SMTL ID : 3bhl.1

E.coli thymidylate synthase complexes with 5-NO2dUMP and tetrahydrofolate at 1.4 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x NDU: 2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE(Non-covalent)

NDU.1: 18 residues within 4Å: Chain A: R.21, W.80, Y.94, L.143, 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: THG.2 15 PLIP interactions: 4 interactions with chain B, 11 interactions with chain A Water bridges: B:R.126, B:R.126, A:H.147, A:N.177 Salt bridges: B:R.126, B:R.127, A:R.21, A:R.166 Hydrogen bonds: A:Y.94, A:Q.165, A:S.167, A:D.169, A:N.177, A:N.177, A:Y.209 NDU.5: 18 residues within 4Å: Chain A: R.126, R.127 Chain B: R.21, W.80, Y.94, L.143, C.146, H.147, Q.165, R.166, S.167, C.168, D.169, G.173, N.177, H.207, Y.209 Ligands: THG.6 16 PLIP interactions: 4 interactions with chain A, 12 interactions with chain B Water bridges: A:R.126, A:R.126, B:H.147, B:N.177 Salt bridges: A:R.126, A:R.127, B:R.21, B:R.166 Hydrogen bonds: B:Y.94, B:Q.165, B:S.167, B:D.169, B:N.177, B:N.177, B:Y.209, B:Y.209

2 x THG: (6S)-5,6,7,8-TETRAHYDROFOLATE(Non-covalent)

THG.2: 13 residues within 4Å: Chain A: T.78, I.79, W.80, W.83, L.143, D.169, L.172, G.173, F.176, Y.209, V.262, A.263 Ligands: NDU.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.79, A:F.176, A:F.176 Hydrogen bonds: A:T.78, A:A.263, A:A.263 Water bridges: A:S.54, A:I.79 Salt bridges: A:K.48, A:H.51, A:D.169 THG.6: 13 residues within 4Å: Chain B: H.51, I.79, W.83, L.143, D.169, L.172, G.173, F.176, Y.209, I.258, V.262, A.263 Ligands: NDU.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.176, B:F.176 Hydrogen bonds: B:H.51, B:A.263, B:A.263, B:A.263 Water bridges: B:R.21, B:K.48 Salt bridges: B:K.48, B:D.169

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: E.223, R.225, H.255 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.223, A:H.255 Salt bridges: A:R.225, A:H.255 SO4.4: 3 residues within 4Å: Chain A: E.250, G.251, Y.252 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.250, A:G.251, A:Y.252 Water bridges: A:I.249 SO4.7: 3 residues within 4Å: Chain B: G.106, R.107, H.108 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.108 Salt bridges: B:H.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arendall III, W.B. et al., Structural Studies of Early Events in Catalysis by Thymidylate Synthase. To be Published

Release Date

2008-12-02

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Thymidylate synthase

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