SMTL ID : 6f30.1 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

4 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: 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 NAG-NAG.2: 4 residues within 4Å: Chain A: G.118, Q.119, Y.127, N.145 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: Y.152, N.154 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 9 residues within 4Å: Chain A: L.82, S.86, H.314, P.396, N.397, N.398, D.621, H.623, L.709 No protein-ligand interaction detected (PLIP)

1 x UD1: URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE(Non-covalent)

UD1.5: 19 residues within 4Å: Chain A: D.33, K.70, A.71, F.72, N.92, L.105, W.137, P.138, Y.155, Y.186, D.191, H.195, D.238, H.239, P.267, T.347, H.348 Ligands: ZN.6, ZN.7 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:P.138, A:Y.186 Hydrogen bonds: A:A.71, A:W.137, A:Y.155, A:Y.155 Salt bridges: A:H.195, A:H.239, A:H.348, A:H.348, A:H.348 pi-Stacking: A:F.72, A:Y.155

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 6 residues within 4Å: Chain A: D.33, A.71, D.191, D.238, H.239 Ligands: UD1.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.33, A:D.33, A:D.238, A:H.239 ZN.7: 4 residues within 4Å: Chain A: D.191, H.195, H.348 Ligands: UD1.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.191, A:D.191, A:H.195, A:H.348

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 5 residues within 4Å: Chain A: D.617, N.619, D.621, H.623, 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.5

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

NAG.9: 3 residues within 4Å: Chain A: N.654, T.656, H.657 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.656

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
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 3

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