data_5V06 # _model_server_result.job_id 8u_HlO7qneRs6nKIiXbjrw _model_server_result.datetime_utc '2024-12-08 18:20:26' _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 5v06 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":402}' # _entry.id 5V06 # _exptl.entry_id 5V06 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 5 _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 5V06 _cell.length_a 74.281 _cell.length_b 74.281 _cell.length_c 179.889 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V06 _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 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 5 _struct_asym.id E _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 metalc ? metalc1 A OD2 ASP 152 Z ASP 152 1_555 D MN MN . Z MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? metalc ? metalc2 A OD1 ASP 152 Z ASP 152 1_555 F MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc3 A OD2 ASP 171 Z ASP 171 1_555 D MN MN . Z MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc4 A OD2 ASP 173 Z ASP 173 1_555 D MN MN . Z MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc5 A O SER 222 Z SER 222 1_555 E NA NA . Z NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc6 A OG SER 229 Z SER 229 1_555 E NA NA . Z NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc7 A O ILE 233 Z ILE 233 1_555 E NA NA . Z NA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc8 D MN MN . Z MN 401 1_555 H O HOH . Z HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc9 D MN MN . Z MN 401 1_555 C OP1 DC 2 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc10 E NA NA . Z NA 402 1_555 H O HOH . Z HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc11 E NA NA . Z NA 402 1_555 B OP2 DT 4 A DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc12 H O HOH . Z HOH 501 1_555 F MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc13 H O HOH . Z HOH 504 1_555 F MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc14 H O HOH . Z HOH 508 1_555 F MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc15 C O3' DT 1 B DT 1 1_555 F MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc16 C OP1 DT 1 B DT 1 1_555 G MN MN . B MN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc17 C OP1 DC 2 B DC 2 1_555 F MN MN . B MN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? hydrog WATSON-CRICK hydrog1 B N3 DC 1 A DC 1 1_555 C N1 DG 10 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 1 A DC 1 1_555 C O6 DG 10 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 1 A DC 1 1_555 C N2 DG 10 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 2 A DG 2 1_555 C N3 DC 9 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 2 A DG 2 1_555 C O2 DC 9 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 2 A DG 2 1_555 C N4 DC 9 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DC 3 A DC 3 1_555 C N1 DG 8 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N4 DC 3 A DC 3 1_555 C O6 DG 8 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O2 DC 3 A DC 3 1_555 C N2 DG 8 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N3 DT 4 A DT 4 1_555 C N1 DA 7 B DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O4 DT 4 A DT 4 1_555 C N6 DA 7 B DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N1 DA 5 A DA 5 1_555 C N3 DT 6 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N6 DA 5 A DA 5 1_555 C O4 DT 6 B DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N1 DG 6 A DG 6 1_555 C N3 DC 5 B DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N2 DG 6 A DG 6 1_555 C O2 DC 5 B DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O6 DG 6 A DG 6 1_555 C N4 DC 5 B DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DT 7 A DT 7 1_555 C N1 DA 4 B DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O4 DT 7 A DT 7 1_555 C N6 DA 4 B DA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N3 DC 8 A DC 8 1_555 C N1 DG 3 B DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N4 DC 8 A DC 8 1_555 C O6 DG 3 B DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B O2 DC 8 A DC 8 1_555 C N2 DG 3 B DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 DG 9 A DG 9 1_555 C N3 DC 2 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N2 DG 9 A DG 9 1_555 C O2 DC 2 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O6 DG 9 A DG 9 1_555 C N4 DC 2 B DC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N1 DA 10 A DA 10 1_555 C N3 DT 1 B DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N6 DA 10 A DA 10 1_555 C O4 DT 1 B DT 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 5V06 _atom_sites.fract_transf_matrix[1][1] 0.013462 _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] 0.013462 _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] 0.005559 _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 4 MN Z 1 401 2 MN MN . E 5 NA Z 1 402 1 NA NA . F 4 MN B 1 101 1 MN MN . G 4 MN B 1 102 3 MN MN . H 6 HOH Z 1 501 4 HOH HOH . H 6 HOH Z 2 502 3 HOH HOH . H 6 HOH Z 3 503 15 HOH HOH . H 6 HOH Z 4 504 2 HOH HOH . H 6 HOH Z 5 505 5 HOH HOH . H 6 HOH Z 6 506 8 HOH HOH . H 6 HOH Z 7 507 6 HOH HOH . H 6 HOH Z 8 508 1 HOH HOH . H 6 HOH Z 9 509 13 HOH HOH . H 6 HOH Z 10 510 10 HOH HOH . H 6 HOH Z 11 511 12 HOH HOH . H 6 HOH Z 12 512 16 HOH HOH . H 6 HOH Z 13 513 9 HOH HOH . H 6 HOH Z 14 514 19 HOH HOH . H 6 HOH Z 15 515 21 HOH HOH . H 6 HOH Z 16 516 20 HOH HOH . I 6 HOH A 1 101 14 HOH HOH . I 6 HOH A 2 102 7 HOH HOH . I 6 HOH A 3 103 17 HOH HOH . I 6 HOH A 4 104 18 HOH HOH . J 6 HOH B 1 201 11 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 E _atom_site.label_entity_id 5 _atom_site.Cartn_x 19.237 _atom_site.Cartn_y 11.853 _atom_site.Cartn_z -12.862 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 76.21 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 402 _atom_site.auth_asym_id Z _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 428 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #