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

Crystal structures of human E-NPP 1: bound to N-{4-[(7-methoxyquinolin-4-yl)oxy]phenyl}sulfuric diamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.73 Å

Oligo State

monomer

Ligands

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

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

NAG-NAG-MAN.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 PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 9 residues within 4Å: Chain A: K.255, T.256, N.277, D.376, H.380, H.535 Ligands: ZN.5, ZN.6, TZV.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.256, A:N.277 Salt bridges: A:H.424, A:H.535

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: D.376, H.380, H.535 Ligands: PO4.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.376, A:D.376, A:H.380, A:H.535 ZN.6: 5 residues within 4Å: Chain A: D.218, T.256, D.423, H.424 Ligands: PO4.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.218, A:T.256, A:D.423, A:H.424

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

NAG.7: 1 residues within 4Å: Chain A: N.731 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.731 NAG.8: 5 residues within 4Å: Chain A: Y.440, L.441, V.444, N.477, R.481 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.481

1 x TZV: N-{4-[(7-methoxyquinolin-4-yl)oxy]phenyl}sulfuric diamide(Non-covalent)

TZV.9: 16 residues within 4Å: Chain A: T.256, F.257, K.295, F.321, W.322, P.323, S.325, D.326, K.338, Y.340, Y.371, E.373, D.376, S.377, H.380 Ligands: PO4.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:T.256, A:F.257, A:Y.340 Hydrogen bonds: A:W.322, A:E.373, A:D.376 pi-Stacking: A:F.257, A:Y.340, A:Y.340

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

EDO.10: 2 residues within 4Å: Chain A: H.493, F.801 No protein-ligand interaction detected (PLIP) EDO.11: 4 residues within 4Å: Chain A: F.708, S.709, Y.737, Q.770 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.737 EDO.12: 5 residues within 4Å: Chain A: R.476, S.479, L.491, R.861, S.865 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.479, A:R.861, A:S.865

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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