data_8RDY # _model_server_result.job_id Dhfy3I8fbU9uoFqwbYiquw _model_server_result.datetime_utc '2024-10-24 06:16:07' _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 8rdy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1201}' # _entry.id 8RDY # _exptl.entry_id 8RDY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 8RDY _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RDY _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? _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 3 _struct_asym.id C _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 metalc ? metalc1 A OG1 THR 160 A THR 123 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc2 C O1B ADP . A ADP 1201 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? # _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 8RDY _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 C 3 ADP A 1 1201 1201 ADP ADP . D 4 MG A 1 1202 1202 MG MG . # 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 . . . C 3 107.689 110.155 130.794 1 54.56 ? PB ADP 1201 A 1 HETATM 2 O O1B ADP . . . C 3 108.665 109.628 129.773 1 56.2 ? O1B ADP 1201 A 1 HETATM 3 O O2B ADP . . . C 3 106.468 109.296 131.005 1 48.2 ? O2B ADP 1201 A 1 HETATM 4 O O3B ADP . . . C 3 107.408 111.629 130.676 1 69.42 ? O3B ADP 1201 A 1 HETATM 5 P PA ADP . . . C 3 110.049 110.392 132.19 1 57.59 ? PA ADP 1201 A 1 HETATM 6 O O1A ADP . . . C 3 110.34 111.254 130.991 1 49.05 ? O1A ADP 1201 A 1 HETATM 7 O O2A ADP . . . C 3 110.839 109.131 132.42 1 60.32 ? O2A ADP 1201 A 1 HETATM 8 O O3A ADP . . . C 3 108.484 110.047 132.182 1 54.2 ? O3A ADP 1201 A 1 HETATM 9 O O5' ADP . . . C 3 110.225 111.303 133.494 1 60.25 ? O5' ADP 1201 A 1 HETATM 10 C C5' ADP . . . C 3 111.526 111.82 133.712 1 64.02 ? C5' ADP 1201 A 1 HETATM 11 C C4' ADP . . . C 3 111.589 112.757 134.908 1 65.56 ? C4' ADP 1201 A 1 HETATM 12 O O4' ADP . . . C 3 112.929 112.752 135.396 1 67.98 ? O4' ADP 1201 A 1 HETATM 13 C C3' ADP . . . C 3 111.23 114.182 134.532 1 64.75 ? C3' ADP 1201 A 1 HETATM 14 O O3' ADP . . . C 3 110.261 114.705 135.442 1 63.45 ? O3' ADP 1201 A 1 HETATM 15 C C2' ADP . . . C 3 112.524 114.964 134.612 1 67.08 ? C2' ADP 1201 A 1 HETATM 16 O O2' ADP . . . C 3 112.358 116.119 135.438 1 68.86 ? O2' ADP 1201 A 1 HETATM 17 C C1' ADP . . . C 3 113.555 114.021 135.211 1 63.99 ? C1' ADP 1201 A 1 HETATM 18 N N9 ADP . . . C 3 114.723 113.854 134.308 1 60.32 ? N9 ADP 1201 A 1 HETATM 19 C C8 ADP . . . C 3 114.756 113.104 133.189 1 58.69 ? C8 ADP 1201 A 1 HETATM 20 N N7 ADP . . . C 3 115.975 113.163 132.6 1 58.48 ? N7 ADP 1201 A 1 HETATM 21 C C5 ADP . . . C 3 116.747 113.962 133.35 1 63.34 ? C5 ADP 1201 A 1 HETATM 22 C C6 ADP . . . C 3 118.14 114.448 133.295 1 67.25 ? C6 ADP 1201 A 1 HETATM 23 N N6 ADP . . . C 3 118.967 114.077 132.29 1 63.77 ? N6 ADP 1201 A 1 HETATM 24 N N1 ADP . . . C 3 118.556 115.274 134.279 1 69.12 ? N1 ADP 1201 A 1 HETATM 25 C C2 ADP . . . C 3 117.745 115.654 135.284 1 66.29 ? C2 ADP 1201 A 1 HETATM 26 N N3 ADP . . . C 3 116.469 115.245 135.39 1 63.87 ? N3 ADP 1201 A 1 HETATM 27 C C4 ADP . . . C 3 115.92 114.416 134.474 1 62.27 ? C4 ADP 1201 A 1 HETATM 28 H "H5'1" ADP . . . C 3 111.833 112.359 132.814 1 62.11 ? "H5'1" ADP 1201 A 1 HETATM 29 H "H5'2" ADP . . . C 3 112.225 110.995 133.861 1 60.44 ? "H5'2" ADP 1201 A 1 HETATM 30 H H4' ADP . . . C 3 110.897 112.401 135.684 1 62.62 ? H4' ADP 1201 A 1 HETATM 31 H H3' ADP . . . C 3 110.846 114.209 133.502 1 63.99 ? H3' ADP 1201 A 1 HETATM 32 H HO3' ADP . . . C 3 109.935 115.555 135.116 1 64.29 ? HO3' ADP 1201 A 1 HETATM 33 H H2' ADP . . . C 3 112.839 115.254 133.6 1 65.89 ? H2' ADP 1201 A 1 HETATM 34 H HO2' ADP . . . C 3 111.793 116.761 134.987 1 68.41 ? HO2' ADP 1201 A 1 HETATM 35 H H1' ADP . . . C 3 113.883 114.422 136.18 1 64.21 ? H1' ADP 1201 A 1 HETATM 36 H H8 ADP . . . C 3 113.928 112.528 132.804 1 60.07 ? H8 ADP 1201 A 1 HETATM 37 H HN61 ADP . . . C 3 118.634 113.459 131.564 1 61.88 ? HN61 ADP 1201 A 1 HETATM 38 H HN62 ADP . . . C 3 119.917 114.419 132.266 1 65.44 ? HN62 ADP 1201 A 1 HETATM 39 H H2 ADP . . . C 3 118.14 116.318 136.043 1 66.06 ? H2 ADP 1201 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 39 #