SMTL ID : 6ael.1

Crystal structure of ENPP1 in complex with 3'3'-cGAMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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.18 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.619 Water bridges: A:D.617, 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 4BW: 2-amino-9-[(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-9-(6-amino-9H-purin-9-yl)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecin-2-yl]-1,9-dihydro-6H-purin-6-one(Non-covalent)

4BW.5: 20 residues within 4Å: Chain A: K.70, A.71, F.72, N.92, L.105, K.106, K.110, W.137, P.138, Y.155, Y.186, D.191, H.195, S.347, G.348, F.349, H.350 Ligands: ZN.6, ZN.7, CL.13 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.70, A:A.71, A:N.92, A:S.347, A:S.347, A:S.347 Water bridges: A:K.106, A:K.110, A:W.137, A:S.140, A:D.141 Salt bridges: A:K.106, A:H.350 pi-Stacking: A:F.72, A:Y.155, A:Y.155, A:H.195, A:H.195

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 5 residues within 4Å: Chain A: D.191, H.195, H.239, H.350 Ligands: 4BW.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.191, A:D.191, A:H.195, A:H.350 ZN.7: 7 residues within 4Å: Chain A: D.33, G.34, A.71, D.191, D.238, H.239 Ligands: 4BW.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.33, A:D.33, A:D.238, A:H.239

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 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.9

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

CL.9: 5 residues within 4Å: Chain A: K.93, M.94, Y.95, R.273 Ligands: EDO.17 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: R.717, Q.718 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain A: S.319, R.321 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain A: Q.300, H.301 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain A: H.195, F.349, H.350 Ligands: 4BW.5 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain A: P.25, N.232, P.368, A.369 Ligand excluded by PLIP

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

EDO.15: 9 residues within 4Å: Chain A: N.386, L.387, D.390, S.402, H.403, G.404, S.405, L.406, N.407 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.404, A:S.405, A:L.406, A:N.407 Water bridges: A:E.383, A:N.386 EDO.16: 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.17: 6 residues within 4Å: Chain A: K.93, K.263, V.265, Y.266, R.273 Ligands: CL.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.93, A:K.93, A:Y.266, A:R.273 Water bridges: A:M.94 EDO.18: 3 residues within 4Å: Chain A: P.398 Ligands: NAG-NAG-MAN.1, NAG-NAG-MAN.1 No protein-ligand interaction detected (PLIP) EDO.19: 5 residues within 4Å: Chain A: V.259, N.261, V.262, F.284, L.289 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.261 EDO.20: 8 residues within 4Å: Chain A: K.70, D.91, Y.266, G.267, P.268, A.269, A.270, R.271 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.91, A:A.269 Water bridges: A:K.93 EDO.21: 3 residues within 4Å: Chain A: A.663, L.664, E.719 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.664, A:E.719, A:E.719 Water bridges: A:L.727 EDO.22: 6 residues within 4Å: Chain A: S.418, H.419, P.420, V.721, L.725, K.728 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.419, A:K.728, A:K.728

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

Related Entries With Identical Sequence