data_1RDZ # _model_server_result.job_id XdxO18kXOJu9ShhMfmcMug _model_server_result.datetime_utc '2024-10-20 19:31:36' _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 1rdz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":339}' # _entry.id 1RDZ # _exptl.entry_id 1RDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 347.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'ADENOSINE MONOPHOSPHATE' _entity.pdbx_number_of_molecules 2 _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 1RDZ _cell.length_a 61.06 _cell.length_b 166.78 _cell.length_c 79.92 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RDZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 61.06 166.78 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # _chem_comp.formula 'C10 H14 N5 O7 P' _chem_comp.formula_weight 347.221 _chem_comp.id AMP _chem_comp.mon_nstd_flag . _chem_comp.name 'ADENOSINE MONOPHOSPHATE' _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 P O1P AMP doub 13 n n P O2P AMP sing 14 n n P O3P AMP sing 15 n n P O5' AMP sing 16 n n O2P HOP2 AMP sing 17 n n O3P HOP3 AMP sing 18 n n O5' C5' AMP sing 19 n n C5' C4' AMP sing 20 n n C5' "H5'1" AMP sing 21 n n C5' "H5'2" AMP sing 22 n n C4' O4' AMP sing 23 n n C4' C3' AMP sing 24 n n C4' H4' AMP sing 25 n n O4' C1' AMP sing 26 n n C3' O3' AMP sing 27 n n C3' C2' AMP sing 28 n n C3' H3' AMP sing 29 n n O3' HO3' AMP sing 30 n n C2' O2' AMP sing 31 n n C2' C1' AMP sing 32 n n C2' H2' AMP sing 33 n n O2' HO2' AMP sing 34 n n C1' N9 AMP sing 35 n n C1' H1' AMP sing 36 n n N9 C8 AMP sing 37 n y N9 C4 AMP sing 38 n y C8 N7 AMP doub 39 n y C8 H8 AMP sing 40 n n N7 C5 AMP sing 41 n y C5 C6 AMP sing 42 n y C5 C4 AMP doub 43 n y C6 N6 AMP sing 44 n n C6 N1 AMP doub 45 n y N6 HN61 AMP sing 46 n n N6 HN62 AMP sing 47 n n N1 C2 AMP sing 48 n y C2 N3 AMP doub 49 n y C2 H2 AMP sing 50 n n N3 C4 AMP sing 51 n y # _atom_sites.entry_id 1RDZ _atom_sites.fract_transf_matrix[1][1] 0.016377 _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] 0.005996 _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] 0.012513 _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 C 2 F6P A 1 338 1 F6P F6P . D 3 AMP A 1 339 3 AMP AMP . E 2 F6P B 1 338 2 F6P F6P . F 3 AMP B 1 339 4 AMP AMP . G 4 HOH A 1 340 1 HOH HOH . G 4 HOH A 2 341 2 HOH HOH . G 4 HOH A 3 342 4 HOH HOH . G 4 HOH A 4 343 5 HOH HOH . G 4 HOH A 5 344 6 