data_9B04 # _model_server_result.job_id ZaJKJiJ_Ogulypg_Zn3zGg _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":"W","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 . . . W 2 113.045 174.535 119.995 1 149.54 ? PB ADP 401 H 1 HETATM 2 O O1B ADP . . . W 2 111.84 173.755 119.531 1 160.65 ? O1B ADP 401 H 1 HETATM 3 O O2B ADP . . . W 2 114.091 174.765 118.932 1 130.68 ? O2B ADP 401 H 1 HETATM 4 O O3B ADP . . . W 2 113.597 174.095 121.329 1 141.74 ? O3B ADP 401 H 1 HETATM 5 P PA ADP . . . W 2 111.339 176.22 121.411 1 154.4 ? PA ADP 401 H 1 HETATM 6 O O1A ADP . . . W 2 109.979 176.094 120.769 1 157.95 ? O1A ADP 401 H 1 HETATM 7 O O2A ADP . . . W 2 111.713 175.367 122.598 1 151.38 ? O2A ADP 401 H 1 HETATM 8 O O3A ADP . . . W 2 112.465 176.005 120.283 1 141.11 ? O3A ADP 401 H 1 HETATM 9 O O5' ADP . . . W 2 111.577 177.757 121.812 1 146.34 ? O5' ADP 401 H 1 HETATM 10 C C5' ADP . . . W 2 111.688 178.131 123.182 1 146.86 ? C5' ADP 401 H 1 HETATM 11 C C4' ADP . . . W 2 111.69 179.648 123.287 1 146.59 ? C4' ADP 401 H 1 HETATM 12 O O4' ADP . . . W 2 112.368 180.215 122.164 1 140.64 ? O4' ADP 401 H 1 HETATM 13 C C3' ADP . . . W 2 110.281 180.217 123.295 1 155.92 ? C3' ADP 401 H 1 HETATM 14 O O3' ADP . . . W 2 109.95 180.706 124.598 1 162.6 ? O3' ADP 401 H 1 HETATM 15 C C2' ADP . . . W 2 110.28 181.336 122.273 1 149.94 ? C2' ADP 401 H 1 HETATM 16 O O2' ADP . . . W 2 109.924 182.583 122.875 1 154.04 ? O2' ADP 401 H 1 HETATM 17 C C1' ADP . . . W 2 111.692 181.389 121.714 1 138.07 ? C1' ADP 401 H 1 HETATM 18 N N9 ADP . . . W 2 111.649 181.433 120.232 1 137.07 ? N9 ADP 401 H 1 HETATM 19 C C8 ADP . . . W 2 111.58 180.361 119.422 1 139.08 ? C8 ADP 401 H 1 HETATM 20 N N7 ADP . . . W 2 111.557 180.745 118.12 1 136.58 ? N7 ADP 401 H 1 HETATM 21 C C5 ADP . . . W 2 111.609 182.088 118.088 1 135.62 ? C5 ADP 401 H 1 HETATM 22 C C6 ADP . . . W 2 111.62 183.132 117.04 1 136.39 ? C6 ADP 401 H 1 HETATM 23 N N6 ADP . . . W 2 111.567 182.808 115.727 1 140.49 ? N6 ADP 401 H 1 HETATM 24 N N1 ADP . . . W 2 111.684 184.421 117.439 1 135.26 ? N1 ADP 401 H 1 HETATM 25 C C2 ADP . . . W 2 111.738 184.766 118.738 1 138.35 ? C2 ADP 401 H 1 HETATM 26 N N3 ADP . . . W 2 111.731 183.864 119.737 1 141.09 ? N3 ADP 401 H 1 HETATM 27 C C4 ADP . . . W 2 111.67 182.537 119.484 1 138.97 ? C4 ADP 401 H 1 HETATM 28 H "H5'1" ADP . . . W 2 110.852 177.717 123.749 1 153.66 ? "H5'1" ADP 401 H 1 HETATM 29 H "H5'2" ADP . . . W 2 112.614 177.73 123.599 1 141.81 ? "H5'2" ADP 401 H 1 HETATM 30 H H4' ADP . . . W 2 112.197 179.939 124.217 1 143.23 ? H4' ADP 401 H 1 HETATM 31 H H3' ADP . . . W 2 109.571 179.439 122.982 1 159.74 ? H3' ADP 401 H 1 HETATM 32 H HO3' ADP . . . W 2 109.009 180.927 124.633 1 163.48 ? HO3' ADP 401 H 1 HETATM 33 H H2' ADP . . . W 2 109.579 181.087 121.463 1 152.87 ? H2' ADP 401 H 1 HETATM 34 H HO2' ADP . . . W 2 108.994 182.562 123.138 1 156.39 ? HO2' ADP 401 H 1 HETATM 35 H H1' ADP . . . W 2 112.197 182.282 122.104 1 140.7 ? H1' ADP 401 H 1 HETATM 36 H H8 ADP . . . W 2 111.549 179.333 119.762 1 138.28 ? H8 ADP 401 H 1 HETATM 37 H HN61 ADP . . . W 2 111.575 183.537 115.027 1 143.67 ? HN61 ADP 401 H 1 HETATM 38 H HN62 ADP . . . W 2 111.519 181.839 115.447 1 140.25 ? HN62 ADP 401 H 1 HETATM 39 H H2 ADP . . . W 2 111.787 185.817 118.992 1 142.01 ? H2 ADP 401 H 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 63 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #