data_3THY # _model_server_result.job_id 1RTbats4dkN0yTt87pKtcw _model_server_result.datetime_utc '2024-11-26 03:28:57' _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 3thy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":935}' # _entry.id 3THY # _exptl.entry_id 3THY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 67.82 _cell.angle_beta 86.98 _cell.angle_gamma 73.35 _cell.entry_id 3THY _cell.length_a 66.27 _cell.length_b 91.106 _cell.length_c 95.628 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3THY _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 PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 hydrog TYPE_28_PAIR hydrog1 C N3 DT 3 D DT 3 1_555 D O6 DG 24 E DG 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog2 C O2 DT 3 D DT 3 1_555 D N1 DG 24 E DG 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog3 C O2 DC 4 D DC 4 1_555 D N2 DG 23 E DG 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog4 C O2 DC 4 D DC 4 1_555 D N2 DG 24 E DG 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog5 C N3 DT 5 D DT 5 1_555 D N1 DA 22 E DA 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C N1 DA 6 D DA 6 1_555 D N3 DT 21 E DT 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N6 DA 6 D DA 6 1_555 D O4 DT 21 E DT 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C N3 DT 7 D DT 7 1_555 D N1 DA 20 E DA 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C O4 DT 7 D DT 7 1_555 D N6 DA 20 E DA 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N3 DC 8 D DC 8 1_555 D N1 DG 19 E DG 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N4 DC 8 D DC 8 1_555 D O6 DG 19 E DG 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C O2 DC 8 D DC 8 1_555 D N2 DG 19 E DG 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DC MISPAIR' hydrog13 C O4 DT 9 D DT 9 1_555 D N4 DC 17 E DC 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog14 C N3 DT 9 D DT 9 1_555 D N1 DA 18 E DA 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C N1 DG 10 D DG 10 1_555 D N3 DC 17 E DC 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N2 DG 10 D DG 10 1_555 D O2 DC 17 E DC 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C O6 DG 10 D DG 10 1_555 D N4 DC 17 E DC 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C N1 DA 11 D DA 11 1_555 D N3 DT 16 E DT 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C N6 DA 11 D DA 11 1_555 D O4 DT 16 E DT 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C N1 DA 12 D DA 12 1_555 D N3 DT 15 E DT 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C N6 DA 12 D DA 12 1_555 D O4 DT 15 E DT 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog22 C N1 DG 13 D DG 13 1_555 D N3 DC 14 E DC 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C N3 DC 14 D DC 14 1_555 D N1 DG 13 E DG 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C N4 DC 14 D DC 14 1_555 D O6 DG 13 E DG 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C O2 DC 14 D DC 14 1_555 D N2 DG 13 E DG 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C N3 DC 15 D DC 15 1_555 D N1 DG 10 E DG 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C N4 DC 15 D DC 15 1_555 D O6 DG 10 E DG 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 C O2 DC 15 D DC 15 1_555 D N2 DG 10 E DG 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 C N1 DG 16 D DG 16 1_555 D N3 DC 9 E DC 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 C N2 DG 16 D DG 16 1_555 D O2 DC 9 E DC 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 C O6 DG 16 D DG 16 1_555 D N4 DC 9 E DC 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 C N1 DA 17 D DA 17 1_555 D N3 DT 8 E DT 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C N6 DA 17 D DA 17 1_555 D O4 DT 8 E DT 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C N3 DT 18 D DT 18 1_555 D N1 DA 7 E DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 C O4 DT 18 D DT 18 1_555 D N6 DA 7 E DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 C N3 DC 19 D DC 19 1_555 D N1 DG 6 E DG 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C N4 DC 19 D DC 19 1_555 D O6 DG 6 E DG 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 C O2 DC 19 D DC 19 1_555 D N2 DG 6 E DG 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 C N1 DG 20 D DG 20 1_555 D N3 DC 5 E DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 C N2 DG 20 D DG 20 1_555 D O2 DC 5 E DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 C O6 DG 20 D DG 20 1_555 D N4 DC 5 E DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 C N1 DA 21 D DA 21 1_555 D N3 DT 4 E DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 C N6 DA 21 D DA 21 1_555 D O4 DT 4 E DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DC MISPAIR' hydrog44 C O4 DT 22 D DT 22 1_555 D N4 DC 2 E DC 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 C N3 DT 22 D DT 22 1_555 D N1 DA 3 E DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 C O4 DT 22 D DT 22 1_555 D N6 DA 3 E DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog47 C N1 DG 23 D DG 23 1_555 D N3 DC 2 E DC 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 3THY _atom_sites.fract_transf_matrix[1][1] 0.01509 _atom_sites.fract_transf_matrix[1][2] -0.004513 _atom_sites.fract_transf_matrix[1][3] 0.000987 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011457 _atom_sites.fract_transf_matrix[2][3] -0.004689 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011315 _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 ADP A 1 935 1 ADP ADP . F 6 HOH A 1 936 9 HOH HOH . F 6 HOH A 2 937 10 HOH HOH . F 6 HOH A 3 938 11 HOH HOH . F 6 HOH A 4 939 13 HOH HOH . F 6 HOH A 5 940 14 HOH HOH . F 6 HOH A 6 941 15 HOH HOH . F 6 HOH A 7 942 16 HOH HOH . G 6 HOH B 1 1 1 HOH HOH . G 6 HOH B 2 2 2 HOH HOH . G 6 HOH B 3 3 3 HOH HOH . G 6 HOH B 4 4 4 HOH HOH . G 6 HOH B 5 5 5 HOH HOH . G 6 HOH B 6 6 6 HOH HOH . G 6 HOH B 7 7 7 HOH HOH . G 6 HOH B 8 12 12 HOH HOH . # 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 PB ADP . . . E 5 0.945 3.094 -22.714 1 75.98 ? PB ADP 935 A 1 HETATM 2 O O1B ADP . . . E 5 1.502 1.74 -22.347 1 75.54 ? O1B ADP 935 A 1 HETATM 3 O O2B ADP . . . E 5 1.142 3.455 -24.167 1 74.62 ? O2B ADP 935 A 1 HETATM 4 O O3B ADP . . . E 5 1.3 4.204 -21.748 1 76.62 ? O3B ADP 935 A 1 HETATM 5 P PA ADP . . . E 5 -1.303 2.236 -21.25 1 79.31 ? PA ADP 935 A 1 HETATM 6 O O1A ADP . . . E 5 -1.46 0.752 -21.486 1 79.04 ? O1A ADP 935 A 1 HETATM 7 O O2A ADP . . . E 5 -0.565 2.725 -20.023 1 79.96 ? O2A ADP 935 A 1 HETATM 8 O O3A ADP . . . E 5 -0.65 2.922 -22.554 1 77.67 ? O3A ADP 935 A 1 HETATM 9 O O5' ADP . . . E 5 -2.775 2.878 -21.235 1 83.29 ? O5' ADP 935 A 1 HETATM 10 C C5' ADP . . . E 5 -3.669 2.491 -20.2 1 88.61 ? C5' ADP 935 A 1 HETATM 11 C C4' ADP . . . E 5 -4.964 3.29 -20.257 1 92.24 ? C4' ADP 935 A 1 HETATM 12 O O4' ADP . . . E 5 -5.54 3.216 -21.562 1 92.06 ? O4' ADP 935 A 1 HETATM 13 C C3' ADP . . . E 5 -5.955 2.706 -19.265 1 94.88 ? C3' ADP 935 A 1 HETATM 14 O O3' ADP . . . E 5 -6.288 3.678 -18.275 1 97.48 ? O3' ADP 935 A 1 HETATM 15 C C2' ADP . . . E 5 -7.174 2.31 -20.071 1 96.15 ? C2' ADP 935 A 1 HETATM 16 O O2' ADP . . . E 5 -8.325 3.029 -19.617 1 98.42 ? O2' ADP 935 A 1 HETATM 17 C C1' ADP . . . E 5 -6.846 2.648 -21.519 1 95.09 ? C1' ADP 935 A 1 HETATM 18 N N9 ADP . . . E 5 -6.78 1.399 -22.313 1 95.38 ? N9 ADP 935 A 1 HETATM 19 C C8 ADP . . . E 5 -5.671 0.651 -22.47 1 95.65 ? C8 ADP 935 A 1 HETATM 20 N N7 ADP . . . E 5 -5.914 -0.432 -23.249 1 95.91 ? N7 ADP 935 A 1 HETATM 21 C C5 ADP . . . E 5 -7.212 -0.385 -23.605 1 96.06 ? C5 ADP 935 A 1 HETATM 22 C C6 ADP . . . E 5 -8.122 -1.22 -24.424 1 96.32 ? C6 ADP 935 A 1 HETATM 23 N N6 ADP . . . E 5 -7.684 -2.349 -25.028 1 95.67 ? N6 ADP 935 A 1 HETATM 24 N N1 ADP . . . E 5 -9.406 -0.815 -24.546 1 96.92 ? N1 ADP 935 A 1 HETATM 25 C C2 ADP . . . E 5 -9.853 0.306 -23.947 1 97.25 ? C2 ADP 935 A 1 HETATM 26 N N3 ADP . . . E 5 -9.086 1.112 -23.19 1 96.95 ? N3 ADP 935 A 1 HETATM 27 C C4 ADP . . . E 5 -7.778 0.825 -22.986 1 96.49 ? C4 ADP 935 A 1 # _model_server_stats.io_time_ms 129 _model_server_stats.parse_time_ms 74 _model_server_stats.create_model_time_ms 134 _model_server_stats.query_time_ms 403 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #