SMTL ID : 4gp6.1

Polynucleotide kinase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 11 residues within 4Å: Chain A: S.17, S.18, G.19, S.20, G.21, K.22, S.23, T.24, R.117, R.121 Ligands: MG.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:G.19, A:S.20, A:G.21, A:K.22, A:S.23, A:T.24, A:T.24, A:R.117 Water bridges: A:K.22, A:K.22, A:R.117, A:R.121, A:R.121, A:R.121, A:R.121 Salt bridges: A:K.22, A:R.121, A:R.121 pi-Cation interactions: A:R.117, A:R.117 ADP.3: 11 residues within 4Å: Chain B: S.17, S.18, G.19, S.20, G.21, K.22, S.23, T.24, R.117, R.121 Ligands: MG.4 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.19, B:S.20, B:G.21, B:K.22, B:S.23, B:T.24, B:T.24 Water bridges: B:K.22, B:K.22, B:K.22, B:T.24, B:R.117, B:R.117, B:R.117, B:R.117, B:R.121, B:R.121, B:R.121, B:R.121, B:T.122 Salt bridges: B:K.22, B:R.121, B:R.121 pi-Cation interactions: B:R.117

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.23 Ligands: ADP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.23, H2O.1, H2O.1, H2O.1, H2O.4 MG.4: 2 residues within 4Å: Chain B: S.23 Ligands: ADP.3 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:S.23, H2O.5, H2O.5, H2O.5, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, L.K. et al., Structure and mechanism of the polynucleotide kinase component of the bacterial Pnkp-Hen1 RNA repair system. Rna (2012)

Release Date

2012-11-14

Peptides

Metallophosphoesterase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Metallophosphoesterase