data_3THX # _model_server_result.job_id JNNZtKX9usvZMig68gmlcQ _model_server_result.datetime_utc '2025-02-18 09:26:18' _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 3thx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":935}' # _entry.id 3THX # _exptl.entry_id 3THX _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 67.88 _cell.angle_beta 86.51 _cell.angle_gamma 72.86 _cell.entry_id 3THX _cell.length_a 67.12 _cell.length_b 91.54 _cell.length_c 95.58 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3THX _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,H _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 'DT-DG MISPAIR' hydrog1 C O2 DT 3 D DT 3 1_555 D N2 DG 25 E DG 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog2 C O2 DC 4 D DC 4 1_555 D N2 DG 24 E DG 49 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog3 C N3 DT 5 D DT 5 1_555 D N1 DA 23 E DA 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N1 DA 6 D DA 6 1_555 D N3 DT 22 E DT 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N6 DA 6 D DA 6 1_555 D O4 DT 22 E DT 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C N3 DT 7 D DT 7 1_555 D N1 DA 21 E DA 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C O4 DT 7 D DT 7 1_555 D N6 DA 21 E DA 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog8 C O2 DC 8 D DC 8 1_555 D N2 DG 20 E DG 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N3 DT 9 D DT 9 1_555 D N1 DA 19 E DA 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C O4 DT 9 D DT 9 1_555 D N6 DA 19 E DA 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N1 DG 10 D DG 10 1_555 D N3 DC 18 E DC 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C N2 DG 10 D DG 10 1_555 D O2 DC 18 E DC 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C O6 DG 10 D DG 10 1_555 D N4 DC 18 E DC 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N1 DA 11 D DA 11 1_555 D N3 DT 17 E DT 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C N6 DA 11 D DA 11 1_555 D O4 DT 17 E DT 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N1 DA 12 D DA 12 1_555 D N3 DT 16 E DT 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C N6 DA 12 D DA 12 1_555 D O4 DT 16 E DT 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog18 C N1 DG 13 D DG 13 1_555 D N3 DC 15 E DC 40 1_555 ? ? ? ? A ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C N3 DC 15 D DC 15 1_555 D N1 DG 10 E DG 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C N4 DC 15 D DC 15 1_555 D O6 DG 10 E DG 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C O2 DC 15 D DC 15 1_555 D N2 DG 10 E DG 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C N1 DG 16 D DG 16 1_555 D N3 DC 9 E DC 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C N2 DG 16 D DG 16 1_555 D O2 DC 9 E DC 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C O6 DG 16 D DG 16 1_555 D N4 DC 9 E DC 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C N1 DA 17 D DA 17 1_555 D N3 DT 8 E DT 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C N6 DA 17 D DA 17 1_555 D O4 DT 8 E DT 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C N3 DT 18 D DT 18 1_555 D N1 DA 7 E DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 C O4 DT 18 D DT 18 1_555 D N6 DA 7 E DA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog29 C O2 DC 19 D DC 19 1_555 D N2 DG 6 E DG 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 C N1 DG 20 D DG 20 1_555 D N3 DC 5 E DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 C N2 DG 20 D DG 20 1_555 D O2 DC 5 E DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 C O6 DG 20 D DG 20 1_555 D N4 DC 5 E DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C N1 DA 21 D DA 21 1_555 D N3 DT 4 E DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C N6 DA 21 D DA 21 1_555 D O4 DT 4 E DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DC MISPAIR' hydrog35 C O4 DT 22 D DT 22 1_555 D N4 DC 2 E DC 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 C N3 DT 22 D DT 22 1_555 D N1 DA 3 E DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C O4 DT 22 D DT 22 1_555 D N6 DA 3 E DA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 C N1 DG 23 D DG 23 1_555 D N3 DC 2 E DC 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 C N2 DG 23 D DG 23 1_555 D O2 DC 2 E DC 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 C O6 DG 23 D DG 23 1_555 D N4 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 3THX _atom_sites.fract_transf_matrix[1][1] 0.014899 _atom_sites.fract_transf_matrix[1][2] -0.004595 _atom_sites.fract_transf_matrix[1][3] 0.000884 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011432 _atom_sites.fract_transf_matrix[2][3] -0.004638 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011312 _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 NA B 1 1 1 NA NA . G 7 HOH A 1 936 14 HOH HOH . G 7 HOH A 2 937 15 HOH HOH . G 7 HOH A 3 938 19 HOH HOH . G 7 HOH A 4 939 20 HOH HOH . G 7 HOH A 5 940 23 HOH HOH . G 7 HOH A 6 941 24 HOH HOH . G 7 HOH A 7 942 25 HOH HOH . G 7 HOH A 8 943 27 HOH HOH . H 7 HOH B 1 2 2 HOH HOH . H 7 HOH B 2 3 3 HOH HOH . H 7 HOH B 3 4 4 HOH HOH . H 7 HOH B 4 5 5 HOH HOH . H 7 HOH B 5 6 6 HOH HOH . H 7 HOH B 6 7 7 HOH HOH . H 7 HOH B 7 8 8 HOH HOH . H 7 HOH B 8 9 9 HOH HOH . H 7 HOH B 9 10 10 HOH HOH . H 7 HOH B 10 11 11 HOH HOH . H 7 HOH B 11 12 12 HOH HOH . H 7 HOH B 12 13 13 HOH HOH . H 7 HOH B 13 16 16 HOH HOH . H 7 HOH B 14 17 17 HOH HOH . H 7 HOH B 15 18 18 HOH HOH . H 7 HOH B 16 22 22 HOH HOH . H 7 HOH B 17 26 26 HOH HOH . H 7 HOH B 18 28 28 HOH HOH . H 7 HOH B 19 1126 1 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 0.998 3.151 -22.585 1 69.1 ? PB ADP 935 A 1 HETATM 2 O O1B ADP . . . E 5 1.491 1.809 -22.102 1 68.47 ? O1B ADP 935 A 1 HETATM 3 O O2B ADP . . . E 5 1.237 3.408 -24.055 1 68.71 ? O2B ADP 935 A 1 HETATM 4 O O3B ADP . . . E 5 1.366 4.299 -21.675 1 69.86 ? O3B ADP 935 A 1 HETATM 5 P PA ADP . . . E 5 -1.283 2.422 -21.148 1 70.89 ? PA ADP 935 A 1 HETATM 6 O O1A ADP . . . E 5 -1.536 0.952 -21.387 1 70.42 ? O1A ADP 935 A 1 HETATM 7 O O2A ADP . . . E 5 -0.487 2.86 -19.941 1 71.3 ? O2A ADP 935 A 1 HETATM 8 O O3A ADP . . . E 5 -0.602 3.05 -22.464 1 70.07 ? O3A ADP 935 A 1 HETATM 9 O O5' ADP . . . E 5 -2.702 3.177 -21.074 1 72.33 ? O5' ADP 935 A 1 HETATM 10 C C5' ADP . . . E 5 -3.446 3.116 -19.859 1 73.72 ? C5' ADP 935 A 1 HETATM 11 C C4' ADP . . . E 5 -4.841 3.676 -20.068 1 75.07 ? C4' ADP 935 A 1 HETATM 12 O O4' ADP . . . E 5 -5.262 3.462 -21.415 1 74.36 ? O4' ADP 935 A 1 HETATM 13 C C3' ADP . . . E 5 -5.831 2.979 -19.152 1 76.33 ? C3' ADP 935 A 1 HETATM 14 O O3' ADP . . . E 5 -6.233 3.849 -18.088 1 78.24 ? O3' ADP 935 A 1 HETATM 15 C C2' ADP . . . E 5 -7.005 2.607 -20.038 1 76.46 ? C2' ADP 935 A 1 HETATM 16 O O2' ADP . . . E 5 -8.157 3.378 -19.683 1 78.35 ? O2' ADP 935 A 1 HETATM 17 C C1' ADP . . . E 5 -6.587 2.93 -21.465 1 75.18 ? C1' ADP 935 A 1 HETATM 18 N N9 ADP . . . E 5 -6.578 1.685 -22.278 1 74.02 ? N9 ADP 935 A 1 HETATM 19 C C8 ADP . . . E 5 -5.493 0.926 -22.525 1 72.67 ? C8 ADP 935 A 1 HETATM 20 N N7 ADP . . . E 5 -5.804 -0.147 -23.298 1 73.73 ? N7 ADP 935 A 1 HETATM 21 C C5 ADP . . . E 5 -7.122 -0.083 -23.56 1 74.48 ? C5 ADP 935 A 1 HETATM 22 C C6 ADP . . . E 5 -8.097 -0.9 -24.32 1 76.71 ? C6 ADP 935 A 1 HETATM 23 N N6 ADP . . . E 5 -7.715 -2.027 -24.968 1 78.77 ? N6 ADP 935 A 1 HETATM 24 N N1 ADP . . . E 5 -9.382 -0.48 -24.342 1 76.87 ? N1 ADP 935 A 1 HETATM 25 C C2 ADP . . . E 5 -9.774 0.638 -23.702 1 75.64 ? C2 ADP 935 A 1 HETATM 26 N N3 ADP . . . E 5 -8.944 1.426 -22.995 1 75.6 ? N3 ADP 935 A 1 HETATM 27 C C4 ADP . . . E 5 -7.628 1.126 -22.888 1 74.34 ? C4 ADP 935 A 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #