SMTL ID : 4eeq.1

Crystal structure of E. faecalis DNA ligase with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: G.123, L.124, A.125, R.141, R.202 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.123, A:A.125 Water bridges: A:R.141, A:R.141, A:R.141, A:R.202, A:R.202 Salt bridges: A:R.202 SO4.2: 3 residues within 4Å: Chain A: P.81, R.129, R.137 4 PLIP interactions: 4 interactions with chain A Water bridges: A:N.149, A:N.149 Salt bridges: A:R.129, A:R.137

1 x NMN: BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE(Non-covalent)

NMN.3: 10 residues within 4Å: Chain A: Y.25, Y.29, Y.30, P.35, V.37, D.39, Y.42, D.43, Y.46, R.158 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.29, A:Y.30 Hydrogen bonds: A:Y.25, A:Y.30, A:D.39, A:Y.42, A:D.43 Water bridges: A:Y.29, A:V.37, A:Y.42, A:R.158 Salt bridges: A:R.158 pi-Stacking: A:Y.29, A:Y.42

1 x 0OX: 4-amino-2-(cyclopentyloxy)pyrimidine-5-carboxamide(Non-covalent)

0OX.4: 11 residues within 4Å: Chain A: L.89, E.118, L.119, K.120, I.121, E.175, Y.227, V.289, K.291, P.308, W.310 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.89, A:Y.227, A:V.289, A:P.308, A:W.310 Hydrogen bonds: A:E.118, A:I.121, A:I.121, A:Y.227, A:K.291 Water bridges: A:L.119, A:K.120 pi-Stacking: A:Y.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, T. et al., Design, Synthesis and Activity Evaluation of Potent NAD+ DNA Ligase Inhibitors as Potential Antibacterial Agents. To be Published

Release Date

2013-04-03

Peptides

DNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase

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