HOH HOH . G 4 HOH A 6 345 7 HOH HOH . G 4 HOH A 7 346 8 HOH HOH . G 4 HOH A 8 347 10 HOH HOH . G 4 HOH A 9 348 11 HOH HOH . G 4 HOH A 10 349 12 HOH HOH . G 4 HOH A 11 350 13 HOH HOH . G 4 HOH A 12 351 14 HOH HOH . G 4 HOH A 13 352 15 HOH HOH . G 4 HOH A 14 353 16 HOH HOH . G 4 HOH A 15 354 17 HOH HOH . G 4 HOH A 16 355 18 HOH HOH . G 4 HOH A 17 356 19 HOH HOH . G 4 HOH A 18 357 20 HOH HOH . G 4 HOH A 19 358 21 HOH HOH . G 4 HOH A 20 359 22 HOH HOH . G 4 HOH A 21 360 23 HOH HOH . G 4 HOH A 22 361 24 HOH HOH . G 4 HOH A 23 362 26 HOH HOH . G 4 HOH A 24 363 27 HOH HOH . G 4 HOH A 25 364 28 HOH HOH . G 4 HOH A 26 365 29 HOH HOH . G 4 HOH A 27 366 30 HOH HOH . G 4 HOH A 28 367 31 HOH HOH . G 4 HOH A 29 368 32 HOH HOH . G 4 HOH A 30 369 33 HOH HOH . G 4 HOH A 31 370 35 HOH HOH . G 4 HOH A 32 371 36 HOH HOH . G 4 HOH A 33 372 37 HOH HOH . G 4 HOH A 34 373 38 HOH HOH . G 4 HOH A 35 374 39 HOH HOH . G 4 HOH A 36 375 40 HOH HOH . G 4 HOH A 37 376 41 HOH HOH . G 4 HOH A 38 377 42 HOH HOH . G 4 HOH A 39 378 43 HOH HOH . G 4 HOH A 40 379 44 HOH HOH . G 4 HOH A 41 380 45 HOH HOH . G 4 HOH A 42 381 46 HOH HOH . G 4 HOH A 43 382 47 HOH HOH . G 4 HOH A 44 383 53 HOH HOH . G 4 HOH A 45 384 56 HOH HOH . G 4 HOH A 46 385 58 HOH HOH . G 4 HOH A 47 386 68 HOH HOH . G 4 HOH A 48 387 69 HOH HOH . G 4 HOH A 49 388 79 HOH HOH . G 4 HOH A 50 389 80 HOH HOH . G 4 HOH A 51 390 100 HOH HOH . G 4 HOH A 52 391 101 HOH HOH . G 4 HOH A 53 392 102 HOH HOH . G 4 HOH A 54 393 103 HOH HOH . G 4 HOH A 55 394 106 HOH HOH . G 4 HOH A 56 395 107 HOH HOH . G 4 HOH A 57 396 108 HOH HOH . G 4 HOH A 58 397 112 HOH HOH . G 4 HOH A 59 398 126 HOH HOH . G 4 HOH A 60 399 128 HOH HOH . G 4 HOH A 61 400 130 HOH HOH . G 4 HOH A 62 401 131 HOH HOH . G 4 HOH A 63 402 132 HOH HOH . G 4 HOH A 64 403 133 HOH HOH . G 4 HOH A 65 404 134 HOH HOH . G 4 HOH A 66 405 137 HOH HOH . G 4 HOH A 67 406 138 HOH HOH . G 4 HOH A 68 407 142 HOH HOH . G 4 HOH A 69 408 146 HOH HOH . G 4 HOH A 70 409 151 HOH HOH . G 4 HOH A 71 410 152 HOH HOH . G 4 HOH A 72 411 154 HOH HOH . G 4 HOH A 73 412 161 HOH HOH . G 4 HOH A 74 413 163 HOH HOH . G 4 HOH A 75 414 164 HOH HOH . G 4 HOH A 76 415 165 HOH HOH . G 4 HOH A 77 416 167 HOH HOH . G 4 HOH A 78 417 168 HOH HOH . G 4 HOH A 79 418 169 HOH HOH . G 4 HOH A 80 419 170 HOH HOH . G 4 HOH A 81 420 171 HOH HOH . G 4 HOH A 82 421 172 HOH HOH . G 4 HOH A 83 422 173 HOH HOH . G 