Entry | Database: PDB / ID: 5kzw |
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Title | Crystal structure of human GAA |
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Components | Lysosomal alpha-glucosidase |
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Keywords | HYDROLASE / Pompe disease / Glycogen storage disease 2 / human acid alpha glucosidase / glycoprotein / N-linked glycosylation / lysosomal enzyme |
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Function / homology | Function and homology information
vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-glucosidase activity / alpha-1,4-glucosidase activity / sucrose metabolic process / glycophagy / Glycogen storage disease type II (GAA) / maltose alpha-glucosidase activity / alpha-glucosidase ...vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-glucosidase activity / alpha-1,4-glucosidase activity / sucrose metabolic process / glycophagy / Glycogen storage disease type II (GAA) / maltose alpha-glucosidase activity / alpha-glucosidase / diaphragm contraction / neuromuscular process controlling posture / tissue development / regulation of the force of heart contraction / glycogen catabolic process / aorta development / azurophil granule membrane / muscle cell cellular homeostasis / Glycogen breakdown (glycogenolysis) / lysosome organization / tertiary granule membrane / neuromuscular process controlling balance / ficolin-1-rich granule membrane / heart morphogenesis / cardiac muscle contraction / lysosomal lumen / locomotory behavior / glucose metabolic process / carbohydrate binding / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular exosome / membrane / plasma membraneSimilarity search - Function : / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain ...: / Spasmolytic Protein, domain 1 / Spasmolytic Protein; domain 1 / P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / glycosyl hydrolase (family 31) / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Few Secondary Structures / Irregular / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha BetaSimilarity search - Domain/homology beta-D-glucopyranose / alpha-D-glucopyranose / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Lysosomal alpha-glucosidaseSimilarity search - Component |
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Biological species | Homo sapiens (human) |
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Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å |
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Model details | Complex with DNJ |
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Authors | Deming, D.T. / Garman, S.C. |
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Funding support | United States, 2items Organization | Grant number | Country |
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National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) | R01 DK76877 | United States | National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | T32 GM008515 | United States |
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Citation | Journal: To be published Title: The structure of human GAA: structural basis of Pompe disease Authors: Deming, D.T. / Garman, S.C. |
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History | Deposition | Jul 25, 2016 | Deposition site: RCSB / Processing site: RCSB |
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Revision 1.0 | Jul 26, 2017 | Provider: repository / Type: Initial release |
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Revision 1.1 | Dec 25, 2019 | Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support Item: _chem_comp.type / _pdbx_audit_support.funding_organization |
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Revision 2.0 | Jul 29, 2020 | Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / 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_unobs_or_zero_occ_atoms / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / 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_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_percent_reflns_obs / _refine_hist.cycle_id / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _reflns.pdbx_CC_half / _reflns_shell.pdbx_CC_half Description: Carbohydrate remediation / Provider: repository / Type: Remediation |
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Revision 2.1 | Oct 4, 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 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession |
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