data_7RKZ # _model_server_result.job_id ePDB6Q5YTBxgp-nOCT3OHg _model_server_result.datetime_utc '2024-12-26 17:47:43' _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 7rkz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1201}' # _entry.id 7RKZ # _exptl.entry_id 7RKZ _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 3 _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 7RKZ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RKZ _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 E N N ? 2 J N N ? 2 R N N # _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 7RKZ _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 E 2 ADP A 1 1201 1201 ADP ADP . F 3 Q5B A 1 1202 1202 Q5B Q5B . G 4 FLC A 1 1203 2201 FLC FLC . H 5 UNL A 1 1204 2301 UNL UNL . I 6 COA A 1 1205 2101 COA COA . J 2 ADP B 1 1201 1201 ADP ADP . K 3 Q5B B 1 1202 1202 Q5B Q5B . L 4 FLC B 1 1203 2201 FLC FLC . M 6 COA B 1 1204 2101 COA COA . N 6 COA C 1 2101 2101 COA COA . O 6 COA C 1 2102 2101 COA COA . P 4 FLC C 1 2103 2201 FLC FLC . Q 5 UNL C 1 2104 2301 UNL UNL . R 2 ADP D 1 1201 1201 ADP ADP . S 3 Q5B D 1 1202 2104 Q5B Q5B . T 4 FLC D 1 1203 2201 FLC FLC . U 7 HOH A 1 1301 48 HOH HOH . U 7 HOH A 2 1302 148 HOH HOH . U 7 HOH A 3 1303 106 HOH HOH . U 7 HOH A 4 1304 49 HOH HOH . U 7 HOH A 5 1305 97 HOH HOH . U 7 HOH A 6 1306 29 HOH HOH . U 7 HOH A 7 1307 161 HOH HOH . U 7 HOH A 8 1308 177 HOH HOH . U 7 HOH A 9 1309 179 HOH HOH . U 7 HOH A 10 1310 152 HOH HOH . U 7 HOH A 11 1311 135 HOH HOH . U 7 HOH A 12 1312 28 HOH HOH . U 7 HOH A 13 1313 16 HOH HOH . U 7 HOH A 14 1314 85 HOH HOH . U 7 HOH A 15 1315 57 HOH HOH . U 7 HOH A 16 1316 154 HOH HOH . U 7 HOH A 17 1317 41 HOH HOH . U 7 HOH A 18 1318 46 HOH HOH . U 7 HOH A 19 1319 89 HOH HOH . U 7 HOH A 20 1320 33 HOH HOH . U 7 HOH A 21 1321 163 HOH HOH . U 7 HOH A 22 1322 172 HOH HOH . U 7 HOH A 23 1323 133 HOH HOH . U 7 HOH A 24 1324 86 HOH HOH . U 7 HOH A 25 1325 119 HOH HOH . U 7 HOH A 26 1326 34 HOH HOH . U 7 HOH A 27 1327 175 HOH HOH . U 7 HOH A 28 1328 93 HOH HOH . U 7 HOH A 29 1329 186 HOH HOH . U 7 HOH A 30 1330 72 HOH HOH . U 7 HOH A 31 1331 149 HOH HOH . U 7 HOH A 32 1332 151 HOH HOH . U 7 HOH A 33 1333 3 HOH HOH . U 7 HOH A 34 1334 1 HOH HOH . U 7 HOH A 35 1335 76 HOH HOH . V 7 HOH B 1 1301 107 HOH HOH . V 7 HOH B 2 1302 44 HOH HOH . V 7 HOH B 3 1303 73 HOH HOH . V 7 HOH B 4 1304 183 HOH HOH . V 7 HOH B 5 1305 25 HOH HOH . V 7 HOH B 6 1306 35 HOH HOH . V 7 HOH B 7 1307 61 HOH HOH . V 7 HOH B 8 1308 23 HOH HOH . V 7 HOH B 9 1309 31 HOH HOH . V 7 HOH B 10 1310 129 HOH HOH . V 7 HOH B 11 1311 156 HOH HOH . V 7 HOH B 12 1312 80 HOH HOH . V 7 HOH B 13 1313 79 HOH HOH . V 7 HOH B 14 1314 60 HOH HOH . V 7 HOH B 15 1315 103 HOH HOH . V 7 HOH B 16 1316 158 HOH HOH . V 7 HOH B 17 1317 78 HOH HOH . V 7 HOH B 18 1318 53 HOH HOH . V 7 HOH B 19 1319 142 HOH HOH . V 7 HOH B 20 1320 56 HOH HOH . V 7 HOH B 21 1321 55 HOH HOH . V 7 HOH B 22 1322 105 HOH HOH . V 7 HOH B 23 1323 173 HOH HOH . V 7 HOH B 24 1324 140 HOH HOH . V 7 HOH B 25 1325 128 HOH HOH . V 7 HOH B 26 1326 71 HOH HOH . V 7 HOH B 27 1327 159 HOH HOH . V 7 HOH B 28 1328 168 HOH HOH . V 7 HOH B 29 1329 36 HOH HOH . V 7 HOH B 30 1330 120 HOH HOH . V 7 HOH B 31 1331 74 HOH HOH . V 7 HOH B 32 1332 95 HOH HOH . V 7 HOH B 33 1333 176 HOH HOH . V 7 HOH B 34 1334 125 HOH HOH . V 7 HOH B 35 1335 96 HOH HOH . V 7 HOH B 36 1336 109 HOH HOH . V 7 HOH B 37 1337 145 HOH HOH . V 7 HOH B 38 1338 87 HOH HOH . V 7 HOH B 39 1339 5 HOH HOH . V 7 HOH B 40 1340 101 HOH HOH . V 7 HOH B 41 1341 147 HOH HOH . V 7 HOH B 42 1342 18 HOH HOH . V 7 HOH B 43 1343 4 HOH HOH . V 7 HOH B 44 1344 32 HOH HOH . V 7 HOH B 45 1345 144 HOH HOH . V 7 HOH B 46 1346 100 HOH HOH . V 7 HOH B 47 1347 69 HOH HOH . W 7 HOH C 1 2201 155 HOH HOH . W 7 HOH C 2 2202 130 HOH HOH . W 7 HOH C 3 2203 45 HOH HOH . W 7 HOH C 4 2204 54 HOH HOH . W 7 HOH C 5 2205 17 HOH HOH . W 7 HOH C 6 2206 184 HOH HOH . W 7 HOH C 7 2207 42 HOH HOH . W 7 HOH C 8 2208 65 HOH HOH . W 7 HOH C 9 2209 104 HOH HOH . W 7 HOH C 10 2210 114 HOH HOH . W 7 HOH C 11 2211 38 HOH HOH . W 7 HOH C 12 2212 116 HOH HOH . W 7 HOH C 13 2213 27 HOH HOH . W 7 HOH C 14 2214 138 HOH HOH . W 7 HOH C 15 2215 30 HOH HOH . W 7 HOH C 16 2216 67 HOH HOH . W 7 HOH C 17 2217 122 HOH HOH . W 7 HOH C 18 2218 102 HOH HOH . W 7 HOH C 19 2219 115 HOH HOH . W 7 HOH C 20 2220 70 HOH HOH . W 7 HOH C 21 2221 118 HOH HOH . W 7 HOH C 22 2222 52 HOH HOH . W 7 HOH C 23 2223 139 HOH HOH . W 7 HOH C 24 2224 83 HOH HOH . W 7 HOH C 25 2225 134 HOH HOH . W 7 HOH C 26 2226 98 HOH HOH . W 7 HOH C 27 2227 66 HOH HOH . W 7 HOH C 28 2228 171 HOH HOH . W 7 HOH C 29 2229 90 HOH HOH . W 7 HOH C 30 2230 22 HOH HOH . W 7 HOH C 31 2231 112 HOH HOH . W 7 HOH C 32 2232 64 HOH HOH . W 7 HOH C 33 2233 99 HOH HOH . W 7 HOH C 34 2234 63 HOH HOH . W 7 HOH C 35 2235 136 HOH HOH . W 7 HOH C 36 2236 165 HOH HOH . W 7 HOH C 37 2237 160 HOH HOH . X 7 HOH D 1 1301 59 HOH HOH . X 7 HOH D 2 1302 180 HOH HOH . X 7 HOH D 3 1303 8 HOH HOH . X 7 HOH D 4 1304 58 HOH HOH . X 7 HOH D 5 1305 19 HOH HOH . X 7 HOH D 6 1306 68 HOH HOH . X 7 HOH D 7 1307 37 HOH HOH . X 7 HOH D 8 1308 94 HOH HOH . X 7 HOH D 9 1309 84 HOH HOH . X 7 HOH D 10 1310 166 HOH HOH . X 7 HOH D 11 1311 167 HOH HOH . X 7 HOH D 12 1312 20 HOH HOH . X 7 HOH D 13 1313 81 HOH HOH . X 7 HOH D 14 1314 50 HOH HOH . X 7 HOH D 15 1315 91 HOH HOH . X 7 HOH D 16 1316 2 HOH HOH . X 7 HOH D 17 1317 181 HOH HOH . X 7 HOH D 18 1318 169 HOH HOH . X 7 HOH D 19 1319 39 HOH HOH . X 7 HOH D 20 1320 77 HOH HOH . X 7 HOH D 21 1321 21 HOH HOH . X 7 HOH D 22 1322 174 HOH HOH . X 7 HOH D 23 1323 127 HOH HOH . X 7 HOH D 24 1324 26 HOH HOH . X 7 HOH D 25 1325 24 HOH HOH . X 7 HOH D 26 1326 40 HOH HOH . X 7 HOH D 27 1327 75 HOH HOH . X 7 HOH D 28 1328 126 HOH HOH . X 7 HOH D 29 1329 143 HOH HOH . X 7 HOH D 30 1330 132 HOH HOH . X 7 HOH D 31 1331 124 HOH HOH . X 7 HOH D 32 1332 108 HOH HOH . X 7 HOH D 33 1333 137 HOH HOH . X 7 HOH D 34 1334 164 HOH HOH . X 7 HOH D 35 1335 146 HOH HOH . X 7 HOH D 36 1336 157 HOH HOH . X 7 HOH D 37 1337 47 HOH HOH . X 7 HOH D 38 1338 153 HOH HOH . X 7 HOH D 39 1339 51 HOH HOH . X 7 HOH D 40 1340 117 HOH HOH . X 7 HOH D 41 1341 7 HOH HOH . X 7 HOH D 42 1342 150 HOH HOH . X 7 HOH D 43 1343 82 HOH HOH . # 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 . . . J 2 132.538 52.171 33.641 1 152.78 ? PB ADP 1201 B 1 HETATM 2 O O1B ADP . . . J 2 133.535 52.158 32.507 1 152.78 ? O1B ADP 1201 B 1 HETATM 3 O O2B ADP . . . J 2 133.134 51.907 35.001 1 152.78 ? O2B ADP 1201 B 1 HETATM 4 O O3B ADP . . . J 2 131.584 53.339 33.6 1 152.78 ? O3B ADP 1201 B 1 HETATM 5 P PA ADP . . . J 2 130.742 50.802 32 1 152.78 ? PA ADP 1201 B 1 HETATM 6 O O1A ADP . . . J 2 131.21 51.919 31.101 1 152.78 ? O1A ADP 1201 B 1 HETATM 7 O O2A ADP . . . J 2 129.282 50.65 32.35 1 152.78 ? O2A ADP 1201 B 1 HETATM 8 O O3A ADP . . . J 2 131.598 50.893 33.361 1 152.78 ? O3A ADP 1201 B 1 HETATM 9 O O5' ADP . . . J 2 131.257 49.428 31.339 1 152.78 ? O5' ADP 1201 B 1 HETATM 10 C C5' ADP . . . J 2 132.103 49.501 30.194 1 152.78 ? C5' ADP 1201 B 1 HETATM 11 C C4' ADP . . . J 2 131.524 48.711 29.028 1 152.78 ? C4' ADP 1201 B 1 HETATM 12 O O4' ADP . . . J 2 130.257 48.135 29.355 1 152.78 ? O4' ADP 1201 B 1 HETATM 13 C C3' ADP . . . J 2 131.292 49.62 27.83 1 152.78 ? C3' ADP 1201 B 1 HETATM 14 O O3' ADP . . . J 2 132.26 49.344 26.814 1 152.78 ? O3' ADP 1201 B 1 HETATM 15 C C2' ADP . . . J 2 129.9 49.295 27.327 1 152.78 ? C2' ADP 1201 B 1 HETATM 16 O O2' ADP . . . J 2 129.947 48.908 25.951 1 152.78 ? O2' ADP 1201 B 1 HETATM 17 C C1' ADP . . . J 2 129.434 48.132 28.186 1 152.78 ? C1' ADP 1201 B 1 HETATM 18 N N9 ADP . . . J 2 127.998 48.272 28.534 1 152.78 ? N9 ADP 1201 B 1 HETATM 19 C C8 ADP . . . J 2 127.491 48.993 29.55 1 152.78 ? C8 ADP 1201 B 1 HETATM 20 N N7 ADP . . . J 2 126.136 48.903 29.586 1 152.78 ? N7 ADP 1201 B 1 HETATM 21 C C5 ADP . . . J 2 125.757 48.106 28.572 1 152.78 ? C5 ADP 1201 B 1 HETATM 22 C C6 ADP . . . J 2 124.474 47.592 28.038 1 152.78 ? C6 ADP 1201 B 1 HETATM 23 N N6 ADP . . . J 2 123.293 47.92 28.613 1 152.78 ? N6 ADP 1201 B 1 HETATM 24 N N1 ADP . . . J 2 124.523 46.783 26.957 1 152.78 ? N1 ADP 1201 B 1 HETATM 25 C C2 ADP . . . J 2 125.69 46.449 26.377 1 152.78 ? C2 ADP 1201 B 1 HETATM 26 N N3 ADP . . . J 2 126.889 46.876 26.808 1 152.78 ? N3 ADP 1201 B 1 HETATM 27 C C4 ADP . . . J 2 126.988 47.694 27.882 1 152.78 ? C4 ADP 1201 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 46 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 27 #