:G.199 Water bridges: A:F.57 Salt bridges: A:K.54 pi-Stacking: A:F.202 D16.4: 10 residues within 4Å: Chain B: F.57, I.85, W.86, D.195, L.198, G.199, F.202, N.203, Y.235 Ligands: UMP.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.57, B:W.86, B:L.198, B:F.202, B:Y.235 Hydrogen bonds: B:G.199 pi-Stacking: B:F.202

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Almog, R. et al., Crystal structure of a deletion mutant of human thymidylate synthase Delta (7-29) and its ternary complex with Tomudex and dUMP. Protein Sci. (2001)

Release Date

2001-05-09

Peptides

THYMIDYLATE SYNTHASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

THYMIDYLATE SYNTHASE

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