SMTL ID : 5kas.1

Murine acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3B) with phosphocholine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

monomer

Ligands

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.1: 4 residues within 4Å: Chain A: W.60, A.61, N.64, Y.68 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: alpha-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-MAN.2: 7 residues within 4Å: Chain A: N.156, E.157, W.208, D.211, V.212, N.215, R.218 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.157

1 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: 9 residues within 4Å: Chain A: D.24, P.25, N.26, P.38, P.88, V.90, E.93, S.94, L.95 No protein-ligand interaction detected (PLIP)

5 x ZN: ZINC ION(Non-covalent)

ZN.4: 8 residues within 4Å: Chain A: D.20, D.85, N.126, H.127, H.228, H.269 Ligands: ZN.5, PC.11 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.85, A:H.228, A:H.269, H2O.1 ZN.5: 8 residues within 4Å: Chain A: D.20, H.22, D.85, H.228, H.269, H.271 Ligands: ZN.4, PC.11 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.20, A:H.22, A:D.85, A:H.271, H2O.1 ZN.6: 5 residues within 4Å: Chain A: H.89, N.126, H.127, K.132 Ligands: PC.11 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.127, H2O.12, H2O.13 ZN.7: 2 residues within 4Å: Chain A: N.335, E.348 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.348, A:E.348, H2O.8 ZN.8: 2 residues within 4Å: Chain A: H.259, R.260 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.259, H2O.3, H2O.4

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.9: 6 residues within 4Å: Chain A: Y.351, R.352, E.355, A.356, R.383, Y.387 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.387, A:Y.387 Water bridges: A:E.355 NO3.10: 6 residues within 4Å: Chain A: G.210, E.250, K.253, V.254, K.257, H.258 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.253 Water bridges: A:G.210, A:K.257, A:H.258

1 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.11: 17 residues within 4Å: Chain A: H.22, D.85, H.89, N.126, H.127, Y.190, F.234, W.242, H.269, H.270, H.271, W.298, T.300, L.302 Ligands: ZN.4, ZN.5, ZN.6 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:N.126 Water bridges: A:Y.190 Salt bridges: A:H.22, A:H.89, A:H.127, A:H.269, A:H.271 pi-Cation interactions: A:H.269, A:H.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorelik, A. et al., Crystal Structure of the Acid Sphingomyelinase-like Phosphodiesterase SMPDL3B Provides Insights into Determinants of Substrate Specificity. J.Biol.Chem. (2016)

Release Date

2016-10-05

Peptides

Acid sphingomyelinase-like phosphodiesterase 3b: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Acid sphingomyelinase-like phosphodiesterase 3b

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