SMTL ID : 3u7e.1

Crystal structure of mPNKP catalytic fragment (D170A)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: A.29, L.30, D.31, T.75, N.76, Q.77, K.118 Ligands: MG.2 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:L.30, A:D.31, A:T.75, A:T.75, A:N.76 Water bridges: A:N.76, A:Q.77, A:K.118, A:K.118, A:K.118 Salt bridges: A:K.118

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: A.29, D.31, G.32, T.33, D.147, F.164 Ligands: PO4.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.31, A:D.147, H2O.17, H2O.17

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 13 residues within 4Å: Chain A: P.119, L.170, P.197, F.199, P.201, E.313, H.317, R.320, Q.377, F.378, S.379, E.380, G.381 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.317, A:R.320, A:S.379, A:S.379, A:E.380, A:E.380 Water bridges: A:F.199 GOL.4: 10 residues within 4Å: Chain A: G.18, V.19, K.20, Q.22, A.65, G.68, Y.69, K.70, L.71, P.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.20, A:Q.22, A:L.71 Water bridges: A:P.104 GOL.5: 8 residues within 4Å: Chain A: R.169, F.179, A.180, T.181, E.184, A.191, A.192, F.194 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.169, A:R.169, A:F.179, A:E.184 Water bridges: A:F.179, A:F.179 GOL.6: 6 residues within 4Å: Chain A: K.60, L.64, E.67, Y.69, V.143, F.185 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.60, A:E.67, A:Y.69 Water bridges: A:D.141, A:S.142 GOL.7: 10 residues within 4Å: Chain A: F.231, P.232, G.233, A.234, G.235, K.236, S.237, T.238, R.322, V.332 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.231, A:G.233, A:A.234, A:G.235, A:K.236, A:K.236 Water bridges: A:R.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coquelle, N. et al., Structural basis for the phosphatase activity of polynucleotide kinase/phosphatase on single- and double-stranded DNA substrates. Proc.Natl.Acad.Sci.USA (2011)

Release Date

2011-12-14

Peptides

Bifunctional polynucleotide phosphatase/kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Bifunctional polynucleotide phosphatase/kinase

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