SMTL ID : 3baa.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: K.120, I.121, E.175 Ligands: 3BA.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.175 Water bridges: A:K.120 Salt bridges: A:K.120 SO4.2: 3 residues within 4Å: Chain A: P.81, R.129, R.137 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.129, A:R.137 SO4.3: 4 residues within 4Å: Chain A: R.190, Q.195, Q.211, R.220 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.195, A:Q.211 Water bridges: A:R.190, A:R.190, A:R.220, A:R.220 Salt bridges: A:R.190, A:R.220 SO4.4: 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

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

NMN.5: 11 residues within 4Å: Chain A: Y.25, Y.29, Y.30, P.35, V.37, E.38, D.39, Y.42, D.43, Y.46, R.158 15 PLIP interactions: 15 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 Water bridges: A:V.37, A:Y.42, A:R.158, A:R.158 Salt bridges: A:R.158 pi-Stacking: A:Y.29, A:Y.42

1 x 3BA: 7-amino-2-tert-butyl-4-{[2-(1H-imidazol-4-yl)ethyl]amino}pyrido[2,3-d]pyrimidine-6-carboxamide(Non-covalent)

3BA.6: 18 residues within 4Å: Chain A: M.86, Y.87, L.89, E.118, L.119, K.120, I.121, A.125, R.141, R.173, E.175, Y.227, V.289, K.291, P.308, W.310 Ligands: SO4.1, GOL.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.89, A:V.289, A:P.308, A:W.310 Hydrogen bonds: A:E.118, A:I.121, A:I.121, A:K.291 Water bridges: A:L.89, A:L.119 pi-Stacking: A:Y.227

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 4 residues within 4Å: Chain A: F.101, R.104, L.301, R.309 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.104 Water bridges: A:A.108, A:R.309 GOL.8: 7 residues within 4Å: Chain A: P.85, M.86, Y.87, R.173, F.303, W.310 Ligands: 3BA.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.87, A:R.173, A:R.173

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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