data_8I5G # _model_server_result.job_id DtHwdFcN4bFyDIqbnJ3ENw _model_server_result.datetime_utc '2025-02-17 01:53:06' _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 8i5g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":2006}' # _entry.id 8I5G # _exptl.entry_id 8I5G _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 22.99 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _entity.pdbx_number_of_molecules 1 _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 8I5G _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8I5G _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA _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 ? _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 # _struct_asym.details ? _struct_asym.entity_id 9 _struct_asym.id O _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 D 1 NAG B 304 NAG 4 n D NAG 2 D 2 NAG B 305 NAG 4 n E NAG 1 E 1 NAG A 2007 NAG 4 n E NAG 2 E 2 NAG A 2008 NAG 4 n F NAG 1 F 1 NAG A 2009 NAG 4 n F NAG 2 F 2 NAG F 2004 NAG # 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 disulf ? disulf1 A SG CYS 21 B CYS 21 1_555 A SG CYS 43 B CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 40 B CYS 40 1_555 A SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 50 C CYS 50 1_555 B SG CYS 127 C CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 B SG CYS 55 C CYS 55 1_555 C SG CYS 895 A CYS 895 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 B SG CYS 72 C CYS 72 1_555 B SG CYS 75 C CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 C SG CYS 275 A CYS 275 1_555 C SG CYS 324 A CYS 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 C SG CYS 315 A CYS 315 1_555 C SG CYS 330 A CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 C SG CYS 897 A CYS 897 1_555 C SG CYS 903 A CYS 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 C SG CYS 935 A CYS 935 1_555 C SG CYS 944 A CYS 944 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf10 C SG CYS 1350 A CYS 1350 1_555 C SG CYS 1370 A CYS 1370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 C SG CYS 1715 A CYS 1715 1_555 C SG CYS 1730 A CYS 1730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 93 B ASN 93 1_555 G C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 110 B ASN 110 1_555 H C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 A ND2 ASN 114 B ASN 114 1_555 I C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 135 B ASN 135 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 C ND2 ASN 283 A ASN 283 1_555 J C1 NAG . A NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale6 C ND2 ASN 1352 A ASN 1352 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 C ND2 ASN 1366 A ASN 1366 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 C ND2 ASN 1375 A ASN 1375 1_555 M C1 NAG . A NAG 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale11 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 C OD1 ASP 361 A ASP 361 1_555 O NA NA . A NA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc2 C OE1 GLU 930 A GLU 930 1_555 O NA NA . A NA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc3 O NA NA . A NA 2006 1_555 DA O HOH . A HOH 2105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? # _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 8I5G _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 G 5 NAG B 1 301 301 NAG NAG . H 5 NAG B 1 302 302 NAG NAG . I 5 NAG B 1 303 303 NAG NAG . J 5 NAG A 1 2001 2006 NAG NAG . K 6 Y01 A 1 2002 2017 Y01 Y01 . L 7 9Z9 A 1 2003 2019 9Z9 9Z9 . M 5 NAG A 1 2004 2021 NAG NAG . N 8 T70 A 1 2005 2023 T70 LIG . O 9 NA A 1 2006 3 NA NA . P 10 LPE A 1 2007 2010 LPE LPE . Q 11 PCW A 1 2008 2013 PCW PCW . R 10 LPE A 1 2009 2014 LPE LPE . S 10 LPE A 1 2010 2015 LPE LPE . T 11 PCW A 1 2011 2016 PCW PCW . U 11 PCW A 1 2012 2018 PCW PCW . V 10 LPE A 1 2013 2019 LPE LPE . W 10 LPE A 1 2014 2020 LPE LPE . X 10 LPE A 1 2015 2021 LPE LPE . Y 10 LPE A 1 2016 2023 LPE LPE . Z 11 PCW A 1 2017 2035 PCW PCW . AA 11 PCW A 1 2018 2036 PCW PCW . BA 6 Y01 A 1 2019 2040 Y01 Y01 . CA 10 LPE A 1 2020 305 LPE LPE . DA 12 HOH A 1 2101 10 HOH HOH . DA 12 HOH A 2 2102 2 HOH HOH . DA 12 HOH A 3 2103 5 HOH HOH . DA 12 HOH A 4 2104 6 HOH HOH . DA 12 HOH A 5 2105 1 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 O _atom_site.label_entity_id 9 _atom_site.Cartn_x 126.916 _atom_site.Cartn_y 132.525 _atom_site.Cartn_z 133.718 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 29.01 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 2006 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 1 #