SMTL ID : 2g8m.1

Escherichia coli thymidylate synthase Y209W in complex with substrate, dUMP, and a cofactor analog, CB3717

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x UMP: 2'-DEOXYURIDINE 5'-MONOPHOSPHATE(Covalent)

UMP.1: 16 residues within 4Å: Chain A: R.21, Y.94, C.146, H.147, Q.165, R.166, S.167, C.168, D.169, G.173, N.177, H.207, W.209 Chain B: R.126, R.127 Ligands: CB3.2 11 PLIP interactions: 8 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Q.165, A:S.167, A:D.169, A:N.177, A:N.177, A:H.207 Salt bridges: A:R.21, A:R.166, B:R.126, B:R.127 Water bridges: B:R.126 UMP.3: 16 residues within 4Å: Chain A: R.126, R.127 Chain B: R.21, Y.94, C.146, H.147, Q.165, R.166, S.167, C.168, D.169, G.173, N.177, H.207, W.209 Ligands: CB3.4 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Q.165, B:S.167, B:D.169, B:N.177, B:N.177, B:H.207 Salt bridges: B:R.21, B:R.166, A:R.126, A:R.127 Water bridges: A:R.126

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

CB3.2: 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, W.209, V.262, A.263 Ligands: UMP.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.79, A:I.79, A:W.83, A:W.83, A:L.143, A:F.176 Hydrogen bonds: A:D.169, A:W.209, A:A.263 Water bridges: A:H.51, A:S.54, A:T.78, A:I.79, A:W.209 Salt bridges: A:K.48, A:H.51, A:D.169 pi-Stacking: A:W.80, A:F.176 CB3.4: 16 residues within 4Å: Chain B: H.51, E.58, I.79, W.80, W.83, L.143, D.169, L.172, G.173, F.176, N.177, W.209, I.258, V.262, A.263 Ligands: UMP.3 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.79, B:I.79, B:W.83, B:W.83, B:L.143, B:F.176 Hydrogen bonds: B:T.78, B:D.169, B:W.209, B:A.263 Water bridges: B:S.54, B:T.78, B:W.209, B:I.258 Salt bridges: B:K.48, B:H.51, B:D.169 pi-Stacking: B:W.80, B:F.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newby, Z. et al., The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2'-deoxyuridine 5'-monophosphate (dUMP)-binding Tyr-261. Biochemistry (2006)

Release Date

2006-03-14

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate synthase

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