SMTL ID : 6kdu.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

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.1: 17 residues within 4Å: Chain A: L.83, S.84, L.85, N.87, E.114, L.115, K.116, I.117, A.121, R.137, E.177, H.229, D.288, V.291, K.293, K.317 Ligands: SO4.3 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:L.85, A:N.87, A:E.114, A:L.115, A:K.116, A:I.117, A:R.137, A:R.137, A:K.293 Salt bridges: A:K.116, A:K.317 pi-Stacking: A:H.229

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

NMN.2: 10 residues within 4Å: Chain A: H.20, Q.21, Y.24, Y.25, P.30, I.32, S.33, D.34, F.37, D.38 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.24, A:Y.25, A:F.37 Hydrogen bonds: A:I.32, A:D.34 Water bridges: A:I.32 pi-Stacking: A:Y.24, A:F.37

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

SO4.3: 5 residues within 4Å: Chain A: G.119, V.120, A.121, R.137 Ligands: AMP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.121 Water bridges: A:R.137 Salt bridges: A:R.137 SO4.4: 5 residues within 4Å: Chain A: R.23, R.27, V.156, P.157, E.158 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.158 Water bridges: A:R.23, A:R.23, A:R.159 Salt bridges: A:R.23, A:R.27 SO4.5: 4 residues within 4Å: Chain A: V.234, E.235, G.236, F.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.236, A:F.237, A:F.237

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

2020-07-01

Peptides

DNA ligase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase A