data_2YGJ # _model_server_result.job_id ToVQa02WxAQ_WxlzrgzD2g _model_server_result.datetime_utc '2024-10-20 03:48:50' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2ygj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1008}' # _entry.id 2YGJ # _exptl.entry_id 2YGJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2YGJ _cell.length_a 9.06 _cell.length_b 13.32 _cell.length_c 42.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YGJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.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.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 A C HM9 1 A HM9 1 1_555 A N ALA 2 A ALA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C SER 3 A SER 3 1_555 A N HM8 4 A HM8 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? covale ? covale3 A C HM8 4 A HM8 4 1_555 A N ALA 5 A ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? metalc ? metalc1 A SAE HM9 1 A HM9 1 1_555 B CU CU . A CU 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc2 A NAB HM9 1 A HM9 1 1_555 B CU CU . A CU 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc3 A NBA HM8 4 A HM8 4 1_555 B CU CU . A CU 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc4 A SBG HM8 4 A HM8 4 1_555 B CU CU . A CU 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc5 A OBY HM8 4 A HM8 4 1_555 C NA NA . A NA 1008 3_345 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc6 A OBY HM8 4 A HM8 4 3_355 C NA NA . A NA 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc7 A OBZ HM8 4 A HM8 4 1_555 D NA NA . A NA 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc8 A O MET 6 A MET 6 1_555 C NA NA . A NA 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc9 A O MET 6 A MET 6 3_345 D NA NA . A NA 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc10 C NA NA . A NA 1008 1_555 E O HOH . A HOH 2002 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc11 C NA NA . A NA 1008 1_555 E O HOH . A HOH 2004 3_345 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc12 C NA NA . A NA 1008 1_555 E O HOH . A HOH 2010 3_355 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc13 C NA NA . A NA 1008 1_555 E O HOH . A HOH 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc14 D NA NA . A NA 1009 1_555 E O HOH . A HOH 2009 4_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc15 D NA NA . A NA 1009 1_555 E O HOH . A HOH 2010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc16 D NA NA . A NA 1009 1_555 E O HOH . A HOH 2012 3_345 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc17 D NA NA . A NA 1009 1_555 E O HOH . A HOH 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2YGJ _atom_sites.fract_transf_matrix[1][1] 0.110375 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.075075 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.023447 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 CU A 1 1007 1007 CU CU . C 3 NA A 1 1008 1008 NA NA . D 3 NA A 1 1009 1009 NA NA . E 4 HOH A 1 2001 2001 HOH HOH . E 4 HOH A 2 2002 2002 HOH HOH . E 4 HOH A 3 2003 2003 HOH HOH . E 4 HOH A 4 2004 2004 HOH HOH . E 4 HOH A 5 2005 2005 HOH HOH . E 4 HOH A 6 2006 2006 HOH HOH . E 4 HOH A 7 2007 2007 HOH HOH . E 4 HOH A 8 2008 2008 HOH HOH . E 4 HOH A 9 2009 2009 HOH HOH . E 4 HOH A 10 2010 2010 HOH HOH . E 4 HOH A 11 2011 2011 HOH HOH . E 4 HOH A 12 2012 2012 HOH HOH . E 4 HOH A 13 2013 2013 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id C _atom_site.label_entity_id 3 _atom_site.Cartn_x -11.899 _atom_site.Cartn_y 2.176 _atom_site.Cartn_z 17.36 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 5.73 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1008 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #