SMTL ID : 4efe.1

crystal structure of DNA ligase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: L.124, A.125, R.141, R.202 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:A.125 Water bridges: A:R.141, A:G.142, A:G.142, A:G.142, A:R.202 Salt bridges: A:R.202 SO4.2: 3 residues within 4Å: Chain A: P.81, R.129, R.137 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.129 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:V.37, A:V.37, A:Y.42, A:R.158 Salt bridges: A:R.158 pi-Stacking: A:Y.29, A:Y.42

1 x 0OV: [4-amino-2-{[(1S,2R)-2-methylcyclohexyl]oxy}-5-oxopyrido[2,3-d]pyrimidin-8(5H)-yl]acetonitrile(Non-covalent)

0OV.4: 14 residues within 4Å: Chain A: S.88, L.89, E.118, L.119, K.120, I.121, A.125, E.175, Y.227, V.289, K.291, P.308, W.310, A.311 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.89, A:L.89, A:K.120, A:V.289, A:W.310, A:A.311 Hydrogen bonds: A:E.118, A:I.121, A:K.291 Water bridges: A:L.119 pi-Stacking: A:Y.227

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, T. et al., crystal structure of DNA ligase. 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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