data_9B0T # _model_server_result.job_id j5rB9kWA1JEdVhpiNlElbg _model_server_result.datetime_utc '2025-02-23 03:10:13' _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 9b0t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":402}' # _entry.id 9B0T # _exptl.entry_id 9B0T _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 9B0T _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9B0T _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 R 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 O1B ADP . A ADP 402 1_555 L MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? metalc ? metalc2 J O2B ADP . A ADP 402 1_555 L MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc3 J O1A ADP . A ADP 402 1_555 L MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc4 N O1B ADP . B ADP 402 1_555 P MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc5 N O2B ADP . B ADP 402 1_555 P MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc6 N O1A ADP . B ADP 402 1_555 P MG MG . B MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc7 R O1B ADP . C ADP 402 1_555 T MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc8 R O2B ADP . C ADP 402 1_555 T MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc9 R O1A ADP . C ADP 402 1_555 T MG MG . C MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc10 V O2B ADP . D ADP 402 1_555 X MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.633 ? metalc ? metalc11 V O3B ADP . D ADP 402 1_555 X MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc12 V O2A ADP . D ADP 402 1_555 X MG MG . D MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc13 Z O2B ADP . E ADP 402 1_555 BA MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc14 Z O3B ADP . E ADP 402 1_555 BA MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc15 Z O2A ADP . E ADP 402 1_555 BA MG MG . E MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc16 DA O2B ADP . F ADP 402 1_555 FA MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? metalc ? metalc17 DA O3B ADP . F ADP 402 1_555 FA MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc18 DA O2A ADP . F ADP 402 1_555 FA MG MG . F MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? metalc ? metalc19 HA O2B ADP . G ADP 402 1_555 JA MG MG . G MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc20 HA O3B ADP . G ADP 402 1_555 JA MG MG . G MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc21 HA O2A ADP . G ADP 402 1_555 JA MG MG . G MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc22 LA O1B ADP . H ADP 402 1_555 NA MG MG . H MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc23 LA O2B ADP . H ADP 402 1_555 NA MG MG . H MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc24 LA O1A ADP . H ADP 402 1_555 NA MG MG . H MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? # _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 9B0T _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 NO3 A 1 403 403 NO3 NO3 . 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 NO3 B 1 403 403 NO3 NO3 . P 5 MG B 1 404 2 MG MG . Q 2 CRN C 1 401 401 CRN CRN . R 3 ADP C 1 402 402 ADP ADP . S 4 NO3 C 1 403 403 NO3 NO3 . 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 NO3 D 1 403 403 NO3 NO3 . 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 NO3 E 1 403 403 NO3 NO3 . 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 NO3 F 1 403 403 NO3 NO3 . 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 NO3 G 1 403 403 NO3 NO3 . 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 NO3 H 1 403 403 NO3 NO3 . 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 . . . N 3 92.592 125.056 151.658 1 141.88 ? PB ADP 402 B 1 HETATM 2 O O1B ADP . . . N 3 92.568 124.049 150.539 1 130.66 ? O1B ADP 402 B 1 HETATM 3 O O2B ADP . . . N 3 93.301 126.334 151.298 1 137.17 ? O2B ADP 402 B 1 HETATM 4 O O3B ADP . . . N 3 92.97 124.488 153.003 1 129.79 ? O3B ADP 402 B 1 HETATM 5 P PA ADP . . . N 3 90.15 126.085 150.661 1 132.76 ? PA ADP 402 B 1 HETATM 6 O O1A ADP . . . N 3 91.014 126.616 149.546 1 125.81 ? O1A ADP 402 B 1 HETATM 7 O O2A ADP . . . N 3 89.095 126.95 151.296 1 139.74 ? O2A ADP 402 B 1 HETATM 8 O O3A ADP . . . N 3 91.057 125.493 151.852 1 138.38 ? O3A ADP 402 B 1 HETATM 9 O O5' ADP . . . N 3 89.433 124.766 150.098 1 130.2 ? O5' ADP 402 B 1 HETATM 10 C C5' ADP . . . N 3 89.019 124.697 148.738 1 128.14 ? C5' ADP 402 B 1 HETATM 11 C C4' ADP . . . N 3 88.199 123.426 148.561 1 125.12 ? C4' ADP 402 B 1 HETATM 12 O O4' ADP . . . N 3 88.281 122.664 149.766 1 122.82 ? O4' ADP 402 B 1 HETATM 13 C C3' ADP . . . N 3 86.726 123.684 148.293 1 128.14 ? C3' ADP 402 B 1 HETATM 14 O O3' ADP . . . N 3 86.313 122.953 147.135 1 119.62 ? O3' ADP 402 B 1 HETATM 15 C C2' ADP . . . N 3 86.005 123.191 149.529 1 125.64 ? C2' ADP 402 B 1 HETATM 16 O O2' ADP . . . N 3 84.786 122.53 149.196 1 125.64 ? O2' ADP 402 B 1 HETATM 17 C C1' ADP . . . N 3 86.985 122.238 150.178 1 118.45 ? C1' ADP 402 B 1 HETATM 18 N N9 ADP . . . N 3 86.894 122.258 151.654 1 112.97 ? N9 ADP 402 B 1 HETATM 19 C C8 ADP . . . N 3 87.676 122.979 152.472 1 118.92 ? C8 ADP 402 B 1 HETATM 20 N N7 ADP . . . N 3 87.344 122.758 153.769 1 119.85 ? N7 ADP 402 B 1 HETATM 21 C C5 ADP . . . N 3 86.333 121.875 153.786 1 125.17 ? C5 ADP 402 B 1 HETATM 22 C C6 ADP . . . N 3 85.516 121.212 154.824 1 134.67 ? C6 ADP 402 B 1 HETATM 23 N N6 ADP . . . N 3 85.716 121.462 156.139 1 140.64 ? N6 ADP 402 B 1 HETATM 24 N N1 ADP . . . N 3 84.561 120.354 154.412 1 129.44 ? N1 ADP 402 B 1 HETATM 25 C C2 ADP . . . N 3 84.347 120.095 153.11 1 124.19 ? C2 ADP 402 B 1 HETATM 26 N N3 ADP . . . N 3 85.057 120.665 152.121 1 118.34 ? N3 ADP 402 B 1 HETATM 27 C C4 ADP . . . N 3 86.045 121.544 152.388 1 117.13 ? C4 ADP 402 B 1 HETATM 28 H "H5'1" ADP . . . N 3 89.894 124.667 148.085 1 127.65 ? "H5'1" ADP 402 B 1 HETATM 29 H "H5'2" ADP . . . N 3 88.434 125.582 148.482 1 130.24 ? "H5'2" ADP 402 B 1 HETATM 30 H H4' ADP . . . N 3 88.616 122.848 147.723 1 123.71 ? H4' ADP 402 B 1 HETATM 31 H H3' ADP . . . N 3 86.535 124.758 148.161 1 131.04 ? H3' ADP 402 B 1 HETATM 32 H HO3' ADP . . . N 3 85.397 123.175 146.919 1 124.44 ? HO3' ADP 402 B 1 HETATM 33 H H2' ADP . . . N 3 85.817 124.038 150.205 1 128.49 ? H2' ADP 402 B 1 HETATM 34 H HO2' ADP . . . N 3 84.166 123.171 148.823 1 127.11 ? HO2' ADP 402 B 1 HETATM 35 H H1' ADP . . . N 3 86.789 121.223 149.804 1 121.66 ? H1' ADP 402 B 1 HETATM 36 H H8 ADP . . . N 3 88.461 123.649 152.142 1 123.59 ? H8 ADP 402 B 1 HETATM 37 H HN61 ADP . . . N 3 86.436 122.11 156.426 1 135.72 ? HN61 ADP 402 B 1 HETATM 38 H HN62 ADP . . . N 3 85.145 121.001 156.832 1 141.82 ? HN62 ADP 402 B 1 HETATM 39 H H2 ADP . . . N 3 83.565 119.395 152.846 1 127.43 ? H2 ADP 402 B 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 88 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #