SMTL ID : 6ksc.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 2.40 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: S.84, L.85, E.114, L.115, R.116, I.117, A.121, R.137, E.177, H.229, V.291, K.293, K.317 Ligands: SO4.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.84, A:L.85, A:E.114, A:K.293 Salt bridges: A:R.116, A:R.137 pi-Stacking: A:H.229, A:H.229

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

SO4.2: 6 residues within 4Å: Chain A: G.119, V.120, A.121, R.137, E.177 Ligands: AMP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.121 Salt bridges: A:R.137 SO4.3: 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

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