data_8B9K # _model_server_result.job_id tYrnOwWTIrxKmvDFuUU56w _model_server_result.datetime_utc '2024-10-20 20:48:18' _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 8b9k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1201}' # _entry.id 8B9K # _exptl.entry_id 8B9K _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 8B9K _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8B9K _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 covale ? covale1 A CA GLY 412 A GLY 412 1_555 C C4' ADP . A ADP 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.494 ? hydrog 'G-C PAIR' hydrog1 B N2 G 1 B G 1 1_555 B O2 C 47 B C 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_18_PAIR hydrog2 B N3 U 2 B U 2 1_555 B N3 C 46 B C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_18_PAIR hydrog3 B O4 U 2 B U 2 1_555 B N4 C 46 B C 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 G 3 B G 3 1_555 B N3 C 44 B C 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 G 3 B G 3 1_555 B O2 C 44 B C 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 G 3 B G 3 1_555 B N4 C 44 B C 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 U 4 B U 4 1_555 B N1 A 43 B A 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B O4 U 4 B U 4 1_555 B N6 A 43 B A 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N1 A 5 B A 5 1_555 B N3 U 42 B U 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N6 A 5 B A 5 1_555 B O4 U 42 B U 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 A 6 B A 6 1_555 B N3 U 41 B U 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N6 A 6 B A 6 1_555 B O4 U 41 B U 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 A 7 B A 7 1_555 B N3 U 40 B U 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N6 A 7 B A 7 1_555 B O4 U 40 B U 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 A 8 B A 8 1_555 B N3 U 39 B U 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N6 A 8 B A 8 1_555 B O4 U 39 B U 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 A 8 B A 8 1_555 B N3 U 40 B U 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N6 A 8 B A 8 1_555 B O4 U 40 B U 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_27_PAIR hydrog19 B N3 U 9 B U 9 1_555 B O6 G 38 B G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_27_PAIR hydrog20 B O4 U 9 B U 9 1_555 B N1 G 38 B G 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N1 G 10 B G 10 1_555 B N3 C 37 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N2 G 10 B G 10 1_555 B O2 C 37 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O6 G 10 B G 10 1_555 B N4 C 37 B C 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N3 U 11 B U 11 1_555 B N1 A 36 B A 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O4 U 11 B U 11 1_555 B N6 A 36 B A 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N3 U 12 B U 12 1_555 B N1 A 35 B A 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B O4 U 12 B U 12 1_555 B N6 A 35 B A 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog28 B N1 G 13 B G 13 1_555 B O2 U 34 B U 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_28_PAIR hydrog29 B O6 G 13 B G 13 1_555 B N3 U 34 B U 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N3 C 14 B C 14 1_555 B N1 G 33 B G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N4 C 14 B C 14 1_555 B O6 G 33 B G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B O2 C 14 B C 14 1_555 B N2 G 33 B G 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B N3 U 15 B U 15 1_555 B N1 A 32 B A 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B O4 U 15 B U 15 1_555 B N6 A 32 B A 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N1 A 16 B A 16 1_555 B N3 U 31 B U 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B N6 A 16 B A 16 1_555 B O4 U 31 B U 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 B N1 G 17 B G 17 1_555 B N3 C 30 B C 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 B N2 G 17 B G 17 1_555 B O2 C 30 B C 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 B O6 G 17 B G 17 1_555 B N4 C 30 B C 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 B N3 C 18 B C 18 1_555 B N1 G 29 B G 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 B N4 C 18 B C 18 1_555 B O6 G 29 B G 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 B O2 C 18 B C 18 1_555 B N2 G 29 B G 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 B N1 A 19 B A 19 1_555 B N3 U 28 B U 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 B N6 A 19 B A 19 1_555 B O4 U 28 B U 26 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 40 n n PB O2B ADP sing 41 n n PB O3B ADP sing 42 n n PB O3A ADP sing 43 n n O2B HOB2 ADP sing 44 n n O3B HOB3 ADP sing 45 n n PA O1A ADP doub 46 n n PA O2A ADP sing 47 n n PA O3A ADP sing 48 n n PA O5' ADP sing 49 n n O2A HOA2 ADP sing 50 n n O5' C5' ADP sing 51 n n C5' C4' ADP sing 52 n n C5' "H5'1" ADP sing 53 n n C5' "H5'2" ADP sing 54 n n C4' O4' ADP sing 55 n n C4' C3' ADP sing 56 n n C4' H4' ADP sing 57 n n O4' C1' ADP sing 58 n n C3' O3' ADP sing 59 n n C3' C2' ADP sing 60 n n C3' H3' ADP sing 61 n n O3' HO3' ADP sing 62 n n C2' O2' ADP sing 63 n n C2' C1' ADP sing 64 n n C2' H2' ADP sing 65 n n O2' HO2' ADP sing 66 n n C1' N9 ADP sing 67 n n C1' H1' ADP sing 68 n n N9 C8 ADP sing 69 n y N9 C4 ADP sing 70 n y C8 N7 ADP doub 71 n y C8 H8 ADP sing 72 n n N7 C5 ADP sing 73 n y C5 C6 ADP sing 74 n y C5 C4 ADP doub 75 n y C6 N6 ADP sing 76 n n C6 N1 ADP doub 77 n y N6 HN61 ADP sing 78 n n N6 HN62 ADP sing 79 n n N1 C2 ADP sing 80 n y C2 N3 ADP doub 81 n y C2 H2 ADP sing 82 n n N3 C4 ADP sing 83 n y # _atom_sites.entry_id 8B9K _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 ALF A 1 1202 1202 ALF ALF . # 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 3 127.95 114.921 112.548 1 20 ? PB ADP 1201 A 1 HETATM 2 O O1B ADP . . . C 3 126.984 114.783 111.395 1 20 ? O1B ADP 1201 A 1 HETATM 3 O O2B ADP . . . C 3 127.633 114.054 113.74 1 20 ? O2B ADP 1201 A 1 HETATM 4 O O3B ADP . . . C 3 128.319 116.342 112.893 1 20 ? O3B ADP 1201 A 1 HETATM 5 P PA ADP . . . C 3 130.7 114.63 112.729 1 20 ? PA ADP 1201 A 1 HETATM 6 O O1A ADP . . . C 3 131.338 115.821 112.063 1 20 ? O1A ADP 1201 A 1 HETATM 7 O O2A ADP . . . C 3 130.473 114.634 114.217 1 20 ? O2A ADP 1201 A 1 HETATM 8 O O3A ADP . . . C 3 129.317 114.301 111.985 1 20 ? O3A ADP 1201 A 1 HETATM 9 O O5' ADP . . . C 3 131.571 113.336 112.365 1 20 ? O5' ADP 1201 A 1 HETATM 10 C C5' ADP . . . C 3 132.937 113.491 112.011 1 20 ? C5' ADP 1201 A 1 HETATM 11 C C4' ADP . . . C 3 133.53 112.145 111.633 1 20 ? C4' ADP 1201 A 1 HETATM 12 O O4' ADP . . . C 3 134.825 112.397 111.095 1 20 ? O4' ADP 1201 A 1 HETATM 13 C C3' ADP . . . C 3 133.711 111.273 112.863 1 20 ? C3' ADP 1201 A 1 HETATM 14 O O3' ADP . . . C 3 133.138 109.982 112.65 1 20 ? O3' ADP 1201 A 1 HETATM 15 C C2' ADP . . . C 3 135.202 111.114 113.062 1 20 ? C2' ADP 1201 A 1 HETATM 16 O O2' ADP . . . C 3 135.548 109.728 113.059 1 20 ? O2' ADP 1201 A 1 HETATM 17 C C1' ADP . . . C 3 135.857 111.809 111.886 1 20 ? C1' ADP 1201 A 1 HETATM 18 N N9 ADP . . . C 3 136.737 112.876 112.415 1 20 ? N9 ADP 1201 A 1 HETATM 19 C C8 ADP . . . C 3 136.318 113.998 113.028 1 20 ? C8 ADP 1201 A 1 HETATM 20 N N7 ADP . . . C 3 137.366 114.774 113.402 1 20 ? N7 ADP 1201 A 1 HETATM 21 C C5 ADP . . . C 3 138.489 114.139 113.024 1 20 ? C5 ADP 1201 A 1 HETATM 22 C C6 ADP . . . C 3 139.942 114.402 113.113 1 20 ? C6 ADP 1201 A 1 HETATM 23 N N6 ADP . . . C 3 140.411 115.531 113.695 1 20 ? N6 ADP 1201 A 1 HETATM 24 N N1 ADP . . . C 3 140.783 113.482 112.595 1 20 ? N1 ADP 1201 A 1 HETATM 25 C C2 ADP . . . C 3 140.327 112.357 112.015 1 20 ? C2 ADP 1201 A 1 HETATM 26 N N3 ADP . . . C 3 139.023 112.052 111.9 1 20 ? N3 ADP 1201 A 1 HETATM 27 C C4 ADP . . . C 3 138.071 112.887 112.379 1 20 ? C4 ADP 1201 A 1 # _model_server_stats.io_time_ms 132 _model_server_stats.parse_time_ms 146 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #