data_5NJR # _model_server_result.job_id d-uG85s4qLZBdv6nK0L14w _model_server_result.datetime_utc '2024-11-23 11:48:48' _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 5njr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":205}' # _entry.id 5NJR # _exptl.entry_id 5NJR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 4 _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 5NJR _cell.length_a 79.61 _cell.length_b 79.61 _cell.length_c 38.3 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NJR _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 NAG NAG C1 O1 . O4 HO4 . 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 2 n B NAG 1 B 1 NAG A 130 CTO 2 n B NAG 2 B 2 NAG A 130 CTO 2 n B NAG 3 B 3 NAG A 130 CTO # 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 6 A CYS 6 1_555 A SG CYS 127 A CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 115 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 80 A CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 76 A CYS 76 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 sing covale ? covale2 B O4 NAG . B NAG 2 1_555 B C1 NAG . B NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.364 sing metalc ? metalc1 A O SER 60 A SER 60 1_555 F NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc2 A O CYS 64 A CYS 64 1_555 F NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc3 A OG SER 72 A SER 72 1_555 F NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc4 A O ARG 73 A ARG 73 1_555 F NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc5 F NA NA . A NA 205 1_555 G O HOH . A HOH 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc6 F NA NA . A NA 205 1_555 G O HOH . A HOH 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? # _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 5NJR _atom_sites.fract_transf_matrix[1][1] 0.012561 _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] 0.012561 _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] 0.02611 _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 C 3 CL A 1 202 131 CL CL . D 3 CL A 1 203 132 CL CL . E 3 CL A 1 204 133 CL CL . F 4 NA A 1 205 134 NA NA . G 5 HOH A 1 301 192 HOH HOH . G 5 HOH A 2 302 165 HOH HOH . G 5 HOH A 3 303 193 HOH HOH . G 5 HOH A 4 304 143 HOH HOH . G 5 HOH A 5 305 136 HOH HOH . G 5 HOH A 6 306 180 HOH HOH . G 5 HOH A 7 307 175 HOH HOH . G 5 HOH A 8 308 155 HOH HOH . G 5 HOH A 9 309 156 HOH HOH . G 5 HOH A 10 310 152 HOH HOH . G 5 HOH A 11 311 169 HOH HOH . G 5 HOH A 12 312 138 HOH HOH . G 5 HOH A 13 313 158 HOH HOH . G 5 HOH A 14 314 172 HOH HOH . G 5 HOH A 15 315 171 HOH HOH . G 5 HOH A 16 316 137 HOH HOH . G 5 HOH A 17 317 150 HOH HOH . G 5 HOH A 18 318 147 HOH HOH . G 5 HOH A 19 319 177 HOH HOH . G 5 HOH A 20 320 154 HOH HOH . G 5 HOH A 21 321 186 HOH HOH . G 5 HOH A 22 322 149 HOH HOH . G 5 HOH A 23 323 163 HOH HOH . G 5 HOH A 24 324 191 HOH HOH . G 5 HOH A 25 325 159 HOH HOH . G 5 HOH A 26 326 135 HOH HOH . G 5 HOH A 27 327 170 HOH HOH . G 5 HOH A 28 328 182 HOH HOH . G 5 HOH A 29 329 139 HOH HOH . G 5 HOH A 30 330 166 HOH HOH . G 5 HOH A 31 331 148 HOH HOH . G 5 HOH A 32 332 174 HOH HOH . G 5 HOH A 33 333 141 HOH HOH . G 5 HOH A 34 334 142 HOH HOH . G 5 HOH A 35 335 168 HOH HOH . G 5 HOH A 36 336 145 HOH HOH . G 5 HOH A 37 337 146 HOH HOH . G 5 HOH A 38 338 153 HOH HOH . G 5 HOH A 39 339 140 HOH HOH . G 5 HOH A 40 340 173 HOH HOH . G 5 HOH A 41 341 184 HOH HOH . G 5 HOH A 42 342 190 HOH HOH . G 5 HOH A 43 343 187 HOH HOH . G 5 HOH A 44 344 185 HOH HOH . G 5 HOH A 45 345 183 HOH HOH . G 5 HOH A 46 346 144 HOH HOH . G 5 HOH A 47 347 164 HOH HOH . G 5 HOH A 48 348 181 HOH HOH . G 5 HOH A 49 349 167 HOH HOH . G 5 HOH A 50 350 161 HOH HOH . G 5 HOH A 51 351 176 HOH HOH . G 5 HOH A 52 352 160 HOH HOH . G 5 HOH A 53 353 157 HOH HOH . G 5 HOH A 54 354 179 HOH HOH . G 5 HOH A 55 355 162 HOH HOH . G 5 HOH A 56 356 151 HOH HOH . G 5 HOH A 57 357 189 HOH HOH . G 5 HOH A 58 358 178 HOH HOH . G 5 HOH A 59 359 188 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 F _atom_site.label_entity_id 4 _atom_site.Cartn_x 14.837 _atom_site.Cartn_y 7.967 _atom_site.Cartn_z -12.944 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 31.39 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 205 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #