SMTL ID : 5kar.1

Murine acid sphingomyelinase-like phosphodiesterase 3b (SMPDL3B)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.14 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: 5 residues within 4Å: Chain A: W.60, A.61, N.64, Y.68, K.71 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.2: 8 residues within 4Å: Chain A: N.156, E.157, A.160, W.208, D.211, V.212, N.215, R.218 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.157, 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: 8 residues within 4Å: Chain A: P.25, N.26, P.38, P.88, V.90, E.93, S.94, L.95 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 7 residues within 4Å: Chain A: D.20, D.85, N.126, H.127, H.228, H.269 Ligands: ZN.5 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, GOL.8 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

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

NO3.6: 5 residues within 4Å: Chain A: Y.351, E.355, A.356, R.383, Y.387 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.387, A:Y.387 Water bridges: A:R.352, A:E.355 NO3.7: 6 residues within 4Å: Chain A: G.210, E.250, K.253, V.254, K.257, H.258 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.253 Water bridges: A:G.210, A:E.250, A:K.257, A:K.257, A:K.257

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 9 residues within 4Å: Chain A: F.234, W.242, H.269, H.270, H.271, W.298, T.300, L.302 Ligands: ZN.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.300 Water bridges: A:H.269, A:T.300, A:T.300

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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