SMTL ID : 6f2v.2 (1 other biounit)

Crystal structure of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3) in complex with AMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 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: 5 residues within 4Å: Chain A: N.100, N.102, Y.262, R.274, I.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.274, A:I.276

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.2: 10 residues within 4Å: Chain A: L.82, Y.83, S.86, H.314, P.396, N.397, N.398, D.621, H.623, L.709 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.621

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 14 residues within 4Å: Chain A: D.33, T.71, F.72, N.92, L.105, Y.155, Y.186, E.188, D.191, H.195, H.239, H.348 Ligands: ZN.4, ZN.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.71, A:N.92, A:D.141, A:S.192 Water bridges: A:K.110 Salt bridges: A:H.195, A:H.348 pi-Stacking: A:F.72, A:Y.155, A:Y.155

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 6 residues within 4Å: Chain A: D.33, T.71, D.191, D.238, H.239 Ligands: AMP.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.33, A:T.71, A:D.238, A:H.239, AMP.3 ZN.5: 4 residues within 4Å: Chain A: D.191, H.195, H.348 Ligands: AMP.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.191, A:D.191, A:H.195, A:H.348, AMP.3

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 6 residues within 4Å: Chain A: D.617, N.619, D.621, H.623, F.624, D.625 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.617, A:D.621, A:H.623, A:D.625, H2O.3

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

NAG.7: 4 residues within 4Å: Chain A: G.118, Q.119, Y.127, N.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.119 NAG.8: 2 residues within 4Å: Chain A: Y.152, N.154 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.152 Hydrogen bonds: A:Y.152, A:N.154 NAG.9: 3 residues within 4Å: Chain A: N.654, T.656, H.657 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dohler, C. et al., Crystal structure and substrate binding mode of ectonucleotide phosphodiesterase/pyrophosphatase-3 (NPP3). Sci Rep (2018)

Release Date

2018-08-01

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Ectonucleotide pyrophosphatase/phosphodiesterase family member 3

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