SMTL ID : 4b56.1

Structure of ectonucleotide pyrophosphatase-phosphodiesterase-1 (NPP1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG-BMA-MAN-MAN.1: 9 residues within 4Å: Chain A: L.163, Y.164, S.167, K.399, P.479, N.480, N.481, R.701, L.789 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.399 NAG-NAG-BMA-MAN-MAN.3: 10 residues within 4Å: Chain B: L.163, Y.164, S.167, H.396, P.479, N.480, N.481, D.699, R.701, L.789 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.701

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: 3 residues within 4Å: Chain A: E.534, K.535, N.538 No protein-ligand interaction detected (PLIP)

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(Non-functional Binders)

NAG-NAG-BMA.4: 5 residues within 4Å: Chain B: N.237, S.239, V.240, P.241, E.244 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.241

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: D.272, H.276, H.320, H.431 Ligands: PO4.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.272, A:D.272, A:H.276, A:H.431 ZN.6: 6 residues within 4Å: Chain A: D.114, T.152, D.272, D.319, H.320 Ligands: PO4.8 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.114, A:D.114, A:T.152, A:D.319, A:H.320 ZN.11: 4 residues within 4Å: Chain B: D.272, H.276, H.431 Ligands: PO4.14 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.272, B:D.272, B:H.276, B:H.431 ZN.12: 6 residues within 4Å: Chain B: D.114, T.152, D.272, D.319, H.320 Ligands: PO4.14 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.114, B:D.114, B:T.152, B:D.319, B:H.320

2 x CA: CALCIUM ION(Non-covalent)

CA.7: 6 residues within 4Å: Chain A: D.695, D.697, D.699, R.701, Y.702, D.703 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.695, A:D.697, A:D.699, A:R.701, A:D.703 CA.13: 6 residues within 4Å: Chain B: D.695, D.697, D.699, R.701, Y.702, D.703 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:D.695, B:D.697, B:D.699, B:R.701, B:D.703

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

PO4.8: 8 residues within 4Å: Chain A: D.114, T.152, N.173, D.272, H.276, H.431 Ligands: ZN.5, ZN.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.152, A:T.152, A:T.152, A:N.173 Salt bridges: A:H.276, A:H.431 PO4.14: 8 residues within 4Å: Chain B: D.114, T.152, N.173, D.272, H.276, H.431 Ligands: ZN.11, ZN.12 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.152, B:T.152, B:N.173 Salt bridges: B:H.276, B:H.431

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

NAG.9: 3 residues within 4Å: Chain A: N.237, S.239, V.240 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.237 NAG.10: 4 residues within 4Å: Chain A: Y.336, L.337, N.373, R.377 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.337, A:R.377 NAG.15: 2 residues within 4Å: Chain B: Y.336, N.373 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.373 NAG.16: 3 residues within 4Å: Chain B: N.181, V.358, P.359 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jansen, S. et al., Structure of Npp1, an Ectonucleotide Pyrophosphatase/Phosphodiesterase Involved in Tissue Calcification. Structure (2012)

Release Date

2012-09-19

Peptides

ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ECTONUCLEOTIDE PYROPHOSPHATASE/PHOSPHODIESTERASE FAMILY MEMBER 1