SMTL ID : 5ege.2 (3 other biounits)

Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUL.1: 6 residues within 4Å: Chain A: W.339, N.341, E.347, G.348, W.349, R.351 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.339, A:W.349 Hydrogen bonds: A:W.349, A:R.351, A:R.351

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 6 residues within 4Å: Chain A: R.82, V.86, Y.309, P.402, N.403, N.404 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.86

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 2 residues within 4Å: Chain A: N.100, Q.265 No protein-ligand interaction detected (PLIP) NAG.4: 4 residues within 4Å: Chain A: P.114, L.115, N.118, L.147 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.147 Hydrogen bonds: A:N.118 Water bridges: A:L.115, A:L.147, A:L.147

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 3 residues within 4Å: Chain A: D.193, H.197, H.354 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.193, A:H.197, A:H.354, H2O.2, H2O.15 ZN.6: 4 residues within 4Å: Chain A: D.32, S.71, D.240, H.241 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.32, A:S.71, A:D.240, A:H.241, H2O.2

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 6 residues within 4Å: Chain A: E.85, N.306, Y.309, Y.310, K.311, K.312 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.310, A:K.311 Water bridges: A:N.306, A:K.312

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morita, J. et al., Structure and biological function of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase. Sci Rep (2016)

Release Date

2016-03-09

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 6: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Ectonucleotide pyrophosphatase/phosphodiesterase family member 6

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