SMTL ID : 6nnr.1

high-resolution structure of wild-type E. coli thymidylate synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-dimer

Ligands

2 x UMC: 2'-deoxy-5'-uridylic acid(Covalent)

UMC.1: 19 residues within 4Å: Chain A: R.21, W.80, Y.94, L.143, A.144, C.146, H.147, Q.165, R.166, S.167, C.168, D.169, G.173, N.177, H.207, Y.209 Chain B: R.126, R.127 Ligands: CB3.2 13 PLIP interactions: 9 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.165, A:S.167, A:D.169, A:N.177, A:N.177, A:H.207, A:Y.209 Salt bridges: A:R.21, A:R.166, B:R.126, B:R.127 Water bridges: B:R.126, B:R.126 UMC.6: 19 residues within 4Å: Chain A: R.126, R.127 Chain B: R.21, W.80, Y.94, L.143, A.144, C.146, H.147, Q.165, R.166, S.167, C.168, D.169, G.173, N.177, H.207, Y.209 Ligands: CB3.7 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.165, B:S.167, B:D.169, B:N.177, B:N.177, B:H.207, B:Y.209 Water bridges: B:Y.94, A:R.126, A:R.126 Salt bridges: B:R.21, B:R.166, A:R.126, A:R.127

2 x CB3: 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID(Non-covalent)

CB3.2: 18 residues within 4Å: Chain A: R.21, T.22, K.48, E.58, T.78, I.79, W.80, W.83, L.143, D.169, L.172, G.173, F.176, N.177, Y.209, V.262, A.263 Ligands: UMC.1 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.79, A:W.80, A:W.83, A:W.83, A:L.143, A:F.176 Hydrogen bonds: A:T.78, A:Y.209, A:A.263, A:A.263, A:A.263 Water bridges: A:K.48, A:T.78, A:I.79 Salt bridges: A:K.48, A:D.169 pi-Stacking: A:F.176 CB3.7: 19 residues within 4Å: Chain B: R.21, T.22, K.48, H.51, E.58, I.79, W.80, W.83, L.143, D.169, L.172, G.173, F.176, N.177, Y.209, I.258, V.262, A.263 Ligands: UMC.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.79, B:I.79, B:W.80, B:W.83, B:W.83, B:L.143, B:F.176 Hydrogen bonds: B:Y.209, B:A.263, B:A.263, B:A.263 Water bridges: B:K.48, B:K.48, B:T.78 Salt bridges: B:K.48, B:H.51, B:D.169 pi-Stacking: B:F.176

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: R.53, S.54, N.76, V.77, T.78 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.53, A:S.54, A:N.76 Water bridges: A:T.78

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 2 residues within 4Å: Chain A: Q.39, E.195 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.39, A:Q.39 Salt bridges: A:E.195, A:E.195 EPE.5: 6 residues within 4Å: Chain A: V.154, A.155, D.156, G.157 Chain B: T.16, Q.17 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.156, A:G.157 Water bridges: B:K.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Z. et al., Mg2+ binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site. J. Am. Chem. Soc. (2013)

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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