SMTL ID : 6f33.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

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.1: 8 residues within 4Å: Chain A: Y.95, N.100, K.101, N.102, Y.262, R.272, R.274, I.276 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 7 residues within 4Å: Chain A: L.82, S.86, H.314, P.396, N.398, D.621, H.623 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.621

1 x ZAN: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

ZAN.3: 19 residues within 4Å: Chain A: D.33, K.70, A.71, F.72, N.92, L.105, K.110, W.137, P.138, D.141, Y.155, N.157, Y.186, D.191, H.195, T.347, H.348 Ligands: ZN.4, ZN.5 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:A.71, A:N.92, A:D.141 Salt bridges: A:K.70, A:H.195, A:H.348 pi-Stacking: A:F.72, A:F.72, A:Y.155, A:Y.155

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 8 residues within 4Å: Chain A: D.33, A.71, D.191, D.238, H.239, H.348 Ligands: ZAN.3, ZN.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.33, A:D.33, A:D.238, A:H.239 ZN.5: 5 residues within 4Å: Chain A: D.191, H.195, H.348 Ligands: ZAN.3, ZN.4 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.6: 7 residues within 4Å: Chain A: D.617, N.619, D.621, H.623, F.624, D.625, E.629 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.617, A:D.621, A:H.623, A:D.625

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

NAG.7: 1 residues within 4Å: Chain A: N.439 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: N.567, E.568 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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