SMTL ID : 6ksd.1

Structural basis for domain rotation during adenylation of active site K123 and fragment library screening against NAD+ -dependent DNA ligase from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x NMN: BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE(Non-covalent)

NMN.1: 9 residues within 4Å: Chain A: H.20, Q.21, Y.24, Y.25, P.30, I.32, D.34, F.37, D.38 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.24, A:F.37 Hydrogen bonds: A:Y.24, A:D.34, A:D.34 pi-Stacking: A:Y.24, A:F.37

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

SO4.2: 6 residues within 4Å: Chain A: R.23, R.27, V.156, P.157, E.158, R.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.158 Salt bridges: A:R.23, A:R.27 SO4.3: 5 residues within 4Å: Chain A: G.119, V.120, A.121, R.137, R.204 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.121, A:R.204 Water bridges: A:R.137, A:R.137, A:R.204 Salt bridges: A:R.137 SO4.4: 6 residues within 4Å: Chain A: I.227, S.257, E.258, H.259, V.283, H.285 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.257, A:E.258 Water bridges: A:R.181, A:H.259, A:D.284 Salt bridges: A:H.259, A:H.285

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Afsar, M. et al., Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD + -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity. Acta Crystallogr D Struct Biol (2021)

Release Date

2020-08-26

Peptides

DNA ligase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase A