SMTL ID : 6kkv.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 2.56 Å

Oligo State

monomer

Ligands

1 x DKR: N-[(4-methylphenyl)methyl]-1H-pyrrole-2-carboxamide(Non-covalent)

DKR.1: 10 residues within 4Å: Chain A: H.20, Q.21, Y.24, Y.25, P.30, I.31, I.32, S.33, D.34, F.37 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:H.20, A:Y.24, A:Y.24, A:P.30, A:I.32, A:F.37, A:F.37, A:F.37 Hydrogen bonds: A:D.34, A:D.34

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

SO4.2: 5 residues within 4Å: Chain A: R.23, R.27, V.156, P.157, E.158 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.158 Salt bridges: A:R.23, A:R.27 SO4.3: 4 residues within 4Å: Chain A: G.119, V.120, A.121, R.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.121 Salt bridges: A:R.137

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shukla, A. et al., Structure based identification of first-in-class fragment inhibitors that target the NMN pocket of M. tuberculosis NAD + -dependent DNA ligase A. J.Struct.Biol. (2021)

Release Date

2020-07-29

Peptides

DNA ligase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase A