SMTL ID : 6kjm.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 2.20 Å

Oligo State

monomer

Ligands

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

NMN.1: 12 residues within 4Å: Chain A: H.27, Q.28, Y.31, Y.32, P.37, I.39, S.40, D.41, F.44, D.45, L.48, G.72 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.31, A:F.44 Hydrogen bonds: A:Q.28, A:Y.32, A:D.41, A:D.41, A:G.72, A:G.72 pi-Stacking: A:Y.31, A:F.44

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 15 residues within 4Å: Chain A: L.90, S.91, L.92, N.94, E.121, L.122, K.123, I.124, A.128, R.144, E.184, H.236, V.298, K.300, K.324 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:L.90, A:N.94, A:E.121, A:L.122, A:K.123, A:I.124, A:R.144, A:R.144, A:E.184, A:H.236, A:K.300 Water bridges: A:A.128 Salt bridges: A:K.123, A:K.324 pi-Stacking: A:H.236, A:H.236

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

SO4.3: 6 residues within 4Å: Chain A: R.30, R.34, V.163, P.164, E.165, R.166 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.165 Water bridges: A:R.30, A:R.166 Salt bridges: A:R.30, A:R.34 SO4.4: 4 residues within 4Å: Chain A: G.126, V.127, A.128, R.144 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.128 Water bridges: A:R.144 Salt bridges: A:R.144 SO4.5: 4 residues within 4Å: Chain A: V.241, E.242, G.243, F.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.241, A:G.243, A:F.244 SO4.6: 2 residues within 4Å: Chain A: R.134, V.178 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.134

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

2020-07-22

Peptides

DNA ligase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

DNA ligase A

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