SMTL ID : 4glw.1

DNA ligase A in complex with inhibitor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: R.224, D.225, K.229 Chain B: L.157, D.158 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.225, B:D.158 Salt bridges: A:R.224, A:K.229 SO4.3: 6 residues within 4Å: Chain A: E.156, L.157, D.158 Chain B: R.224, D.225, K.229 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.225, A:D.158, A:D.158 Water bridges: B:R.224, B:R.224, B:R.224 Salt bridges: B:R.224, B:K.229

2 x 0XT: 7-methoxy-6-methylpteridine-2,4-diamine(Non-covalent)

0XT.2: 10 residues within 4Å: Chain A: Y.77, L.79, E.107, L.108, R.162, Y.216, Q.217, V.276, K.278, W.297 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.77, A:L.79 Hydrogen bonds: A:L.108, A:E.164, A:K.278 Water bridges: A:L.108 Salt bridges: A:E.107 pi-Stacking: A:Y.216, A:Y.216 pi-Cation interactions: A:Y.216 0XT.4: 11 residues within 4Å: Chain B: Y.77, L.79, E.107, L.108, K.109, E.164, Y.216, Q.217, V.276, K.278, W.297 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.77, B:L.79 Hydrogen bonds: B:L.108, B:E.164, B:K.278 Salt bridges: B:E.107 pi-Stacking: B:Y.216, B:Y.216 pi-Cation interactions: B:Y.216

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

NMN.5: 9 residues within 4Å: Chain B: D.53, K.121, G.122, I.123, T.152, L.153, P.154, E.155, E.156 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:I.123, B:E.156 Hydrogen bonds: B:D.53, B:T.152, B:T.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Surivet, J.P. et al., Structure-guided design, synthesis and biological evaluation of novel DNA ligase inhibitors with in vitro and in vivo anti-staphylococcal activity. Bioorg.Med.Chem.Lett. (2012)

Release Date

2012-10-10

Peptides

DNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA ligase