SMTL ID : 2fto.1

Y94F mutant of thymidylate synthase bound to thymidine-5'-phosphate and 10-propargyl-5,8-dideazafolid acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 3 residues within 4Å: Chain A: R.49, P.256, G.257 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.257 PO4.2: 3 residues within 4Å: Chain A: L.52, F.244, F.247 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:F.247, A:I.249 Water bridges: A:F.244, A:F.247 PO4.5: 3 residues within 4Å: Chain B: R.49, P.256, G.257 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.257 PO4.6: 3 residues within 4Å: Chain B: L.52, F.244, F.247 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:F.247, B:I.249 Water bridges: B:F.244, B:F.247

2 x TMP: THYMIDINE-5'-PHOSPHATE(Non-covalent)

TMP.3: 16 residues within 4Å: Chain A: R.21, W.80, 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: CB3.4 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.80 Hydrogen bonds: A:Q.165, A:S.167, A:D.169, A:N.177, A:N.177, A:Y.209, A:Y.209 Salt bridges: A:R.21, A:R.166, B:R.126, B:R.127 TMP.7: 16 residues within 4Å: Chain A: R.126, R.127 Chain B: R.21, W.80, C.146, H.147, Q.165, R.166, S.167, C.168, D.169, G.173, N.177, H.207, Y.209 Ligands: CB3.8 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.80 Hydrogen bonds: B:Q.165, B:S.167, B:D.169, B:N.177, B:N.177, B:Y.209 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)

CB3.4: 14 residues within 4Å: Chain A: E.58, 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: TMP.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.79, A:I.79, A:W.83, A:L.143, A:F.176 Hydrogen bonds: A:D.169, A:Y.209, A:A.263, A:A.263 Water bridges: A:S.54 Salt bridges: A:K.48, A:H.51, A:D.169 pi-Stacking: A:F.176 CB3.8: 14 residues within 4Å: Chain B: E.58, 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: TMP.7 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.79, B:I.79, B:W.83, B:L.143, B:F.176 Hydrogen bonds: B:A.263, B:A.263 Water bridges: B:S.54 Salt bridges: B:K.48, B:H.51, B:D.169 pi-Stacking: B:F.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Roberts, S.A. et al., Structure of the Y94F mutant of Escherichia coli thymidylate synthase. ACTA CRYSTALLOGR.,SECT.F (2006)

Release Date

2006-05-02

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

Thymidylate synthase

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