SMTL ID : 5tt5.1

Escherichia coli LigA (K115M) in complex with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 25 residues within 4Å: Chain A: H.38, E.39, Y.42, H.43, P.48, I.50, P.51, D.52, Y.55, D.56, L.100, S.101, L.102, E.133, L.134, M.135, L.136, A.140, R.156, E.193, Y.245, V.308, K.310, K.334 Ligands: MG.3 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:Y.42, A:Y.55 Hydrogen bonds: A:D.52, A:D.52, A:D.56, A:L.100, A:L.102, A:E.133, A:E.133, A:L.136, A:Y.245, A:K.310, A:K.334 Water bridges: A:Y.42, A:Y.42, A:Y.42, A:I.50, A:R.156, A:R.156, A:R.156, A:Y.245, A:Y.245 Salt bridges: A:H.43, A:R.156, A:K.334 pi-Stacking: A:Y.42, A:Y.55, A:Y.245

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.428, C.431, C.446, C.452 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.428, A:C.431, A:C.446, A:C.452

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.305 Ligands: NAD.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unciuleac, M.C. et al., Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NAD(+)-dependent polynucleotide ligases. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-03-08

Peptides

DNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase