data_5YJ9 # _model_server_result.job_id BvbbWfgMA7T2omFjpwMHGg _model_server_result.datetime_utc '2024-11-25 10:38:09' _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 5yj9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5YJ9 # _exptl.entry_id 5YJ9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.82 _cell.angle_gamma 90 _cell.entry_id 5YJ9 _cell.length_a 138.028 _cell.length_b 59.79 _cell.length_c 50.822 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YJ9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 x,y,z _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 A SG CYS 369 D CYS 516 1_555 A SG CYS 401 D CYS 548 2_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A C LYS 49 D LYS 196 1_555 A N MSE 50 D MSE 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 A C MSE 50 D MSE 197 1_555 A N MSE 51 D MSE 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C MSE 51 D MSE 198 1_555 A N PHE 52 D PHE 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 A C SER 60 D SER 207 1_555 A N MSE 61 D MSE 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 A C MSE 61 D MSE 208 1_555 A N GLU 62 D GLU 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 A C ALA 66 D ALA 213 1_555 A N MSE 67 D MSE 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale7 A C MSE 67 D MSE 214 1_555 A N TYR 68 D TYR 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 A C ARG 75 D ARG 222 1_555 A N MSE 76 D MSE 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale9 A C MSE 76 D MSE 223 1_555 A N TYR 77 D TYR 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale10 A C MSE 141 D MSE 288 1_555 A N SER 142 D SER 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 A C LEU 146 D LEU 293 1_555 A N MSE 147 D MSE 294 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale12 A C MSE 147 D MSE 294 1_555 A N LYS 148 D LYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale13 A C HIS 180 D HIS 327 1_555 A N MSE 181 D MSE 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale14 A C MSE 181 D MSE 328 1_555 A N THR 182 D THR 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale15 A C GLU 232 D GLU 379 1_555 A N MSE 233 D MSE 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale16 A C MSE 233 D MSE 380 1_555 A N ASP 234 D ASP 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale17 A C LEU 241 D LEU 388 1_555 A N MSE 242 D MSE 389 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale18 A C MSE 242 D MSE 389 1_555 A N ALA 243 D ALA 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OE2 GLU 70 D GLU 217 1_555 C MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.886 ? metalc ? metalc2 A OD1 ASN 195 D ASN 342 1_555 D MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc3 A OD1 ASP 212 D ASP 359 1_555 C MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc4 A OD2 ASP 212 D ASP 359 1_555 C MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc5 A OD2 ASP 212 D ASP 359 1_555 D MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc6 B O2B ANP . D ANP 601 1_555 C MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc7 B O1G ANP . D ANP 601 1_555 D MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc8 B O1A ANP . D ANP 601 1_555 D MG MG . D MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc9 C MG MG . D MG 602 1_555 E O HOH . D HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc10 D MG MG . D MG 603 1_555 E O HOH . D HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc11 D MG MG . D MG 603 1_555 E O HOH . D HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? # _chem_comp.formula 'C10 H17 N6 O12 P3' _chem_comp.formula_weight 506.196 _chem_comp.id ANP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 PG O1G ANP doub 13 n n PG O2G ANP sing 14 n n PG O3G ANP sing 15 n n PG N3B ANP sing 16 n n O2G HOG2 ANP sing 17 n n O3G HOG3 ANP sing 18 n n PB O1B ANP doub 19 n n PB O2B ANP sing 20 n n PB N3B ANP sing 21 n n PB O3A ANP sing 22 n n O2B HOB2 ANP sing 23 n n N3B HNB1 ANP sing 24 n n PA O1A ANP doub 25 n n PA O2A ANP sing 26 n n PA O3A ANP sing 27 n n PA O5' ANP sing 28 n n O2A HOA2 ANP sing 29 n n O5' C5' ANP sing 30 n n C5' C4' ANP sing 31 n n C5' "H5'1" ANP sing 32 n n C5' "H5'2" ANP sing 33 n n C4' O4' ANP sing 34 n n C4' C3' ANP sing 35 n n C4' H4' ANP sing 36 n n O4' C1' ANP sing 37 n n C3' O3' ANP sing 38 n n C3' C2' ANP sing 39 n n C3' H3' ANP sing 40 n n O3' HO3' ANP sing 41 n n C2' O2' ANP sing 42 n n C2' C1' ANP sing 43 n n C2' H2' ANP sing 44 n n O2' HO2' ANP sing 45 n n C1' N9 ANP sing 46 n n C1' H1' ANP sing 47 n n N9 C8 ANP sing 48 n y N9 C4 ANP sing 49 n y C8 N7 ANP doub 50 n y C8 H8 ANP sing 51 n n N7 C5 ANP sing 52 n y C5 C6 ANP sing 53 n y C5 C4 ANP doub 54 n y C6 N6 ANP sing 55 n n C6 N1 ANP doub 56 n y N6 HN61 ANP sing 57 n n N6 HN62 ANP sing 58 n n N1 C2 ANP sing 59 n y C2 N3 ANP doub 60 n y C2 H2 ANP sing 61 n n N3 C4 ANP sing 62 n y # _atom_sites.entry_id 5YJ9 _atom_sites.fract_transf_matrix[1][1] 0.007245 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001516 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016725 _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] 0.020103 _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 B 2 ANP D 1 601 401 ANP ANP . C 3 MG D 1 602 1 MG MG . D 3 MG D 1 603 2 MG MG . E 4 HOH D 1 701 2 HOH HOH . E 4 HOH D 2 702 1 HOH HOH . E 4 HOH D 3 703 3 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 PG ANP . . . B 2 38.483 58.025 12.703 1 98.83 ? PG ANP 601 D 1 HETATM 2 O O1G ANP . . . B 2 39.217 57.724 11.335 1 144.19 ? O1G ANP 601 D 1 HETATM 3 O O2G ANP . . . B 2 37.275 57.026 12.876 1 135.63 ? O2G ANP 601 D 1 HETATM 4 O O3G ANP . . . B 2 37.961 59.428 12.686 1 102.51 ? O3G ANP 601 D 1 HETATM 5 P PB ANP . . . B 2 40.845 58.899 13.902 1 69.48 ? PB ANP 601 D 1 HETATM 6 O O1B ANP . . . B 2 40.353 60.291 14.39 1 82.64 ? O1B ANP 601 D 1 HETATM 7 O O2B ANP . . . B 2 41.97 58.433 14.768 1 69.34 ? O2B ANP 601 D 1 HETATM 8 N N3B ANP . . . B 2 39.57 57.811 13.986 1 75.34 ? N3B ANP 601 D 1 HETATM 9 P PA ANP . . . B 2 42.589 58.257 11.856 1 73.73 ? PA ANP 601 D 1 HETATM 10 O O1A ANP . . . B 2 42.181 56.797 11.645 1 71.5 ? O1A ANP 601 D 1 HETATM 11 O O2A ANP . . . B 2 43.809 58.469 12.669 1 73.39 1 O2A ANP 601 D 1 HETATM 12 O O3A ANP . . . B 2 41.338 59.047 12.434 1 149.6 ? O3A ANP 601 D 1 HETATM 13 O O5' ANP . . . B 2 42.791 58.973 10.471 1 61.2 ? O5' ANP 601 D 1 HETATM 14 C C5' ANP . . . B 2 41.706 59.747 9.928 1 62.83 ? C5' ANP 601 D 1 HETATM 15 C C4' ANP . . . B 2 41.855 59.794 8.432 1 62.07 ? C4' ANP 601 D 1 HETATM 16 O O4' ANP . . . B 2 42.862 60.768 8.081 1 62.94 ? O4' ANP 601 D 1 HETATM 17 C C3' ANP . . . B 2 42.322 58.496 7.784 1 59.78 ? C3' ANP 601 D 1 HETATM 18 O O3' ANP . . . B 2 41.23 57.621 7.524 1 60.22 ? O3' ANP 601 D 1 HETATM 19 C C2' ANP . . . B 2 42.981 59.003 6.503 1 59 ? C2' ANP 601 D 1 HETATM 20 O O2' ANP . . . B 2 42.007 59.269 5.499 1 60.17 ? O2' ANP 601 D 1 HETATM 21 C C1' ANP . . . B 2 43.638 60.298 6.994 1 61.3 ? C1' ANP 601 D 1 HETATM 22 N N9 ANP . . . B 2 45.012 60.12 7.459 1 61.69 ? N9 ANP 601 D 1 HETATM 23 C C8 ANP . . . B 2 45.426 59.818 8.728 1 61.11 ? C8 ANP 601 D 1 HETATM 24 N N7 ANP . . . B 2 46.729 59.711 8.85 1 59.98 ? N7 ANP 601 D 1 HETATM 25 C C5 ANP . . . B 2 47.202 59.957 7.573 1 60.89 ? C5 ANP 601 D 1 HETATM 26 C C6 ANP . . . B 2 48.501 59.993 7.031 1 61.43 ? C6 ANP 601 D 1 HETATM 27 N N6 ANP . . . B 2 49.609 59.77 7.743 1 60.61 ? N6 ANP 601 D 1 HETATM 28 N N1 ANP . . . B 2 48.625 60.269 5.713 1 61.89 ? N1 ANP 601 D 1 HETATM 29 C C2 ANP . . . B 2 47.52 60.492 4.995 1 61.87 ? C2 ANP 601 D 1 HETATM 30 N N3 ANP . . . B 2 46.246 60.484 5.395 1 61.49 ? N3 ANP 601 D 1 HETATM 31 C C4 ANP . . . B 2 46.153 60.21 6.7 1 61.15 ? C4 ANP 601 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #