SMTL ID : 6nhx.1

mycobacterial DNA ligase D complexed with ATP and MES

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 17 residues within 4Å: Chain A: E.29, G.30, M.31, W.32, R.36, R.51, E.80, F.109, I.166, K.168, R.179, W.183, K.185, K.187, R.293, R.296 Ligands: MES.2 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:E.29, A:E.29, A:W.32, A:K.168 Water bridges: A:R.36, A:R.179, A:K.185, A:K.185, A:K.185, A:R.296, A:R.296, A:R.296, A:R.296, A:R.296, A:R.296, A:K.299 Salt bridges: A:R.51, A:R.179, A:K.185, A:K.185, A:K.185, A:K.187, A:R.293, A:R.296 pi-Stacking: A:F.109

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 10 residues within 4Å: Chain A: D.33, G.34, Y.35, R.36, R.51, E.80, F.92, R.293, R.296 Ligands: ATP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.34, A:R.36 Salt bridges: A:R.51, A:E.80

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unciuleac, M.C. et al., Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates. J. Biol. Chem. (2019)

Release Date

2019-02-13

Peptides

ATP-dependent DNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-dependent DNA ligase