SMTL ID : 4d05.1 (1 other biounit)

Structure and activity of a minimal-type ATP-dependent DNA ligase from a psychrotolerant bacterium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: Q.71, Q.72, F.73, E.74 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.71, A:F.73, A:E.74 Water bridges: A:T.75 SO4.2: 2 residues within 4Å: Chain A: R.253, R.255 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.253, A:R.255 SO4.3: 1 residues within 4Å: Chain A: K.205 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.211 Salt bridges: A:K.205 SO4.4: 6 residues within 4Å: Chain A: L.8, A.9, K.42, R.168, K.174 Ligands: AMP.6 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.31, A:K.42, A:K.42, A:R.168, A:R.168 Salt bridges: A:K.42, A:R.168, A:K.174 SO4.5: 6 residues within 4Å: Chain A: T.60, A.61, L.100, K.102, S.103, K.113 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.61 Water bridges: A:K.102, A:S.103, A:K.113 Salt bridges: A:K.113

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.6: 17 residues within 4Å: Chain A: L.8, A.9, S.24, E.25, K.26, L.27, R.31, E.65, F.98, I.129, Q.131, E.153, M.156, L.172, K.174, K.176 Ligands: SO4.4 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:E.25, A:L.27 Water bridges: A:A.9, A:K.26, A:R.31, A:R.31, A:R.31, A:K.42, A:Q.131 Salt bridges: A:K.26, A:K.174, A:K.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williamson, A. et al., Enzyme-Adenylate Structure of a Bacterial ATP-Dependent DNA Ligase with a Minimized DNA-Binding Surface. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-11-12

Peptides

ATP-DEPENDENT DNA LIGASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ATP-DEPENDENT DNA LIGASE

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