data_1RDY # _model_server_result.job_id gF-sXWn7f-ewDlXCiA_i6w _model_server_result.datetime_utc '2024-11-24 00:35:48' _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 1rdy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":339}' # _entry.id 1RDY # _exptl.entry_id 1RDY _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 1RDY _cell.length_a 61.2 _cell.length_b 166.75 _cell.length_c 79.84 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RDY _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 61.2 166.75 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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 112 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 112 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id F _struct_conn.ptnr2_label_atom_id O3P _struct_conn.ptnr2_label_comp_id AMP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id AMP _struct_conn.ptnr2_auth_seq_id 339 _struct_conn.ptnr2_symmetry 1_555 _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 1.864 _struct_conn.pdbx_value_order ? # _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 ? # _atom_sites.entry_id 1RDY _atom_sites.fract_transf_matrix[1][1] 0.01634 _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] 0.005997 _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] 0.012525 _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 3 HOH HOH . G 4 HOH A 4 343 4 HOH HOH . G 4 HOH A 5 344 5 HOH HOH . G 4 HOH A 6 345 6 HOH HOH . G 4 HOH A 7 346 7 HOH HOH . G 4 HOH A 8 347 8 HOH HOH . G 4 HOH A 9 348 10 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 20 HOH HOH . G 4 HOH A 18 357 21 HOH HOH . G 4 HOH A 19 358 22 HOH HOH . G 4 HOH A 20 359 23 HOH HOH . G 4 HOH A 21 360 24 HOH HOH . G 4 HOH A 22 361 25 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 79 HOH HOH . G 4 HOH A 45 384 100 HOH HOH . G 4 HOH A 46 385 106 HOH HOH . G 4 HOH A 47 386 107 HOH HOH . G 4 HOH A 48 387 109 HOH HOH . G 4 HOH A 49 388 111 HOH HOH . H 4 HOH B 1 340 9 HOH HOH . H 4 HOH B 2 341 11 HOH HOH . H 4 HOH B 3 342 19 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 53 HOH HOH . H 4 HOH B 11 350 54 HOH HOH . H 4 HOH B 12 351 55 HOH HOH . H 4 HOH B 13 352 56 HOH HOH . H 4 HOH B 14 353 57 HOH HOH . H 4 HOH B 15 354 58 HOH HOH . H 4 HOH B 16 355 59 HOH HOH . H 4 HOH B 17 356 60 HOH HOH . H 4 HOH B 18 357 61 HOH HOH . H 4 HOH B 19 358 62 HOH HOH . H 4 HOH B 20 359 63 HOH HOH . H 4 HOH B 21 360 64 HOH HOH . H 4 HOH B 22 361 65 HOH HOH . H 4 HOH B 23 362 66 HOH HOH . H 4 HOH B 24 363 67 HOH HOH . H 4 HOH B 25 364 68 HOH HOH . H 4 HOH B 26 365 69 HOH HOH . H 4 HOH B 27 366 70 HOH HOH . H 4 HOH B 28 367 71 HOH HOH . H 4 HOH B 29 368 72 HOH HOH . H 4 HOH B 30 369 73 HOH HOH . H 4 HOH B 31 370 74 HOH HOH . H 4 HOH B 32 371 75 HOH HOH . H 4 HOH B 33 372 76 HOH HOH . H 4 HOH B 34 373 77 HOH HOH . H 4 HOH B 35 374 78 HOH HOH . H 4 HOH B 36 375 80 HOH HOH . H 4 HOH B 37 376 81 HOH HOH . H 4 HOH B 38 377 82 HOH HOH . H 4 HOH B 39 378 83 HOH HOH . H 4 HOH B 40 379 84 HOH HOH . H 4 HOH B 41 380 85 HOH HOH . H 4 HOH B 42 381 86 HOH HOH . H 4 HOH B 43 382 87 HOH HOH . H 4 HOH B 44 383 88 HOH HOH . H 4 HOH B 45 384 89 HOH HOH . H 4 HOH B 46 385 90 HOH HOH . H 4 HOH B 47 386 91 HOH HOH . H 4 HOH B 48 387 92 HOH HOH . H 4 HOH B 49 388 93 HOH HOH . H 4 HOH B 50 389 94 HOH HOH . H 4 HOH B 51 390 95 HOH HOH . H 4 HOH B 52 391 96 HOH HOH . H 4 HOH B 53 392 97 HOH HOH . H 4 HOH B 54 393 98 HOH HOH . H 4 HOH B 55 394 99 HOH HOH . H 4 HOH B 56 395 101 HOH HOH . H 4 HOH B 57 396 102 HOH HOH . H 4 HOH B 58 397 103 HOH HOH . H 4 HOH B 59 398 104 HOH HOH . H 4 HOH B 60 399 105 HOH HOH . H 4 HOH B 61 400 108 HOH HOH . H 4 HOH B 62 401 115 HOH HOH . H 4 HOH B 63 402 116 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 . . . D 3 36.111 90.773 -13.392 0.94 7.57 ? P AMP 339 A 1 HETATM 2 O O1P AMP . . . D 3 37.487 90.628 -12.886 0.94 13.71 ? O1P AMP 339 A 1 HETATM 3 O O2P AMP . . . D 3 36.061 89.953 -14.646 0.94 11.13 ? O2P AMP 339 A 1 HETATM 4 O O3P AMP . . . D 3 35.249 89.956 -12.383 0.94 18.39 ? O3P AMP 339 A 1 HETATM 5 O O5' AMP . . . D 3 35.632 92.287 -13.616 0.94 16.83 ? O5' AMP 339 A 1 HETATM 6 C C5' AMP . . . D 3 34.29 92.521 -14.17 0.94 15.68 ? C5' AMP 339 A 1 HETATM 7 C C4' AMP . . . D 3 33.811 93.839 -13.828 0.94 19.62 ? C4' AMP 339 A 1 HETATM 8 O O4' AMP . . . D 3 32.438 93.696 -13.438 0.94 29.17 ? O4' AMP 339 A 1 HETATM 9 C C3' AMP . . . D 3 34.394 94.461 -12.556 0.94 19.95 ? C3' AMP 339 A 1 HETATM 10 O O3' AMP . . . D 3 35.59 95.175 -12.75 0.94 26.53 ? O3' AMP 339 A 1 HETATM 11 C C2' AMP . . . D 3 33.284 95.455 -12.184 0.94 27.87 ? C2' AMP 339 A 1 HETATM 12 O O2' AMP . . . D 3 33.344 96.695 -12.871 0.94 37.14 ? O2' AMP 339 A 1 HETATM 13 C C1' AMP . . . D 3 31.992 94.716 -12.564 0.94 27.83 ? C1' AMP 339 A 1 HETATM 14 N N9 AMP . . . D 3 31.3 94.228 -11.3 0.94 26.82 ? N9 AMP 339 A 1 HETATM 15 C C8 AMP . . . D 3 30.25 94.808 -10.605 0.94 30.94 ? C8 AMP 339 A 1 HETATM 16 N N7 AMP . . . D 3 29.863 94.039 -9.522 0.94 21.4 ? N7 AMP 339 A 1 HETATM 17 C C5 AMP . . . D 3 30.72 92.976 -9.584 0.94 25.37 ? C5 AMP 339 A 1 HETATM 18 C C6 AMP . . . D 3 30.753 91.815 -8.779 0.94 26.31 ? C6 AMP 339 A 1 HETATM 19 N N6 AMP . . . D 3 30.045 91.657 -7.685 0.94 30.84 ? N6 AMP 339 A 1 HETATM 20 N N1 AMP . . . D 3 31.682 90.865 -9.194 0.94 34.57 ? N1 AMP 339 A 1 HETATM 21 C C2 AMP . . . D 3 32.445 90.984 -10.33 0.94 26.16 ? C2 AMP 339 A 1 HETATM 22 N N3 AMP . . . D 3 32.435 92.118 -11.067 0.94 12.98 ? N3 AMP 339 A 1 HETATM 23 C C4 AMP . . . D 3 31.519 93.045 -10.732 0.94 22.83 ? C4 AMP 339 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 23 #