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

Crystal structures of human E-NPP 1: bound to N-{[1-(6,7-dimethoxy-5,8-dihydroquinazolin-4-yl)piperidin-4-yl]methyl}sulfuric diamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.1: 10 residues within 4Å: Chain A: L.267, S.271, H.500, K.503, P.583, N.584, N.585, D.804, R.806, H.894 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.503

1 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: 3 residues within 4Å: Chain A: N.341, S.343, V.344 No protein-ligand interaction detected (PLIP)

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.3: 2 residues within 4Å: Chain A: N.285, P.463 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: D.376, H.380, H.424, H.535 Ligands: PO4.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.376, A:D.376, A:H.380, A:H.535

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 5 residues within 4Å: Chain A: D.800, D.802, D.804, R.806, D.808 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.800, A:D.804, A:R.806, A:D.808

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

NAG.6: 5 residues within 4Å: Chain A: Y.440, L.441, V.444, N.477, R.481 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.440, A:R.481

1 x TZS: N-{[1-(6,7-dimethoxy-5,8-dihydroquinazolin-4-yl)piperidin-4-yl]methyl}sulfuric diamide(Non-covalent)

TZS.7: 17 residues within 4Å: Chain A: D.218, T.256, F.257, L.290, K.295, F.321, W.322, P.323, S.325, D.326, K.338, Y.340, Y.371, E.373, D.376, S.377 Ligands: PO4.8 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.256, A:Y.340 Hydrogen bonds: A:W.322, A:E.373 pi-Stacking: A:F.257, A:F.257, A:Y.340

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 7 residues within 4Å: Chain A: D.218, T.256, D.376, H.380, H.535 Ligands: ZN.4, TZS.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.256, A:T.256, A:T.256 Salt bridges: A:H.380, A:H.535

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dennis, M.L. et al., Crystal structures of human ENPP1 in apo and bound forms. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-09-09

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AbA

Ectonucleotide pyrophosphatase/phosphodiesterase family member 1

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