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

Crystal structures of human E-NPP 1: apo

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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.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: 4 residues within 4Å: Chain A: N.341, S.343, V.344, P.345 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: T.256, D.376, H.380, H.535 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.256, A:D.376, A:D.376, A:H.380, A:H.535

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

NAG.4: 4 residues within 4Å: Chain A: N.731, N.732, T.733, Q.767 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.733 Hydrogen bonds: A:N.731 NAG.5: 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:R.481 Water bridges: A:N.477 NAG.6: 2 residues within 4Å: Chain A: N.285, P.463 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.463

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

EDO.7: 7 residues within 4Å: Chain A: E.472, A.475, R.476, S.479, L.491, R.861, S.865 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.472, A:S.479, A:S.479, A:R.861, A:S.865 EDO.8: 3 residues within 4Å: Chain A: H.493, F.801, T.829 No protein-ligand interaction detected (PLIP) EDO.9: 5 residues within 4Å: Chain A: F.321, W.322, P.323, Y.340, Y.371 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.322, A:Y.371 EDO.10: 2 residues within 4Å: Chain A: S.709, Y.737 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.737

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
AaA

Ectonucleotide pyrophosphatase/phosphodiesterase family member 1

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