data_3IYD # _model_server_result.job_id he3W-7A-in-op10Us-DqEQ _model_server_result.datetime_utc '2024-11-05 00:22:57' _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 3iyd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":680}' # _entry.id 3IYD # _exptl.entry_id 3IYD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 329.206 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE" _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 3IYD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IYD _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 decameric _pdbx_struct_assembly.oligomeric_count 10 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _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 ? 9 K N N ? 9 L N 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 hydrog 'DC-DG PAIR' hydrog1 I N3 DC 3 I DC 3 1_555 J N1 DG 96 J DG 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DA MISPAIR' hydrog2 I N1 DA 9 I DA 9 1_555 J N6 DA 89 J DA 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 I N3 DT 10 I DT 10 1_555 J N1 DA 89 J DA 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 I O4 DT 10 I DT 10 1_555 J N6 DA 89 J DA 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 I N3 DT 26 I DT 26 1_555 J N1 DA 73 J DA 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 I O4 DT 26 I DT 26 1_555 J N6 DA 73 J DA 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 I N3 DT 28 I DT 28 1_555 J N1 DA 71 J DA 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 I O4 DT 28 I DT 28 1_555 J N6 DA 71 J DA 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog9 I O6 DG 31 I DG 31 1_555 J N4 DC 68 J DC 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog10 I N2 DG 32 I DG 32 1_555 J O2 DC 67 J DC 67 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog11 I N6 DA 35 I DA 35 1_555 J O4 DT 63 J DT 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog12 I N1 DA 35 I DA 35 1_555 J N3 DT 64 J DT 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog13 I N1 DA 36 I DA 36 1_555 J N3 DT 63 J DT 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 I N1 DA 37 I DA 37 1_555 J N3 DT 62 J DT 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 I N6 DA 37 I DA 37 1_555 J O4 DT 62 J DT 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog16 I N1 DA 38 I DA 38 1_555 J N3 DT 61 J DT 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 I N1 DA 39 I DA 39 1_555 J N3 DT 60 J DT 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 I N6 DA 39 I DA 39 1_555 J O4 DT 60 J DT 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog19 I N2 DG 40 I DG 40 1_555 J N3 DC 59 J DC 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog20 I N2 DG 41 I DG 41 1_555 J N3 DC 58 J DC 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DG MISPAIR' hydrog21 I N1 DA 48 I DA 48 1_555 J N1 DG 50 J DG 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog22 I N3 DT 51 I DT 51 1_555 J N1 DA 47 J DA 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DA MISPAIR' hydrog23 I N6 DA 53 I DA 53 1_555 J N1 DA 45 J DA 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog24 I N6 DA 53 I DA 53 1_555 J O2 DT 46 J DT 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog25 I O2 DT 57 I DT 57 1_555 J N6 DA 42 J DA 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog26 I O2 DC 60 I DC 60 1_555 J N2 DG 39 J DG 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog27 I N2 DG 61 I DG 61 1_555 J O2 DC 38 J DC 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DG MISPAIR' hydrog28 I N1 DG 87 I DG 87 1_555 J O6 DG 11 J DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog29 I N1 DG 89 I DG 89 1_555 J O2 DC 10 J DC 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog30 I N1 DG 90 I DG 90 1_555 J O2 DC 9 J DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 I N3 DT 92 I DT 92 1_555 J N1 DA 7 J DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 I O4 DT 92 I DT 92 1_555 J N6 DA 7 J DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog33 I N6 DA 93 I DA 93 1_555 J O4 DT 6 J DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog34 I N1 DA 94 I DA 94 1_555 J N1 DG 4 J DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog35 I N6 DA 94 I DA 94 1_555 J O6 DG 4 J DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 I N1 DA 97 I DA 97 1_555 J N3 DT 2 J DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 I N6 DA 97 I DA 97 1_555 J O4 DT 2 J DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 I N1 DG 98 I DG 98 1_555 J N3 DC 1 J DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 I N2 DG 98 I DG 98 1_555 J O2 DC 1 J DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 I O6 DG 98 I DG 98 1_555 J N4 DC 1 J DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DA MISPAIR' hydrog41 J O2 DC 88 J DC 88 1_555 J N6 DA 89 J DA 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H12 N5 O6 P' _chem_comp.formula_weight 329.206 _chem_comp.id CMP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'CYCLIC AMP;CAMP' # 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 P O1P CMP doub 70 n n P O2P CMP sing 71 n n P O5' CMP sing 72 n n P O3' CMP sing 73 n n O2P HOP2 CMP sing 74 n n O5' C5' CMP sing 75 n n C5' C4' CMP sing 76 n n C5' "H5'1" CMP sing 77 n n C5' "H5'2" CMP sing 78 n n C4' O4' CMP sing 79 n n C4' C3' CMP sing 80 n n C4' H4' CMP sing 81 n n O4' C1' CMP sing 82 n n C3' O3' CMP sing 83 n n C3' C2' CMP sing 84 n n C3' H3' CMP sing 85 n n C2' O2' CMP sing 86 n n C2' C1' CMP sing 87 n n C2' H2' CMP sing 88 n n O2' HO2' CMP sing 89 n n C1' N9 CMP sing 90 n n C1' H1' CMP sing 91 n n N9 C8 CMP sing 92 n y N9 C4 CMP sing 93 n y C8 N7 CMP doub 94 n y C8 H8 CMP sing 95 n n N7 C5 CMP sing 96 n y C5 C6 CMP sing 97 n y C5 C4 CMP doub 98 n y C6 N6 CMP sing 99 n n C6 N1 CMP doub 100 n y N6 HN61 CMP sing 101 n n N6 HN62 CMP sing 102 n n N1 C2 CMP sing 103 n y C2 N3 CMP doub 104 n y C2 H2 CMP sing 105 n n N3 C4 CMP sing 106 n y # _atom_sites.entry_id 3IYD _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 # 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 K 9 CMP G 1 679 679 CMP CMP . L 9 CMP H 1 680 680 CMP CMP . # 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 P P CMP . . . L 9 57.897 -12.528 -34.291 1 0 ? P CMP 680 H 1 HETATM 2 O O1P CMP . . . L 9 56.624 -11.952 -34.865 1 0 ? O1P CMP 680 H 1 HETATM 3 O O2P CMP . . . L 9 57.912 -12.395 -32.786 1 0 ? O2P CMP 680 H 1 HETATM 4 O O5' CMP . . . L 9 58.048 -14.079 -34.729 1 0 ? O5' CMP 680 H 1 HETATM 5 C C5' CMP . . . L 9 58.586 -14.463 -35.999 1 0 ? C5' CMP 680 H 1 HETATM 6 C C4' CMP . . . L 9 59.873 -13.671 -36.168 1 0 ? C4' CMP 680 H 1 HETATM 7 O O4' CMP . . . L 9 60.623 -13.923 -37.355 1 0 ? O4' CMP 680 H 1 HETATM 8 C C3' CMP . . . L 9 59.532 -12.204 -36.251 1 0 ? C3' CMP 680 H 1 HETATM 9 O O3' CMP . . . L 9 59.175 -11.789 -34.941 1 0 ? O3' CMP 680 H 1 HETATM 10 C C2' CMP . . . L 9 60.791 -11.598 -36.832 1 0 ? C2' CMP 680 H 1 HETATM 11 O O2' CMP . . . L 9 61.679 -11.196 -35.787 1 0 ? O2' CMP 680 H 1 HETATM 12 C C1' CMP . . . L 9 61.398 -12.746 -37.634 1 0 ? C1' CMP 680 H 1 HETATM 13 N N9 CMP . . . L 9 61.344 -12.438 -39.085 1 0 ? N9 CMP 680 H 1 HETATM 14 C C8 CMP . . . L 9 60.336 -12.755 -39.92 1 0 ? C8 CMP 680 H 1 HETATM 15 N N7 CMP . . . L 9 60.594 -12.33 -41.183 1 0 ? N7 CMP 680 H 1 HETATM 16 C C5 CMP . . . L 9 61.796 -11.725 -41.168 1 0 ? C5 CMP 680 H 1 HETATM 17 C C6 CMP . . . L 9 62.666 -11.053 -42.162 1 0 ? C6 CMP 680 H 1 HETATM 18 N N6 CMP . . . L 9 62.291 -10.941 -43.46 1 0 ? N6 CMP 680 H 1 HETATM 19 N N1 CMP . . . L 9 63.846 -10.555 -41.73 1 0 ? N1 CMP 680 H 1 HETATM 20 C C2 CMP . . . L 9 64.23 -10.659 -40.444 1 0 ? C2 CMP 680 H 1 HETATM 21 N N3 CMP . . . L 9 63.491 -11.254 -39.491 1 0 ? N3 CMP 680 H 1 HETATM 22 C C4 CMP . . . L 9 62.286 -11.798 -39.783 1 0 ? C4 CMP 680 H 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #