data_8BW5 # _model_server_result.job_id M4Gxx9oG-DwUy3AmEFITgA _model_server_result.datetime_utc '2024-12-26 18:48:35' _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 8bw5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":101}' # _entry.id 8BW5 # _exptl.entry_id 8BW5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 6 _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 8BW5 _cell.length_a 68.06 _cell.length_b 75.49 _cell.length_c 114.31 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8BW5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 2 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 _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 ? 6 F N N ? 6 G N N # _pdbx_entity_branch.entity_id 4 _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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 4 5 4 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 4 6 5 GAL NAG C1 O1 . O4 HO4 . sing 6 ? 4 7 6 SIA GAL C2 O2 . O6 HO6 . sing 7 ? 4 8 3 MAN BMA C1 O1 . O3 HO3 . 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 A 1 NAG A 1 NAG 4 n D NAG 2 A 2 NAG A 2 NAG 4 n D BMA 3 A 3 BMA A 3 BMA 4 n D MAN 4 A 4 MAN A 4 MAN 4 n D NAG 5 A 5 NAG A 5 NAG 4 n D GAL 6 A 6 GAL A 6 GAL 4 n D SIA 7 A 7 SIA A 7 SIA 4 n D MAN 8 A 8 MAN A 8 MAN # 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 9 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? covale ? covale1 B NE2 HIS 43 H HIS 57 1_555 E C3 0G6 . H 0G6 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale2 B ND2 ASN 53 H ASN 60 1_555 D C1 NAG . A NAG 1 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale3 B OG SER 205 H SER 195 1_555 E C2 0G6 . H 0G6 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale4 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 D O4 NAG . A NAG 2 1_555 D C1 BMA . A BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 D O6 BMA . A BMA 3 1_555 D C1 MAN . A MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 D O3 BMA . A BMA 3 1_555 D C1 MAN . A MAN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale8 D O2 MAN . A MAN 4 1_555 D C1 NAG . A NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale9 D O4 NAG . A NAG 5 1_555 D C1 GAL . A GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale10 D O6 GAL . A GAL 6 1_555 D C2 SIA . A SIA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? metalc ? metalc1 B O ARG 233 H ARG 221 1_555 F NA NA . H NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc2 B O LYS 236 H LYS 224 1_555 F NA NA . H NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? metalc ? metalc3 F NA NA . H NA 302 1_555 H O HOH . H HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc4 C O6 DG 14 F DG 14 1_555 G NA NA . F NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc5 C O6 DG 15 F DG 15 1_555 G NA NA . F NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? metalc ? metalc6 C O6 DG 18 F DG 18 1_555 G NA NA . F NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc7 C O6 DG 19 F DG 19 1_555 G NA NA . F NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc8 C O6 DG 22 F DG 22 1_555 G NA NA . F NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc9 C O6 DG 23 F DG 23 1_555 G NA NA . F NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc10 C O6 DG 26 F DG 26 1_555 G NA NA . F NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc11 C O6 DG 27 F DG 27 1_555 G NA NA . F NA 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? hydrog 'DG-DC PAIR' hydrog1 C O6 DG 1 F DG 1 1_555 C N4 DC 40 F DC 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog2 C N2 DG 2 F DG 2 1_555 C O2 DC 40 F DC 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C N3 DT 3 F DT 3 1_555 C N1 DA 39 F DA 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C O4 DT 3 F DT 3 1_555 C N6 DA 39 F DA 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog5 C O2 DC 4 F DC 4 1_555 C N1 DG 38 F DG 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog6 C N1 DA 5 F DA 5 1_555 C N3 DT 37 F DT 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog7 C N1 DG 6 F DG 6 1_555 C N1 DA 36 F DA 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog8 C O6 DG 6 F DG 6 1_555 C N6 DA 36 F DA 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DG MISPAIR' hydrog9 C N1 DA 7 F DA 7 1_555 C N1 DG 35 F DG 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog10 C N6 DA 10 F DA 10 1_555 C O4 DT 33 F DT 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N3 DT 11 F DT 11 1_555 C N1 DA 32 F DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C O4 DT 11 F DT 11 1_555 C N6 DA 32 F DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog13 C N2 DG 12 F DG 12 1_555 C N7 DA 31 F DA 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_11_PAIR hydrog14 C N3 DG 12 F DG 12 1_555 C N6 DA 31 F DA 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog15 C N1 DG 14 F DG 14 1_555 C O6 DG 19 F DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog16 C N2 DG 14 F DG 14 1_555 C N7 DG 19 F DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog17 C N7 DG 14 F DG 14 1_555 C N2 DG 27 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog18 C O6 DG 14 F DG 14 1_555 C N1 DG 27 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog19 C N7 DG 15 F DG 15 1_555 C N2 DG 18 F DG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog20 C O6 DG 15 F DG 15 1_555 C N1 DG 18 F DG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog21 C N1 DG 15 F DG 15 1_555 C O6 DG 26 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog22 C N2 DG 15 F DG 15 1_555 C N7 DG 26 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog23 C N7 DG 18 F DG 18 1_555 C N2 DG 23 F DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog24 C O6 DG 18 F DG 18 1_555 C N1 DG 23 F DG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog25 C N1 DG 19 F DG 19 1_555 C O6 DG 22 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog26 C N2 DG 19 F DG 19 1_555 C N7 DG 22 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DG MISPAIR' hydrog27 C N2 DG 20 F DG 20 1_555 C O6 DG 22 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DA MISPAIR' hydrog28 C N1 DG 20 F DG 20 1_555 C N1 DA 28 F DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog29 C N1 DG 22 F DG 22 1_555 C O6 DG 27 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog30 C N2 DG 22 F DG 22 1_555 C N7 DG 27 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog31 C N7 DG 23 F DG 23 1_555 C N2 DG 26 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog32 C O6 DG 23 F DG 23 1_555 C N1 DG 26 F DG 26 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 8BW5 _atom_sites.fract_transf_matrix[1][1] 0.014693 _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] 0.013247 _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] 0.008748 _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 E 5 0G6 H 1 301 301 0G6 0G6 . F 6 NA H 1 302 302 NA NA . G 6 NA F 1 101 101 NA NA . H 7 HOH H 1 401 412 HOH HOH . H 7 HOH H 2 402 417 HOH HOH . H 7 HOH H 3 403 414 HOH HOH . H 7 HOH H 4 404 410 HOH HOH . H 7 HOH H 5 405 411 HOH HOH . H 7 HOH H 6 406 404 HOH HOH . H 7 HOH H 7 407 407 HOH HOH . H 7 HOH H 8 408 419 HOH HOH . H 7 HOH H 9 409 409 HOH HOH . H 7 HOH H 10 410 408 HOH HOH . H 7 HOH H 11 411 406 HOH HOH . H 7 HOH H 12 412 401 HOH HOH . H 7 HOH H 13 413 405 HOH HOH . H 7 HOH H 14 414 416 HOH HOH . H 7 HOH H 15 415 420 HOH HOH . H 7 HOH H 16 416 413 HOH HOH . H 7 HOH H 17 417 402 HOH HOH . H 7 HOH H 18 418 415 HOH HOH . H 7 HOH H 19 419 418 HOH HOH . H 7 HOH H 20 420 403 HOH HOH . I 7 HOH F 1 201 201 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 G _atom_site.label_entity_id 6 _atom_site.Cartn_x 12.244 _atom_site.Cartn_y -3.338 _atom_site.Cartn_z -33.379 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 71.24 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 101 _atom_site.auth_asym_id F _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 366 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 1 #