SMTL ID : 3b9h.1

E. coli thymidylate synthase complexed with 5-NITRO-2'-DEOXY URIDINE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 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: 4 residues within 4Å: Chain A: L.52, F.244, F.247, E.248 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.248 PO4.4: 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 PO4.5: 4 residues within 4Å: Chain B: L.52, F.244, F.247, E.248 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.248

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

NDU.3: 17 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 14 PLIP interactions: 10 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:H.147, 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 Water bridges: B:R.126, B:R.126 NDU.6: 17 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 13 PLIP interactions: 9 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:H.147, 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 Water bridges: A:R.126, A:R.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

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

Release Date

2008-11-25

Peptides

Thymidylate synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Thymidylate synthase

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