SMTL ID : 5ven.1 (1 other biounit)

Murine ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

monomer

Ligands

1 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

NAG-NAG-BMA-MAN-MAN.1: 5 residues within 4Å: Chain A: P.277, N.278, D.307, E.308, W.310 No protein-ligand interaction detected (PLIP)

2 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: 6 residues within 4Å: Chain A: K.351, A.353, M.354, N.355, D.358, N.380 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 7 residues within 4Å: Chain A: L.69, F.70, N.73, H.292, P.373, H.374, N.375 No protein-ligand interaction detected (PLIP)

1 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.4: 4 residues within 4Å: Chain A: F.82, N.87, K.88, S.89 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.82 Hydrogen bonds: A:S.89, A:S.89 Water bridges: A:S.89

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: D.177, H.181, H.225, M.227, H.325 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.177, A:D.177, A:H.181, H2O.1, H2O.12 ZN.6: 7 residues within 4Å: Chain A: D.22, G.23, T.58, H.62, D.224, H.225, H.325 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.22, A:T.58, A:D.224, A:H.225, H2O.1 ZN.7: 3 residues within 4Å: Chain A: E.145, E.174, D.178 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.145, A:E.145, A:D.178, A:D.178, H2O.11 ZN.8: 1 residues within 4Å: Chain A: D.182 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.182, A:D.182, H2O.11, H2O.11, H2O.12

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

NAG.9: 3 residues within 4Å: Chain A: N.144, S.146, V.147 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.144 NAG.10: 3 residues within 4Å: Chain A: N.315, K.316, S.317 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.316 Hydrogen bonds: A:N.315, A:S.317, A:S.317

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.11: 6 residues within 4Å: Chain A: Y.139, L.141, P.142, K.155, E.158, W.159 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.155, A:W.159 Water bridges: A:Y.140, A:E.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorelik, A. et al., A key tyrosine substitution restricts nucleotide hydrolysis by the ectoenzyme NPP5. FEBS J. (2017)

Release Date

2017-09-20

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 5

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