SMTL ID : 6aek.1

Crystal structure of ENPP1 in complex with pApG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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.1: 11 residues within 4Å: Chain A: L.82, Y.83, S.86, H.315, P.398, N.399, N.400, D.617, R.619, L.707 Ligands: EDO.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.619 Water bridges: A:D.617, A:R.619, A:R.619

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

NAG.2: 3 residues within 4Å: Chain A: N.100, P.278, E.279 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.278 Hydrogen bonds: A:N.100 NAG.3: 4 residues within 4Å: Chain A: N.156, S.158, V.159, P.160 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.156 NAG.4: 3 residues within 4Å: Chain A: A.288, K.291, N.292 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.292

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.5: 20 residues within 4Å: Chain A: D.33, K.70, A.71, F.72, N.92, L.105, K.110, W.137, P.138, Y.155, Y.186, E.188, D.191, H.195, D.238, H.239, H.350 Ligands: 5GP.6, ZN.7, ZN.8 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:A.71, A:N.92 Water bridges: A:K.110, A:W.137, A:W.137, A:G.139 Salt bridges: A:H.239, A:H.350 pi-Stacking: A:F.72, A:Y.155, A:Y.155

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.6: 6 residues within 4Å: Chain A: N.92, H.195, S.347, G.348 Ligands: AMP.5, CL.14 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.92, A:S.347, A:S.347, A:S.347 Water bridges: A:N.92, A:Y.266 pi-Stacking: A:H.195, A:H.195

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: D.191, H.195, H.239, H.350 Ligands: AMP.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.191, A:D.191, A:H.195, A:H.350, AMP.5 ZN.8: 7 residues within 4Å: Chain A: D.33, G.34, A.71, D.191, D.238, H.239 Ligands: AMP.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.33, A:D.33, A:D.238, A:H.239, AMP.5

1 x CA: CALCIUM ION(Non-covalent)

CA.9: 6 residues within 4Å: Chain A: D.613, D.615, D.617, R.619, Y.620, D.621 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.613, A:D.615, A:D.617, A:R.619, A:D.621, H2O.4

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

CL.10: 5 residues within 4Å: Chain A: K.93, M.94, Y.95, R.273 Ligands: EDO.19 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: R.717, Q.718 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: G.88, K.117, S.319, R.321 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain A: Q.300, H.301 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: H.195, F.349, H.350 Ligands: 5GP.6 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain A: P.25, N.232, P.368, A.369 Ligand excluded by PLIP

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

EDO.16: 9 residues within 4Å: Chain A: N.386, L.387, D.390, S.402, H.403, G.404, S.405, L.406, N.407 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.402, A:G.404, A:S.405, A:L.406, A:N.407 Water bridges: A:N.386, A:N.407 EDO.17: 7 residues within 4Å: Chain A: L.501, M.502, V.536, H.537, Y.542, I.575, P.577 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.575 Water bridges: A:L.501 EDO.18: 4 residues within 4Å: Chain A: R.303, E.693, L.694, L.697 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.303, A:S.680, A:L.697 EDO.19: 5 residues within 4Å: Chain A: K.93, K.263, V.265, Y.266 Ligands: CL.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.263, A:Y.266, A:R.273 Water bridges: A:M.94, A:S.102 EDO.20: 3 residues within 4Å: Chain A: P.398 Ligands: NAG-NAG-MAN.1, NAG-NAG-MAN.1 No protein-ligand interaction detected (PLIP) EDO.21: 4 residues within 4Å: Chain A: V.259, N.261, F.284, L.289 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.261

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato, K. et al., Structural insights into cGAMP degradation by Ecto-nucleotide pyrophosphatase phosphodiesterase 1. Nat Commun (2018)

Release Date

2019-03-06

Peptides

Ectonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Ectonucleotide pyrophosphatase/phosphodiesterase 1, isoform CRA_d

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