SMTL ID : 3zvm.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

DT-DC-DA-DC.1: 11 residues within 4Å: Chain A: D.66, F.78, N.111, Q.112, M.113, G.114, R.117, K.119, R.152, F.199 Ligands: MG.4 Protein-ligand interaction information (PLIP) not available

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

ADP.2: 17 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: MG.5 21 PLIP interactions: 21 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:S.272, A:T.273, A:T.360, A:H.364, A:R.397, A:Q.399 Salt bridges: A:K.271, A:R.357, A:R.357

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 7 residues within 4Å: Chain A: P.267, R.289, D.290, W.295, N.316, T.317, H.364 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.290, A:N.316 Water bridges: A:R.289, A:D.290, A:W.295, A:N.316, A:S.323, A:S.323 Salt bridges: A:R.289

2 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.64, D.66, D.182 Ligands: DT-DC-DA-DC.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.64, A:D.66, A:D.182, H2O.2, H2O.2 MG.5: 3 residues within 4Å: Chain A: S.272, D.290 Ligands: ADP.2 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.272, A:D.290, H2O.17, H2O.17, H2O.18

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: E.91, L.222, K.223 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.91, A:E.91 Water bridges: A:W.224 GOL.7: 9 residues within 4Å: Chain A: A.148, G.149, R.152, K.153, P.154, V.155, R.355, M.359, S.414 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.149, A:R.152 Water bridges: A:E.358, A:E.358, A:E.358 GOL.8: 4 residues within 4Å: Chain A: R.73, S.83, W.85, K.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.73, A:S.83 GOL.9: 8 residues within 4Å: Chain A: G.53, V.54, K.55, Q.57, A.100, Y.104, K.105, L.106 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.53, A:K.55, A:Q.57, A:Y.104, A:L.106

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

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