SMTL ID : 3zvn.1

The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

5 x DG- DT- DC- DA: 5'-D(*GP*TP*CP*AP*CP)-3'(Non-covalent)(Non-functional Binders)

DG-DT-DC-DA.1: 18 residues within 4Å: Chain A: R.289, D.290, W.295, Q.296, N.316, T.317, R.326, H.364, V.367, M.370, V.371, Q.378 Ligands: DG-DT-DC-DA-DC.2, DG-DT-DC-DA-DC.4, DG-DT-DC-DA-DC.5, DG-DT-DC-DA-DC.5, DG-DT-DC-DA-DC.5, MN.6 Protein-ligand interaction information (PLIP) not available DG-DT-DC-DA.2: 8 residues within 4Å: Ligands: DG-DT-DC-DA.1, DG-DT-DC-DA.1, DG-DT-DC-DA-DC.4, DG-DT-DC-DA-DC.4, DG-DT-DC-DA-DC.4, DG-DT-DC-DA-DC.4, DG-DT-DC-DA-DC.4, DG-DT-DC-DA-DC.5 Protein-ligand interaction information (PLIP) not available DG-DT-DC-DA.3: 17 residues within 4Å: Chain A: V.77, F.78, T.110, N.111, Q.112, M.113, G.114, R.117, K.119, L.120, A.148, R.152, F.199, E.358, M.370 Ligands: DG-DT-DC-DA-DC.5, DG-DT-DC-DA-DC.5 Protein-ligand interaction information (PLIP) not available DG-DT-DC-DA.4: 11 residues within 4Å: Chain A: G.293, S.294, Q.296, R.297 Ligands: DG-DT-DC-DA.1, DG-DT-DC-DA-DC.2, DG-DT-DC-DA-DC.2, DG-DT-DC-DA-DC.2, DG-DT-DC-DA-DC.2, DG-DT-DC-DA-DC.2, DG-DT-DC-DA-DC.5 Protein-ligand interaction information (PLIP) not available DG-DT-DC-DA.5: 13 residues within 4Å: Chain A: M.370, F.373, S.374, R.376, K.377 Ligands: DG-DT-DC-DA.1, DG-DT-DC-DA.1, DG-DT-DC-DA.1, DG-DT-DC-DA.1, DG-DT-DC-DA-DC.2, DG-DT-DC-DA-DC.3, DG-DT-DC-DA-DC.3, DG-DT-DC-DA-DC.4 Protein-ligand interaction information (PLIP) not available

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.6: 3 residues within 4Å: Chain A: S.272 Ligands: DG-DT-DC-DA.1, ADP.8 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.272, H2O.4, H2O.5, H2O.5, H2O.8

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 10 residues within 4Å: Chain A: A.269, G.270, T.273, F.274, F.343, I.394, P.395, F.396, R.397 Ligands: ADP.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.394, A:P.395, A:R.397 GOL.9: 1 residues within 4Å: Chain A: W.224 No protein-ligand interaction detected (PLIP)

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

ADP.8: 18 residues within 4Å: Chain A: F.266, P.267, G.268, A.269, G.270, K.271, S.272, T.273, N.353, F.356, R.357, F.396, R.397, L.398, Q.399, Y.410 Ligands: MN.6, GOL.7 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:F.266, A:G.268, A:A.269, A:G.270, A:K.271, A:S.272, A:T.273, A:T.273, A:R.397, A:Q.399 Water bridges: A:K.271, A:K.271, A:K.271, A:R.357, A:R.357 Salt bridges: A:K.271, A:R.357, A:R.357

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garces, F. et al., The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase. Mol. Cell (2011)

Release Date

2011-11-16

Peptides

BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

BIFUNCTIONAL POLYNUCLEOTIDE PHOSPHATASE/KINASE