SMTL ID : 3zvl.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: R.73, S.83, W.85, R.86, K.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.73, A:W.85 GOL.10: 5 residues within 4Å: Chain A: K.95, L.99, Y.104, F.220 Ligands: GOL.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.95, A:K.95 Water bridges: A:K.95, A:Y.104, A:Y.104 GOL.11: 7 residues within 4Å: Chain A: G.53, V.54, K.55, Q.57, Y.104, K.105, L.106 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.53, A:K.55, A:K.55, A:Q.57, A:L.106 Water bridges: A:P.139 GOL.12: 7 residues within 4Å: Chain A: P.232, F.234, H.352, R.355, F.413, S.414, E.415 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.234, A:E.348, A:H.352, A:R.355, A:S.414, A:E.415 Water bridges: A:F.234 GOL.13: 9 residues within 4Å: Chain A: D.66, G.67, I.70, T.71, T.72, P.79, D.84, W.85, K.128 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.66, A:T.72, A:D.84, A:K.128 Water bridges: A:G.67, A:T.71, A:T.71, A:T.72 GOL.14: 5 residues within 4Å: Chain A: P.213, F.214, A.215 Ligands: CL.5, GOL.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.214, A:F.214

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.64, D.66, D.182 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.64, A:D.66, A:D.182, H2O.2, H2O.2, H2O.2

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: D.64, N.111, K.153 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: N.111, Q.112, M.113, R.152 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: P.213, F.214 Ligands: GOL.14 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain A: K.310 Ligand excluded by PLIP

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.6: 2 residues within 4Å: Chain A: N.257, P.337 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.257 Water bridges: A:S.255, A:S.255 ACT.7: 5 residues within 4Å: Chain A: P.79, S.81, P.82, L.120, K.128 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.120, A:K.128 Salt bridges: A:K.128 ACT.8: 4 residues within 4Å: Chain A: A.269, P.395, F.396, R.397 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.269, A:R.397 Water bridges: A:R.397 ACT.9: 7 residues within 4Å: Chain A: F.266, P.267, G.268, A.269, G.270, K.271, S.272 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.271 Hydrogen bonds: A:G.268, A:A.269, A:G.270, A:K.271, A:S.272, A:S.272, A:R.357 Water bridges: A:N.353

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

Related Entries With Identical Sequence