SMTL ID : 5vem.1 (2 other biounits)

Human ectonucleotide pyrophosphatase / phosphodiesterase 5 (ENPP5, NPP5)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

monomer

Ligands

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.1: 8 residues within 4Å: Chain A: L.69, F.70, E.72, N.73, H.292, P.373, H.374, N.375 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

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

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

NAG.5: 3 residues within 4Å: Chain A: N.144, S.146, V.147 No protein-ligand interaction detected (PLIP) NAG.6: 5 residues within 4Å: Chain A: P.277, N.278, D.307, E.308, W.310 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.307 Hydrogen bonds: A:W.310 NAG.7: 6 residues within 4Å: Chain A: K.351, A.353, M.354, N.355, D.358, N.380 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.351, A:N.380

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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