data_9B04 # _model_server_result.job_id NDjzOdafoGqL4bq_BmHUxw _model_server_result.datetime_utc '2025-03-02 23:52:13' _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 9b04 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":401}' # _entry.id 9B04 # _exptl.entry_id 9B04 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 8 _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 9B04 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9B04 _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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,M,N,O,P,Q,R,S,T,U,V,W,X _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q N N ? 2 S N N ? 2 U N N ? 2 W 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 metalc ? metalc1 I O3B ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc2 I O2A ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc3 K O3B ADP . B ADP 401 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc4 K O2A ADP . B ADP 401 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc5 M O3B ADP . C ADP 401 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc6 M O2A ADP . C ADP 401 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc7 O O3B ADP . D ADP 401 1_555 P MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc8 O O2A ADP . D ADP 401 1_555 P MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc9 Q O3B ADP . E ADP 401 1_555 R MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc10 Q O2A ADP . E ADP 401 1_555 R MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc11 S O3B ADP . F ADP 401 1_555 T MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc12 S O2A ADP . F ADP 401 1_555 T MG MG . F MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc13 U O3B ADP . G ADP 401 1_555 V MG MG . G MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc14 U O2A ADP . G ADP 401 1_555 V MG MG . G MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc15 W O3B ADP . H ADP 401 1_555 X MG MG . H MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc16 W O2A ADP . H ADP 401 1_555 X MG MG . H MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? # _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 9B04 _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 I 2 ADP A 1 401 402 ADP ADP . J 3 MG A 1 402 1 MG MG . K 2 ADP B 1 401 402 ADP ADP . L 3 MG B 1 402 2 MG MG . M 2 ADP C 1 401 402 ADP ADP . N 3 MG C 1 402 3 MG MG . O 2 ADP D 1 401 402 ADP ADP . P 3 MG D 1 402 4 MG MG . Q 2 ADP E 1 401 402 ADP ADP . R 3 MG E 1 402 5 MG MG . S 2 ADP F 1 401 402 ADP ADP . T 3 MG F 1 402 6 MG MG . U 2 ADP G 1 401 402 ADP ADP . V 3 MG G 1 402 7 MG MG . W 2 ADP H 1 401 402 ADP ADP . X 3 MG H 1 402 8 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 . . . O 2 97.854 159.343 152.391 1 149.52 ? PB ADP 401 D 1 HETATM 2 O O1B ADP . . . O 2 98.624 160.549 152.874 1 160.59 ? O1B ADP 401 D 1 HETATM 3 O O2B ADP . . . O 2 97.622 158.286 153.442 1 130.92 ? O2B ADP 401 D 1 HETATM 4 O O3B ADP . . . O 2 98.308 158.807 151.056 1 142.92 ? O3B ADP 401 D 1 HETATM 5 P PA ADP . . . O 2 96.167 161.046 150.973 1 153.94 ? PA ADP 401 D 1 HETATM 6 O O1A ADP . . . O 2 96.297 162.405 151.616 1 157.72 ? O1A ADP 401 D 1 HETATM 7 O O2A ADP . . . O 2 97.016 160.673 149.782 1 149.4 ? O2A ADP 401 D 1 HETATM 8 O O3A ADP . . . O 2 96.382 159.918 152.098 1 140.74 ? O3A ADP 401 D 1 HETATM 9 O O5' ADP . . . O 2 94.628 160.812 150.576 1 144.55 ? O5' ADP 401 D 1 HETATM 10 C C5' ADP . . . O 2 94.25 160.7 149.207 1 144.68 ? C5' ADP 401 D 1 HETATM 11 C C4' ADP . . . O 2 92.732 160.698 149.108 1 145.1 ? C4' ADP 401 D 1 HETATM 12 O O4' ADP . . . O 2 92.169 160.017 150.231 1 138.65 ? O4' ADP 401 D 1 HETATM 13 C C3' ADP . . . O 2 92.164 162.108 149.105 1 153.71 ? C3' ADP 401 D 1 HETATM 14 O O3' ADP . . . O 2 91.663 162.437 147.806 1 161.46 ? O3' ADP 401 D 1 HETATM 15 C C2' ADP . . . O 2 91.054 162.11 150.137 1 147.55 ? C2' ADP 401 D 1 HETATM 16 O O2' ADP . . . O 2 89.803 162.472 149.545 1 151.49 ? O2' ADP 401 D 1 HETATM 17 C C1' ADP . . . O 2 91.001 160.696 150.693 1 136.13 ? C1' ADP 401 D 1 HETATM 18 N N9 ADP . . . O 2 90.972 160.733 152.175 1 136.68 ? N9 ADP 401 D 1 HETATM 19 C C8 ADP . . . O 2 92.052 160.757 152.977 1 139.35 ? C8 ADP 401 D 1 HETATM 20 N N7 ADP . . . O 2 91.678 160.788 154.282 1 136.98 ? N7 ADP 401 D 1 HETATM 21 C C5 ADP . . . O 2 90.335 160.786 154.324 1 136.35 ? C5 ADP 401 D 1 HETATM 22 C C6 ADP . . . O 2 89.301 160.809 155.382 1 138.28 ? C6 ADP 401 D 1 HETATM 23 N N6 ADP . . . O 2 89.643 160.843 156.691 1 141.55 ? N6 ADP 401 D 1 HETATM 24 N N1 ADP . . . O 2 88.007 160.794 154.996 1 137.28 ? N1 ADP 401 D 1 HETATM 25 C C2 ADP . . . O 2 87.649 160.759 153.699 1 138.67 ? C2 ADP 401 D 1 HETATM 26 N N3 ADP . . . O 2 88.541 160.738 152.692 1 140.56 ? N3 ADP 401 D 1 HETATM 27 C C4 ADP . . . O 2 89.873 160.749 152.932 1 138.3 ? C4 ADP 401 D 1 HETATM 28 H "H5'1" ADP . . . O 2 94.662 161.534 148.636 1 151.97 ? "H5'1" ADP 401 D 1 HETATM 29 H "H5'2" ADP . . . O 2 94.648 159.772 148.789 1 140.14 ? "H5'2" ADP 401 D 1 HETATM 30 H H4' ADP . . . O 2 92.437 160.194 148.178 1 141.76 ? H4' ADP 401 D 1 HETATM 31 H H3' ADP . . . O 2 92.945 162.819 149.41 1 158 ? H3' ADP 401 D 1 HETATM 32 H HO3' ADP . . . O 2 91.449 163.379 147.768 1 161.88 ? HO3' ADP 401 D 1 HETATM 33 H H2' ADP . . . O 2 91.311 162.809 150.945 1 151.36 ? H2' ADP 401 D 1 HETATM 34 H HO2' ADP . . . O 2 89.829 163.4 149.275 1 154.58 ? HO2' ADP 401 D 1 HETATM 35 H H1' ADP . . . O 2 90.103 160.194 150.311 1 139.3 ? H1' ADP 401 D 1 HETATM 36 H H8 ADP . . . O 2 93.079 160.751 152.631 1 138.01 ? H8 ADP 401 D 1 HETATM 37 H HN61 ADP . . . O 2 88.926 160.859 157.402 1 144.26 ? HN61 ADP 401 D 1 HETATM 38 H HN62 ADP . . . O 2 90.618 160.853 156.958 1 140.59 ? HN62 ADP 401 D 1 HETATM 39 H H2 ADP . . . O 2 86.594 160.751 153.454 1 142.83 ? H2 ADP 401 D 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #