SMTL ID : 6c01.1 (1 other biounit)

Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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.1: 10 residues within 4Å: Chain A: Y.192, N.197, K.198, N.199, Y.360, R.370, H.372, N.373, I.374, P.375 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.372, A:I.374

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: G.215, Q.216, Y.224, N.242 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 13 residues within 4Å: Chain A: L.179, Y.180, E.182, S.183, G.215, H.412, P.494, N.495, N.496, D.719, G.720, H.721, L.807 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.183

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

NAG-NAG-FUC.3: 7 residues within 4Å: Chain A: F.353, P.354, F.358, E.385, I.386, N.389, R.393 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.6: 5 residues within 4Å: Chain A: N.253, S.255, V.256, P.257, E.260 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.260, A:E.260 NAG-NAG-FUC.8: 4 residues within 4Å: Chain A: N.752, S.754, H.755, P.761 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.755

1 x NAG- NAG- BMA- MAN- FUC: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-FUC.5: 12 residues within 4Å: Chain A: H.542, P.621, P.622, V.624, N.662, R.663, T.664, S.665, D.666, Q.668, Y.669, L.672 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.624, A:Y.669 Hydrogen bonds: A:S.665, A:D.666

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.7: 7 residues within 4Å: Chain A: F.527, A.528, N.529, P.530, Q.554, N.557, T.559 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.9: 5 residues within 4Å: Chain A: D.288, H.292, H.336, M.338, H.446 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.288, A:D.288, A:H.292, A:H.446 ZN.10: 7 residues within 4Å: Chain A: D.130, T.168, H.172, D.288, D.335, H.336, H.446 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.130, A:D.130, A:T.168, A:D.335, A:H.336

1 x CA: CALCIUM ION(Non-covalent)

CA.11: 5 residues within 4Å: Chain A: D.715, N.717, D.719, H.721, D.723 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.715, A:D.719, A:H.721, A:D.723, H2O.15

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

NAG.12: 3 residues within 4Å: Chain A: N.545, T.547, Q.548 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.547

1 x NA: SODIUM ION(Non-functional Binders)

NA.13: 6 residues within 4Å: Chain A: Y.645, L.646, D.648, K.649, I.651, T.652 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.651 Water bridges: A:I.651

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorelik, A. et al., Structural basis for nucleotide recognition by the ectoenzyme CD203c. FEBS J. (2018)

Release Date

2018-05-02

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 3

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