SMTL ID : 5egh.1 (1 other biounit)

Structure of ENPP6, a choline-specific glycerophosphodiester-phosphodiesterase in complex with phosphocholine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: P.114, L.115, N.118, L.147, K.314 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: R.82, Y.309, P.402, N.403, N.404 No protein-ligand interaction detected (PLIP)

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.2: 7 residues within 4Å: Chain A: W.339, N.341, S.342, E.347, G.348, W.349, R.351 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.347, A:W.349 Water bridges: A:R.351

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: D.193, H.197, H.241, H.354 Ligands: PC.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.193, A:D.193, A:H.197, A:H.354 ZN.5: 6 residues within 4Å: Chain A: D.32, S.71, D.193, D.240, H.241 Ligands: PC.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.32, A:D.32, A:S.71, A:D.240, A:H.241

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

EDO.6: 6 residues within 4Å: Chain A: E.85, N.306, Y.309, Y.310, K.311, K.312 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.309, A:Y.310, A:K.311 Water bridges: A:E.85, A:N.306 EDO.7: 8 residues within 4Å: Chain A: L.70, G.91, N.92, Y.93, K.268, D.269, V.273, S.275 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.92, A:Y.93, A:D.269, A:S.275 Water bridges: A:S.275, A:Y.310 EDO.9: 6 residues within 4Å: Chain A: Y.72, G.106, P.140, G.141, E.143, Y.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.106, A:G.141

1 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.8: 15 residues within 4Å: Chain A: D.32, S.71, Y.72, Y.75, N.92, Y.157, Y.188, E.190, D.193, H.197, D.240, H.241, H.354 Ligands: ZN.4, ZN.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.71, A:S.71, A:N.92 Salt bridges: A:E.190, A:H.241, A:H.354

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
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 6

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