4 HOH A 84 423 174 HOH HOH . G 4 HOH A 85 424 175 HOH HOH . G 4 HOH A 86 425 176 HOH HOH . G 4 HOH A 87 426 177 HOH HOH . G 4 HOH A 88 427 178 HOH HOH . H 4 HOH B 1 340 3 HOH HOH . H 4 HOH B 2 341 9 HOH HOH . H 4 HOH B 3 342 25 HOH HOH . H 4 HOH B 4 343 34 HOH HOH . H 4 HOH B 5 344 48 HOH HOH . H 4 HOH B 6 345 49 HOH HOH . H 4 HOH B 7 346 50 HOH HOH . H 4 HOH B 8 347 51 HOH HOH . H 4 HOH B 9 348 52 HOH HOH . H 4 HOH B 10 349 54 HOH HOH . H 4 HOH B 11 350 55 HOH HOH . H 4 HOH B 12 351 57 HOH HOH . H 4 HOH B 13 352 59 HOH HOH . H 4 HOH B 14 353 60 HOH HOH . H 4 HOH B 15 354 61 HOH HOH . H 4 HOH B 16 355 62 HOH HOH . H 4 HOH B 17 356 63 HOH HOH . H 4 HOH B 18 357 64 HOH HOH . H 4 HOH B 19 358 65 HOH HOH . H 4 HOH B 20 359 66 HOH HOH . H 4 HOH B 21 360 67 HOH HOH . H 4 HOH B 22 361 70 HOH HOH . H 4 HOH B 23 362 71 HOH HOH . H 4 HOH B 24 363 72 HOH HOH . H 4 HOH B 25 364 73 HOH HOH . H 4 HOH B 26 365 74 HOH HOH . H 4 HOH B 27 366 75 HOH HOH . H 4 HOH B 28 367 76 HOH HOH . H 4 HOH B 29 368 77 HOH HOH . H 4 HOH B 30 369 78 HOH HOH . H 4 HOH B 31 370 81 HOH HOH . H 4 HOH B 32 371 82 HOH HOH . H 4 HOH B 33 372 83 HOH HOH . H 4 HOH B 34 373 84 HOH HOH . H 4 HOH B 35 374 85 HOH HOH . H 4 HOH B 36 375 86 HOH HOH . H 4 HOH B 37 376 87 HOH HOH . H 4 HOH B 38 377 88 HOH HOH . H 4 HOH B 39 378 89 HOH HOH . H 4 HOH B 40 379 90 HOH HOH . H 4 HOH B 41 380 91 HOH HOH . H 4 HOH B 42 381 92 HOH HOH . H 4 HOH B 43 382 93 HOH HOH . H 4 HOH B 44 383 94 HOH HOH . H 4 HOH B 45 384 95 HOH HOH . H 4 HOH B 46 385 96 HOH HOH . H 4 HOH B 47 386 97 HOH HOH . H 4 HOH B 48 387 98 HOH HOH . H 4 HOH B 49 388 99 HOH HOH . H 4 HOH B 50 389 104 HOH HOH . H 4 HOH B 51 390 105 HOH HOH . H 4 HOH B 52 391 109 HOH HOH . H 4 HOH B 53 392 110 HOH HOH . H 4 HOH B 54 393 111 HOH HOH . H 4 HOH B 55 394 113 HOH HOH . H 4 HOH B 56 395 114 HOH HOH . H 4 HOH B 57 396 115 HOH HOH . H 4 HOH B 58 397 116 HOH HOH . H 4 HOH B 59 398 117 HOH HOH . H 4 HOH B 60 399 118 HOH HOH . H 4 HOH B 61 400 119 HOH HOH . H 4 HOH B 62 401 120 HOH HOH . H 4 HOH B 63 402 121 HOH HOH . H 4 HOH B 64 403 122 HOH HOH . H 4 HOH B 65 404 123 HOH HOH . H 4 HOH B 66 405 124 HOH HOH . H 4 HOH B 67 406 125 HOH HOH . H 4 HOH B 68 407 127 HOH HOH . H 4 HOH B 69 408 129 HOH HOH . H 4 HOH B 70 409 135 HOH HOH . H 4 HOH B 71 410 136 HOH HOH . H 4 HOH B 72 411 139 HOH HOH . H 4 HOH B 73 412 140 HOH HOH . H 4 HOH B 74 413 141 