data_9B0U # _model_server_result.job_id OEJIbYjNuZAJQ7d429JrKQ _model_server_result.datetime_utc '2025-03-02 23:51:52' _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 9b0u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"LA","auth_seq_id":402}' # _entry.id 9B0U # _exptl.entry_id 9B0U _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 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 9B0U _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9B0U _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,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA _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 ? 3 J N N ? 3 N N N ? 3 Q N N ? 3 V N N ? 3 Z N N ? 3 DA N N ? 3 HA N N ? 3 LA 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 J O3B ADP . A ADP 402 1_555 L MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.882 ? metalc ? metalc2 J O2A ADP . A ADP 402 1_555 L MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.71 ? metalc ? metalc3 K O4 PO4 . A PO4 403 1_555 L MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.845 ? metalc ? metalc4 N O3B ADP . B ADP 402 1_555 P MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc5 N O2A ADP . B ADP 402 1_555 P MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.851 ? metalc ? metalc6 O O3 PO4 . B PO4 403 1_555 P MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc7 Q O3B ADP . C ADP 401 1_555 T MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc8 Q O2A ADP . C ADP 401 1_555 T MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc9 R O1 PO4 . C PO4 402 1_555 T MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc10 V O3B ADP . D ADP 402 1_555 X MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc11 V O2A ADP . D ADP 402 1_555 X MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc12 W O3 PO4 . D PO4 403 1_555 X MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc13 Z O1B ADP . E ADP 402 1_555 BA MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.841 ? metalc ? metalc14 Z O3B ADP . E ADP 402 1_555 BA MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc15 Z O2A ADP . E ADP 402 1_555 BA MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc16 AA O3 PO4 . E PO4 403 1_555 BA MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? metalc ? metalc17 DA O3B ADP . F ADP 402 1_555 FA MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? metalc ? metalc18 DA O2A ADP . F ADP 402 1_555 FA MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.733 ? metalc ? metalc19 EA O3 PO4 . F PO4 403 1_555 FA MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc20 HA O3B ADP . G ADP 402 1_555 JA MG MG . G MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.865 ? metalc ? metalc21 HA O2A ADP . G ADP 402 1_555 JA MG MG . G MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.702 ? metalc ? metalc22 IA O4 PO4 . G PO4 403 1_555 JA MG MG . G MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc23 LA O3B ADP . H ADP 402 1_555 NA MG MG . H MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc24 LA O2A ADP . H ADP 402 1_555 NA MG MG . H MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? metalc ? metalc25 MA O1 PO4 . H PO4 403 1_555 NA MG MG . H MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? # _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 9B0U _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 CRN A 1 401 401 CRN CRN . J 3 ADP A 1 402 402 ADP ADP . K 4 PO4 A 1 403 403 PO4 PO4 . L 5 MG A 1 404 1 MG MG . M 2 CRN B 1 401 401 CRN CRN . N 3 ADP B 1 402 402 ADP ADP . O 4 PO4 B 1 403 403 PO4 PO4 . P 5 MG B 1 404 2 MG MG . Q 3 ADP C 1 401 402 ADP ADP . R 4 PO4 C 1 402 403 PO4 PO4 . S 2 CRN C 1 403 404 CRN CRN . T 5 MG C 1 404 3 MG MG . U 2 CRN D 1 401 401 CRN CRN . V 3 ADP D 1 402 402 ADP ADP . W 4 PO4 D 1 403 403 PO4 PO4 . X 5 MG D 1 404 4 MG MG . Y 2 CRN E 1 401 401 CRN CRN . Z 3 ADP E 1 402 402 ADP ADP . AA 4 PO4 E 1 403 403 PO4 PO4 . BA 5 MG E 1 404 5 MG MG . CA 2 CRN F 1 401 401 CRN CRN . DA 3 ADP F 1 402 402 ADP ADP . EA 4 PO4 F 1 403 403 PO4 PO4 . FA 5 MG F 1 404 6 MG MG . GA 2 CRN G 1 401 401 CRN CRN . HA 3 ADP G 1 402 402 ADP ADP . IA 4 PO4 G 1 403 403 PO4 PO4 . JA 5 MG G 1 404 7 MG MG . KA 2 CRN H 1 401 401 CRN CRN . LA 3 ADP H 1 402 402 ADP ADP . MA 4 PO4 H 1 403 403 PO4 PO4 . NA 5 MG H 1 404 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 . . . LA 3 125.853 179.829 152.315 1 169.14 ? PB ADP 402 H 1 HETATM 2 O O1B ADP . . . LA 3 127.187 180.005 153.004 1 175.31 ? O1B ADP 402 H 1 HETATM 3 O O2B ADP . . . LA 3 124.749 179.245 153.162 1 146.85 ? O2B ADP 402 H 1 HETATM 4 O O3B ADP . . . LA 3 125.946 179.252 150.924 1 154.93 ? O3B ADP 402 H 1 HETATM 5 P PA ADP . . . LA 3 126.042 182.128 150.833 1 146.69 ? PA ADP 402 H 1 HETATM 6 O O1A ADP . . . LA 3 127.151 182.999 151.361 1 151.92 ? O1A ADP 402 H 1 HETATM 7 O O2A ADP . . . LA 3 126.293 181.121 149.741 1 147.79 ? O2A ADP 402 H 1 HETATM 8 O O3A ADP . . . LA 3 125.374 181.333 152.05 1 147.66 ? O3A ADP 402 H 1 HETATM 9 O O5' ADP . . . LA 3 124.813 183.055 150.392 1 144.59 ? O5' ADP 402 H 1 HETATM 10 C C5' ADP . . . LA 3 124.23 182.918 149.104 1 142.8 ? C5' ADP 402 H 1 HETATM 11 C C4' ADP . . . LA 3 123.075 183.896 149.021 1 140.57 ? C4' ADP 402 H 1 HETATM 12 O O4' ADP . . . LA 3 122.31 183.842 150.226 1 137.12 ? O4' ADP 402 H 1 HETATM 13 C C3' ADP . . . LA 3 123.587 185.315 148.875 1 143.22 ? C3' ADP 402 H 1 HETATM 14 O O3' ADP . . . LA 3 123.255 185.833 147.583 1 144.94 ? O3' ADP 402 H 1 HETATM 15 C C2' ADP . . . LA 3 122.918 186.107 149.978 1 139.65 ? C2' ADP 402 H 1 HETATM 16 O O2' ADP . . . LA 3 122.238 187.247 149.454 1 143.25 ? O2' ADP 402 H 1 HETATM 17 C C1' ADP . . . LA 3 121.933 185.159 150.628 1 137.47 ? C1' ADP 402 H 1 HETATM 18 N N9 ADP . . . LA 3 121.985 185.313 152.101 1 133.97 ? N9 ADP 402 H 1 HETATM 19 C C8 ADP . . . LA 3 122.728 184.576 152.945 1 134.94 ? C8 ADP 402 H 1 HETATM 20 N N7 ADP . . . LA 3 122.536 184.981 154.226 1 133.94 ? N7 ADP 402 H 1 HETATM 21 C C5 ADP . . . LA 3 121.656 185.995 154.209 1 136.36 ? C5 ADP 402 H 1 HETATM 22 C C6 ADP . . . LA 3 121.019 186.872 155.213 1 141.77 ? C6 ADP 402 H 1 HETATM 23 N N6 ADP . . . LA 3 121.297 186.741 156.53 1 148.3 ? N6 ADP 402 H 1 HETATM 24 N N1 ADP . . . LA 3 120.155 187.808 154.771 1 142.57 ? N1 ADP 402 H 1 HETATM 25 C C2 ADP . . . LA 3 119.866 187.954 153.466 1 142.49 ? C2 ADP 402 H 1 HETATM 26 N N3 ADP . . . LA 3 120.412 187.187 152.507 1 141.55 ? N3 ADP 402 H 1 HETATM 27 C C4 ADP . . . LA 3 121.296 186.21 152.806 1 137.24 ? C4 ADP 402 H 1 HETATM 28 H "H5'1" ADP . . . LA 3 124.968 183.138 148.329 1 144.59 ? "H5'1" ADP 402 H 1 HETATM 29 H "H5'2" ADP . . . LA 3 123.869 181.897 148.961 1 141.83 ? "H5'2" ADP 402 H 1 HETATM 30 H H4' ADP . . . LA 3 122.447 183.645 148.155 1 139.88 ? H4' ADP 402 H 1 HETATM 31 H H3' ADP . . . LA 3 124.674 185.323 149.026 1 146.43 ? H3' ADP 402 H 1 HETATM 32 H HO3' ADP . . . LA 3 123.77 186.633 147.411 1 147.15 ? HO3' ADP 402 H 1 HETATM 33 H H2' ADP . . . LA 3 123.666 186.401 150.725 1 143.48 ? H2' ADP 402 H 1 HETATM 34 H HO2' ADP . . . LA 3 122.872 187.818 149.003 1 145.64 ? HO2' ADP 402 H 1 HETATM 35 H H1' ADP . . . LA 3 120.923 185.389 150.261 1 139.86 ? H1' ADP 402 H 1 HETATM 36 H H8 ADP . . . LA 3 123.387 183.771 152.645 1 138.8 ? H8 ADP 402 H 1 HETATM 37 H HN61 ADP . . . LA 3 120.854 187.35 157.202 1 149.4 ? HN61 ADP 402 H 1 HETATM 38 H HN62 ADP . . . LA 3 121.948 186.035 156.84 1 145.96 ? HN62 ADP 402 H 1 HETATM 39 H H2 ADP . . . LA 3 119.163 188.724 153.175 1 144.58 ? H2 ADP 402 H 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 39 #