SMTL ID : 7k72.4 (3 other biounits)

Structure of DNA ligase A from Mycobacterium tuberculosis bound to NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 25 residues within 4Å: Chain A: H.35, Y.39, Y.40, P.45, I.47, S.48, D.49, F.52, D.53, S.99, L.100, N.102, E.129, L.130, K.131, I.132, A.136, R.152, E.192, H.244, V.306, K.308, K.332 Ligands: MG.2, MG.4 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:Y.39, A:F.52 Hydrogen bonds: A:I.47, A:D.53, A:L.98, A:L.100, A:E.129, A:I.132, A:R.152, A:K.308, A:K.332, A:K.332 Water bridges: A:Y.40, A:I.47, A:K.131, A:K.131, A:K.131, A:K.131 Salt bridges: A:K.131, A:R.152, A:K.332 pi-Stacking: A:Y.39, A:F.52, A:H.244, A:H.244

3 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: K.131 Ligands: NAD.1 No protein-ligand interaction detected (PLIP) MG.3: 1 residues within 4Å: Chain A: E.34 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.34, A:E.34, H2O.1, H2O.5, H2O.5 MG.4: 5 residues within 4Å: Chain A: Q.36, Y.40, F.52, G.80 Ligands: NAD.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Y.40

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.5: 8 residues within 4Å: Chain A: G.81, F.84, T.86, G.153, D.154, T.157, G.158, E.159 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.159 Hydrogen bonds: A:F.84, A:F.84

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Delker, S.L. et al., Structure of DNA ligase A from Mycobacterium tuberculosis bound to NAD. To Be Published

Release Date

2020-12-02

Peptides

DNA ligase A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

DNA ligase A

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