data_8YH2 # _model_server_result.job_id JAdbV2-_BkAqnu_brK6gqQ _model_server_result.datetime_utc '2024-12-01 02:07:54' _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 8yh2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":801}' # _entry.id 8YH2 # _exptl.entry_id 8YH2 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 267.241 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE _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 8YH2 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YH2 _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 _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 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 108 B CYS 103 1_555 A SG CYS 119 B CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 119 B CYS 114 1_555 A SG CYS 126 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf3 A SG CYS 126 B CYS 121 1_555 A SG CYS 154 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 C SG CYS 108 R CYS 83 1_555 C SG CYS 190 R CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 E SG CYS 22 S CYS 22 1_555 E SG CYS 96 S CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 E SG CYS 159 S CYS 147 1_555 E SG CYS 229 S CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? # _chem_comp.formula 'C10 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id ADN _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O5' C5' ADN sing 1 n n O5' HO5' ADN sing 2 n n C5' C4' ADN sing 3 n n C5' "H5'1" ADN sing 4 n n C5' "H5'2" ADN sing 5 n n C4' O4' ADN sing 6 n n C4' C3' ADN sing 7 n n C4' H4' ADN sing 8 n n O4' C1' ADN sing 9 n n C3' O3' ADN sing 10 n n C3' C2' ADN sing 11 n n C3' H3' ADN sing 12 n n O3' HO3' ADN sing 13 n n C2' O2' ADN sing 14 n n C2' C1' ADN sing 15 n n C2' H2' ADN sing 16 n n O2' HO2' ADN sing 17 n n C1' N9 ADN sing 18 n n C1' H1' ADN sing 19 n n N9 C8 ADN sing 20 n y N9 C4 ADN sing 21 n y C8 N7 ADN doub 22 n y C8 H8 ADN sing 23 n n N7 C5 ADN sing 24 n y C5 C6 ADN sing 25 n y C5 C4 ADN doub 26 n y C6 N6 ADN sing 27 n n C6 N1 ADN doub 28 n y N6 HN61 ADN sing 29 n n N6 HN62 ADN sing 30 n n N1 C2 ADN sing 31 n y C2 N3 ADN doub 32 n y C2 H2 ADN sing 33 n n N3 C4 ADN sing 34 n y # _atom_sites.entry_id 8YH2 _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 # _pdbx_nonpoly_scheme.asym_id F _pdbx_nonpoly_scheme.entity_id 5 _pdbx_nonpoly_scheme.mon_id ADN _pdbx_nonpoly_scheme.pdb_strand_id R _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 801 _pdbx_nonpoly_scheme.auth_seq_num 400 _pdbx_nonpoly_scheme.pdb_mon_id ADN _pdbx_nonpoly_scheme.auth_mon_id ADO _pdbx_nonpoly_scheme.pdb_ins_code . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O5' ADN . . . F 5 118.045 121.382 147.906 1 49.43 ? O5' ADN 801 R 1 HETATM 2 C C5' ADN . . . F 5 119.011 121.015 146.927 1 49.43 ? C5' ADN 801 R 1 HETATM 3 C C4' ADN . . . F 5 120.405 121.416 147.341 1 49.43 ? C4' ADN 801 R 1 HETATM 4 O O4' ADN . . . F 5 120.321 122.39 148.403 1 49.43 ? O4' ADN 801 R 1 HETATM 5 C C3' ADN . . . F 5 121.261 120.295 147.895 1 49.43 ? C3' ADN 801 R 1 HETATM 6 O O3' ADN . . . F 5 121.968 119.671 146.825 1 49.43 ? O3' ADN 801 R 1 HETATM 7 C C2' ADN . . . F 5 122.25 121.046 148.782 1 49.43 ? C2' ADN 801 R 1 HETATM 8 O O2' ADN . . . F 5 123.422 121.473 148.123 1 49.43 ? O2' ADN 801 R 1 HETATM 9 C C1' ADN . . . F 5 121.417 122.233 149.29 1 49.43 ? C1' ADN 801 R 1 HETATM 10 N N9 ADN . . . F 5 120.899 122.077 150.651 1 49.43 ? N9 ADN 801 R 1 HETATM 11 C C8 ADN . . . F 5 119.671 121.882 150.819 1 49.43 ? C8 ADN 801 R 1 HETATM 12 N N7 ADN . . . F 5 119.499 121.796 152.144 1 49.43 ? N7 ADN 801 R 1 HETATM 13 C C5 ADN . . . F 5 120.852 121.974 152.821 1 49.43 ? C5 ADN 801 R 1 HETATM 14 C C6 ADN . . . F 5 121.486 122.016 154.052 1 49.43 ? C6 ADN 801 R 1 HETATM 15 N N6 ADN . . . F 5 120.712 121.838 155.266 1 49.43 ? N6 ADN 801 R 1 HETATM 16 N N1 ADN . . . F 5 122.784 122.215 154.119 1 49.43 ? N1 ADN 801 R 1 HETATM 17 C C2 ADN . . . F 5 123.515 122.379 153.042 1 49.43 ? C2 ADN 801 R 1 HETATM 18 N N3 ADN . . . F 5 123.016 122.358 151.823 1 49.43 ? N3 ADN 801 R 1 HETATM 19 C C4 ADN . . . F 5 121.716 122.165 151.638 1 49.43 ? C4 ADN 801 R 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 19 #