SMTL ID : 3qwu.1

Putative ATP-dependent DNA ligase from Aquifex aeolicus.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x ADN: ADENOSINE(Non-covalent)

ADN.1: 14 residues within 4Å: Chain A: Y.54, I.57, E.78, E.79, K.80, V.81, N.85, R.100, E.132, F.157, V.185, V.217, K.219, K.229 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.54, A:E.78, A:E.78, A:K.80, A:V.81, A:N.85, A:R.100, A:R.100, A:K.219 pi-Stacking: A:F.157, A:F.157 ADN.4: 13 residues within 4Å: Chain B: Y.54, I.57, E.78, E.79, K.80, V.81, N.85, R.100, E.132, F.157, V.185, V.217, K.219 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.54, B:I.57, B:E.78, B:K.80, B:V.81, B:N.85, B:R.100, B:K.219 pi-Stacking: B:F.157

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 5 residues within 4Å: Chain A: D.82, E.143, E.214, A.235, D.239 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.82, A:E.143, A:D.239, H2O.2, H2O.2 CA.5: 3 residues within 4Å: Chain B: D.82, E.143, D.239 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.82, B:E.143, B:D.239, H2O.5

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: E.79, V.81, Y.147, F.155, H.184, V.185, E.186, R.213 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.184, A:E.186 GOL.6: 7 residues within 4Å: Chain B: E.79, Y.147, F.155, H.184, V.185, E.186, R.213 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.79, B:E.186, B:E.186, B:E.186, B:R.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., Putative ATP-dependent DNA ligase from Aquifex aeolicus. To be Published

Release Date

2011-03-16

Peptides

DNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

DNA ligase