SMTL ID : 6c02.1 (1 other biounit)

Human ectonucleotide pyrophosphatase / phosphodiesterase 3 (ENPP3, NPP3, CD203c), inactive (T205A), N594S, with alpha,beta-methylene-ATP (AMPCPP)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.94 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: 9 residues within 4Å: Chain A: Y.192, N.197, K.198, N.199, Y.360, R.370, H.372, N.373, I.374 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.372 NAG-NAG.4: 14 residues within 4Å: Chain A: L.179, Y.180, E.182, S.183, H.214, G.215, H.412, P.494, N.495, N.496, D.719, G.720, H.721, L.807 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.721

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

NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: G.215, Q.216, Y.224, N.242 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 7 residues within 4Å: Chain A: F.353, P.354, F.358, E.385, I.386, N.389, R.393 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.5: 10 residues within 4Å: Chain A: H.542, V.624, N.662, R.663, T.664, S.665, D.666, Q.668, Y.669, L.672 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.624 Hydrogen bonds: A:D.666

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

NAG-FUC.6: 5 residues within 4Å: Chain A: N.253, S.255, V.256, P.257, E.260 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.253, A:E.260, A:E.260 Water bridges: A:N.253, A:S.255, A:E.260, A:E.260 NAG-FUC.7: 3 residues within 4Å: Chain A: N.752, S.754, H.755 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.754

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 7 residues within 4Å: Chain A: D.288, H.292, H.336, M.338, H.446 Ligands: ZN.9, APC.17 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.288, A:D.288, A:H.292, A:H.446 ZN.9: 9 residues within 4Å: Chain A: D.130, G.131, A.168, D.288, D.335, H.336, H.446 Ligands: ZN.8, APC.17 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.130, A:D.130, A:D.335, A:H.336

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 6 residues within 4Å: Chain A: D.715, N.717, D.719, H.721, F.722, D.723 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.715, A:D.719, A:H.721, A:D.723, H2O.12

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 7 residues within 4Å: Chain A: Y.645, L.646, D.648, K.649, I.651, T.652 Ligands: CL.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.651

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 4 residues within 4Å: Chain A: Y.645, L.646, T.652 Ligands: NA.11 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: R.774, P.775, T.776, V.778 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: Q.114, N.323, H.325, N.326 Ligand excluded by PLIP

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.15: 4 residues within 4Å: Chain A: K.751, N.752, G.762, W.763 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.763 Water bridges: A:N.752 SO4.16: 4 residues within 4Å: Chain A: V.778, C.781, P.782, E.783 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.783

1 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.17: 20 residues within 4Å: Chain A: D.130, K.167, A.168, F.169, N.189, N.190, L.202, Q.207, F.233, W.234, P.235, E.238, Y.252, Y.283, E.285, D.288, H.292, H.446 Ligands: ZN.8, ZN.9 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.167, A:A.168, A:N.189, A:N.190, A:F.233, A:Y.252 Water bridges: A:N.190, A:G.236, A:S.289, A:N.445 pi-Stacking: A:F.169, A:F.169, A:Y.252, A:Y.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorelik, A. et al., Structural basis for nucleotide recognition by the ectoenzyme CD203c. FEBS J. (2018)

Release Date

2018-05-02

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase family member 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase family member 3

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