Entry | Database: PDB / ID: 5jg8 |
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Title | Crystal structure of human acid sphingomyelinase |
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Components | Sphingomyelin phosphodiesterase |
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Keywords | HYDROLASE / Lysosomal hydrolase / Neimann-Pick disease / Sphingolipid / Saposin |
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Function / homology | Function and homology information
acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin metabolic process / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / lamellar body / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction ...acid sphingomyelin phosphodiesterase activity / sphingomyelin catabolic process / sphingomyelin metabolic process / sphingomyelin phosphodiesterase / sphingomyelin phosphodiesterase activity / lamellar body / phospholipase C / phosphatidylcholine phospholipase C activity / endolysosome / termination of signal transduction / glycosphingolipid catabolic process / ceramide biosynthetic process / plasma membrane repair / Glycosphingolipid catabolism / response to type I interferon / hydrolase activity, acting on glycosyl bonds / response to ionizing radiation / positive regulation of endocytosis / response to tumor necrosis factor / : / negative regulation of MAP kinase activity / cellular response to calcium ion / response to interleukin-1 / cholesterol metabolic process / lysosomal lumen / lipid droplet / response to cocaine / wound healing / response to virus / cellular response to UV / nervous system development / endosome / positive regulation of viral entry into host cell / lysosome / response to xenobiotic stimulus / symbiont entry into host cell / positive regulation of apoptotic process / signal transduction / extracellular space / zinc ion binding / extracellular exosome / plasma membraneSimilarity search - Function Sphingomyelin phosphodiesterase / Acid sphingomyelinase/endopolyphosphatase, metallophosphatase domain / Sphingomyelin phosphodiesterase, C-terminal domain / Acid sphingomyelin phosphodiesterase C-terminal region / Saposin (B) Domains / Saposin B type domain / Saposin-like / Saposin B type domain profile. / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-likeSimilarity search - Domain/homology |
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Biological species | Homo sapiens (human) |
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Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å |
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Authors | Xiong, Z.J. / Prive, G.G. |
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Citation | Journal: J.Mol.Biol. / Year: 2016 Title: Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis. Authors: Xiong, Z.J. / Huang, J. / Poda, G. / Pomes, R. / Prive, G.G. |
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History | Deposition | Apr 19, 2016 | Deposition site: RCSB / Processing site: RCSB |
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Revision 1.0 | Jul 6, 2016 | Provider: repository / Type: Initial release |
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Revision 1.1 | Jul 13, 2016 | Group: Database references |
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Revision 1.2 | Aug 17, 2016 | Group: Database references |
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Revision 2.0 | Jul 29, 2020 | Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation |
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Revision 2.1 | Sep 27, 2023 | Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id |
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