SMTL ID : 6krh.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 2.60 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 16 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, Y.229, V.291, K.293, A.315, K.317 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:L.83, A:N.87, A:L.115, A:I.117, A:Y.229, A:K.293 Water bridges: A:R.137 Salt bridges: A:K.116, A:K.317 pi-Stacking: A:Y.229, A:Y.229 pi-Cation interactions: A:K.116

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, A:D.38 pi-Stacking: A:Y.24, A:F.37

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

SO4.3: 4 residues within 4Å: Chain A: V.125, R.127, T.132, R.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.132 Salt bridges: A:R.127, A:R.133 SO4.4: 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 SO4.5: 5 residues within 4Å: Chain A: H.259, V.283, D.284, H.285 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.284, A:D.284 Salt bridges: A:H.259, A:H.285 SO4.6: 6 residues within 4Å: Chain A: I.227, S.257, E.258, H.259, H.285 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.258 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