SMTL ID : 6nhz.1

mycobacterial DNA ligase D complexed with ATP and Mg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: H.15, E.29, G.30, M.31, W.32, R.36, R.51, E.80, F.109, E.163, I.166, K.168, R.179, W.183, K.185, K.187 Ligands: MG.2, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:E.29, A:E.29, A:W.32, A:R.51, A:K.168 Water bridges: A:R.36, A:R.179, A:K.187, A:K.187 Salt bridges: A:H.15, A:R.51, A:R.179, A:K.185, A:K.185, A:K.185, A:K.187

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: R.51 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.3: 4 residues within 4Å: Chain A: E.163, K.187, R.295 Ligands: ATP.1 No protein-ligand interaction detected (PLIP)

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