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

Crystal structures of human E-NPP 1: apo

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- BMA: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA.1: 10 residues within 4Å: Chain A: L.267, S.271, H.500, K.503, P.583, N.584, N.585, D.804, R.806, H.894 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.503, A:D.804

1 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.2: 4 residues within 4Å: Chain A: N.341, S.343, V.344, P.345 No protein-ligand interaction detected (PLIP)

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.3: 2 residues within 4Å: Chain A: N.285, P.463 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 5 residues within 4Å: Chain A: D.376, H.380, H.424, H.535 Ligands: AMP.9 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.376, A:D.376, A:H.380, A:H.535, AMP.9 ZN.5: 6 residues within 4Å: Chain A: D.218, T.256, D.376, D.423, H.424 Ligands: AMP.9 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.218, A:T.256, A:D.423, A:H.424, AMP.9

1 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.800, D.802, D.804, R.806, D.808 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.800, A:D.804, A:R.806, A:D.808

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

NAG.7: 1 residues within 4Å: Chain A: N.731 No protein-ligand interaction detected (PLIP) NAG.8: 5 residues within 4Å: Chain A: Y.440, L.441, V.444, N.477, R.481 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.440, A:R.481

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.9: 17 residues within 4Å: Chain A: D.218, T.256, F.257, N.277, L.290, K.295, W.322, P.323, Y.340, Y.371, E.373, D.376, H.380, H.424, H.535 Ligands: ZN.4, ZN.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.277, A:Y.340 Water bridges: A:W.322, A:W.322 Salt bridges: A:H.380, A:H.535 pi-Stacking: A:F.257, A:Y.340, A:Y.340

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.10: 10 residues within 4Å: Chain A: E.472, A.475, R.476, S.479, P.489, Y.490, L.491, R.861, S.865, E.866 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.479, A:P.489, A:R.861, A:R.861, A:S.865

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 3 residues within 4Å: Chain A: H.493, F.801, T.829 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.493 EDO.12: 4 residues within 4Å: Chain A: F.708, S.736, Y.737, Q.770 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.736, A:Q.770

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dennis, M.L. et al., Crystal structures of human ENPP1 in apo and bound forms. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-09-09

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AcA

Ectonucleotide pyrophosphatase/phosphodiesterase family member 1

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