SMTL ID : 3bab.1

Structural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: P.81, R.129, R.137 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.81 Salt bridges: A:R.129, A:R.137 SO4.2: 4 residues within 4Å: Chain A: R.190, Q.195, Q.211, R.220 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.195, A:Q.211 Salt bridges: A:R.190, A:R.220 SO4.3: 3 residues within 4Å: Chain A: Q.24, H.27, K.32 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.24 Salt bridges: A:H.27, A:K.32 SO4.4: 8 residues within 4Å: Chain A: P.81, H.82, D.83, S.127, R.129, R.137, E.171, R.173 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.83, A:S.127, A:E.171 Water bridges: A:R.137 Salt bridges: A:H.82, A:R.129, A:R.137, A:R.173

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

NMN.5: 12 residues within 4Å: Chain A: Y.25, S.26, Y.29, Y.30, P.35, V.37, E.38, D.39, Y.42, D.43, Y.46, R.158 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.29, A:Y.30, A:Y.42 Hydrogen bonds: A:Y.30, A:D.39, A:D.39, A:Y.42, A:D.43 Salt bridges: A:R.158 pi-Stacking: A:Y.29, A:Y.42

1 x 3BD: 7-amino-2-tert-butyl-4-(4-pyrimidin-2-ylpiperazin-1-yl)pyrido[2,3-d]pyrimidine-6-carboxamide(Non-covalent)

3BD.6: 14 residues within 4Å: Chain A: Y.87, S.88, L.89, E.118, L.119, K.120, I.121, A.125, R.141, E.175, Y.227, V.289, K.291, W.310 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.89, A:V.289, A:W.310 Hydrogen bonds: A:E.118, A:I.121, A:I.121, A:K.291 Water bridges: A:L.119, A:A.125, A:R.141 pi-Stacking: A:Y.227 pi-Cation interactions: A:R.141

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: N.23, H.27, R.68, P.161, M.162, R.163 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.23, A:R.68, A:M.162, A:R.163, A:R.163 Water bridges: A:H.27

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pinko, C. et al., Structural Basis for the Inhibition of Bacterial NAD+ Dependent DNA Ligase. To be Published

Release Date

2008-11-11

Peptides

DNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase

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