data_6X9H # _model_server_result.job_id 2hiUz0wwPbRMRW16dN0lzQ _model_server_result.datetime_utc '2025-01-09 19:06:01' _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 6x9h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":503}' # _entry.id 6X9H # _exptl.entry_id 6X9H _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 6X9H _cell.length_a 91.786 _cell.length_b 116.149 _cell.length_c 227.79 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6X9H _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,F,G,H,I,J _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 # 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 69 A CYS 94 1_555 A SG CYS 170 A CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf2 A SG CYS 148 A CYS 173 1_555 A SG CYS 155 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf3 A SG CYS 266 A CYS 291 1_555 A SG CYS 341 A CYS 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf4 A SG CYS 284 A CYS 309 1_555 A SG CYS 337 A CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf5 A SG CYS 288 A CYS 313 1_555 A SG CYS 335 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 A SG CYS 297 A CYS 322 1_555 A SG CYS 319 A CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf7 A SG CYS 299 A CYS 324 1_555 A SG CYS 311 A CYS 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf8 B SG CYS 69 B CYS 94 1_555 B SG CYS 170 B CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf9 B SG CYS 148 B CYS 173 1_555 B SG CYS 155 B CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf10 B SG CYS 266 B CYS 291 1_555 B SG CYS 341 B CYS 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf11 B SG CYS 284 B CYS 309 1_555 B SG CYS 337 B CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf12 B SG CYS 288 B CYS 313 1_555 B SG CYS 335 B CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf13 B SG CYS 297 B CYS 322 1_555 B SG CYS 319 B CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf14 B SG CYS 299 B CYS 324 1_555 B SG CYS 311 B CYS 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf15 C SG CYS 69 C CYS 94 1_555 C SG CYS 170 C CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf16 C SG CYS 148 C CYS 173 1_555 C SG CYS 155 C CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf17 C SG CYS 266 C CYS 291 1_555 C SG CYS 341 C CYS 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf18 C SG CYS 284 C CYS 309 1_555 C SG CYS 337 C CYS 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf19 C SG CYS 288 C CYS 313 1_555 C SG CYS 335 C CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf20 C SG CYS 297 C CYS 322 1_555 C SG CYS 319 C CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf21 C SG CYS 299 C CYS 324 1_555 C SG CYS 311 C CYS 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 342 A ASN 367 1_555 D C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? covale ? covale2 B ND2 ASN 342 B ASN 367 1_555 G C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 C ND2 ASN 342 C ASN 367 1_555 I C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? metalc ? metalc1 A OD1 ASP 408 A ASP 433 1_555 F NA NA . A NA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc2 F NA NA . A NA 503 1_555 B OD1 ASP 408 B ASP 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc3 F NA NA . A NA 503 1_555 C OD1 ASP 408 C ASP 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.958 ? # _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 6X9H _atom_sites.fract_transf_matrix[1][1] 0.010895 _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] 0.00861 _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] 0.00439 _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 D 2 NAG A 1 501 501 NAG NAG . E 3 UZG A 1 502 1 UZG LIG . F 4 NA A 1 503 1 NA NA . G 2 NAG B 1 501 501 NAG NAG . H 3 UZG B 1 502 1 UZG LIG . I 2 NAG C 1 501 501 NAG NAG . J 3 UZG C 1 502 1 UZG LIG . # _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 -23.652 _atom_site.Cartn_y -15.505 _atom_site.Cartn_z 54.785 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 79.63 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 503 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 1 #