HOH HOH . H 4 HOH B 75 414 143 HOH HOH . H 4 HOH B 76 415 144 HOH HOH . H 4 HOH B 77 416 145 HOH HOH . H 4 HOH B 78 417 147 HOH HOH . H 4 HOH B 79 418 148 HOH HOH . H 4 HOH B 80 419 149 HOH HOH . H 4 HOH B 81 420 150 HOH HOH . H 4 HOH B 82 421 153 HOH HOH . H 4 HOH B 83 422 155 HOH HOH . H 4 HOH B 84 423 156 HOH HOH . H 4 HOH B 85 424 157 HOH HOH . H 4 HOH B 86 425 158 HOH HOH . H 4 HOH B 87 426 159 HOH HOH . H 4 HOH B 88 427 160 HOH HOH . H 4 HOH B 89 428 162 HOH HOH . H 4 HOH B 90 429 166 HOH HOH . H 4 HOH B 91 430 179 HOH HOH . H 4 HOH B 92 431 180 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 P AMP . . . F 3 26.414 91.11 52.527 1 18.61 ? P AMP 339 B 1 HETATM 2 O O1P AMP . . . F 3 26.168 90.544 53.888 1 26.2 ? O1P AMP 339 B 1 HETATM 3 O O2P AMP . . . F 3 26.528 90.009 51.494 1 17.86 ? O2P AMP 339 B 1 HETATM 4 O O3P AMP . . . F 3 25.224 91.918 52.199 1 17.72 ? O3P AMP 339 B 1 HETATM 5 O O5' AMP . . . F 3 27.773 91.859 52.634 1 14.1 ? O5' AMP 339 B 1 HETATM 6 C C5' AMP . . . F 3 27.574 93.087 53.382 1 19.64 ? C5' AMP 339 B 1 HETATM 7 C C4' AMP . . . F 3 28.608 94.031 53.082 1 17.86 ? C4' AMP 339 B 1 HETATM 8 O O4' AMP . . . F 3 29.886 93.361 52.972 1 21.07 ? O4' AMP 339 B 1 HETATM 9 C C3' AMP . . . F 3 28.388 94.743 51.761 1 20.91 ? C3' AMP 339 B 1 HETATM 10 O O3' AMP . . . F 3 27.51 95.847 51.824 1 24.96 ? O3' AMP 339 B 1 HETATM 11 C C2' AMP . . . F 3 29.826 95.144 51.449 1 22.75 ? C2' AMP 339 B 1 HETATM 12 O O2' AMP . . . F 3 30.198 96.42 51.918 1 26.51 ? O2' AMP 339 B 1 HETATM 13 C C1' AMP . . . F 3 30.675 93.954 51.994 1 23.81 ? C1' AMP 339 B 1 HETATM 14 N N9 AMP . . . F 3 30.849 92.951 50.878 1 28.14 ? N9 AMP 339 B 1 HETATM 15 C C8 AMP . . . F 3 30.119 91.82 50.64 1 31.38 ? C8 AMP 339 B 1 HETATM 16 N N7 AMP . . . F 3 30.501 91.257 49.445 1 35.44 ? N7 AMP 339 B 1 HETATM 17 C C5 AMP . . . F 3 31.461 92.105 48.934 1 34.01 ? C5 AMP 339 B 1 HETATM 18 C C6 AMP . . . F 3 32.197 92.057 47.693 1 34.74 ? C6 AMP 339 B 1 HETATM 19 N N6 AMP . . . F 3 32.064 91.107 46.781 1 31.67 ? N6 AMP 339 B 1 HETATM 20 N N1 AMP . . . F 3 33.102 93.096 47.48 1 35.07 ? N1 AMP 339 B 1 HETATM 21 C C2 AMP . . . F 3 33.273 94.099 48.411 1 32.64 ? C2 AMP 339 B 1 HETATM 22 N N3 AMP . . . F 3 32.569 94.13 49.58 1 33.55 ? N3 AMP 339 B 1 HETATM 23 C C4 AMP . . . F 3 31.667 93.14 49.824 1 29.98 ? C4 AMP 339 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #