data_8XOM # _model_server_result.job_id fRCX756rw-efB4BUBgQeBw _model_server_result.datetime_utc '2025-01-03 04:03:12' _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 8xom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1401}' # _entry.id 8XOM # _exptl.entry_id 8XOM _exptl.method 'ELECTRON MICROSCOPY' # _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 90 _cell.angle_gamma 90 _cell.entry_id 8XOM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XOM _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,I,J,K,L,M,N,O,P,Q,R,S _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 metalc ? metalc1 B O2B ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.967 ? metalc ? metalc2 B O1A ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc3 B O2A ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc4 B O3A ANP . A ANP 1401 1_555 S MG MG . A MG 1418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? # _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 8XOM _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 B 2 ANP A 1 1401 1401 ANP ANP . C 3 MTX A 1 1402 1501 MTX MTX . D 4 DU0 A 1 1403 1 DU0 DU0 . E 4 DU0 A 1 1404 2 DU0 DU0 . F 4 DU0 A 1 1405 3 DU0 DU0 . G 4 DU0 A 1 1406 4 DU0 DU0 . H 4 DU0 A 1 1407 5 DU0 DU0 . I 4 DU0 A 1 1408 6 DU0 DU0 . J 4 DU0 A 1 1409 7 DU0 DU0 . K 4 DU0 A 1 1410 8 DU0 DU0 . L 4 DU0 A 1 1411 9 DU0 DU0 . M 4 DU0 A 1 1412 10 DU0 DU0 . N 4 DU0 A 1 1413 11 DU0 DU0 . O 4 DU0 A 1 1414 12 DU0 DU0 . P 4 DU0 A 1 1415 13 DU0 DU0 . Q 4 DU0 A 1 1416 14 DU0 DU0 . R 5 PLM A 1 1417 16 PLM PLM . S 6 MG A 1 1418 1 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 PG ANP . . . B 2 105.173 95.658 50.493 1 298.21 ? PG ANP 1401 A 1 HETATM 2 O O1G ANP . . . B 2 105.075 95.922 48.991 1 293.93 ? O1G ANP 1401 A 1 HETATM 3 O O2G ANP . . . B 2 106.353 94.779 50.897 1 285.91 ? O2G ANP 1401 A 1 HETATM 4 O O3G ANP . . . B 2 105.028 96.899 51.375 1 290.94 ? O3G ANP 1401 A 1 HETATM 5 P PB ANP . . . B 2 103.139 94.438 52.456 1 275.28 ? PB ANP 1401 A 1 HETATM 6 O O1B ANP . . . B 2 103.2 95.688 53.281 1 272.8 ? O1B ANP 1401 A 1 HETATM 7 O O2B ANP . . . B 2 103.65 93.14 53.024 1 270.2 ? O2B ANP 1401 A 1 HETATM 8 N N3B ANP . . . B 2 103.697 94.724 50.911 1 283.22 ? N3B ANP 1401 A 1 HETATM 9 P PA ANP . . . B 2 100.571 93.493 53.391 1 266 ? PA ANP 1401 A 1 HETATM 10 O O1A ANP . . . B 2 100.043 92.158 52.986 1 267.56 ? O1A ANP 1401 A 1 HETATM 11 O O2A ANP . . . B 2 101.266 93.662 54.728 1 262.22 ? O2A ANP 1401 A 1 HETATM 12 O O3A ANP . . . B 2 101.473 94.189 52.253 1 268.79 ? O3A ANP 1401 A 1 HETATM 13 O O5' ANP . . . B 2 99.271 94.511 53.344 1 263.29 ? O5' ANP 1401 A 1 HETATM 14 C C5' ANP . . . B 2 98.694 94.955 54.549 1 261.01 ? C5' ANP 1401 A 1 HETATM 15 C C4' ANP . . . B 2 97.362 94.292 54.836 1 259.35 ? C4' ANP 1401 A 1 HETATM 16 O O4' ANP . . . B 2 97.53 93.026 55.483 1 257.33 ? O4' ANP 1401 A 1 HETATM 17 C C3' ANP . . . B 2 96.417 95.065 55.761 1 255 ? C3' ANP 1401 A 1 HETATM 18 O O3' ANP . . . B 2 95.776 96.137 55.161 1 254.26 ? O3' ANP 1401 A 1 HETATM 19 C C2' ANP . . . B 2 95.511 93.947 56.244 1 253.1 ? C2' ANP 1401 A 1 HETATM 20 O O2' ANP . . . B 2 94.655 93.561 55.208 1 256.65 ? O2' ANP 1401 A 1 HETATM 21 C C1' ANP . . . B 2 96.586 92.876 56.497 1 252.69 ? C1' ANP 1401 A 1 HETATM 22 N N9 ANP . . . B 2 97.263 93.059 57.775 1 250.03 ? N9 ANP 1401 A 1 HETATM 23 C C8 ANP . . . B 2 98.596 93.279 57.989 1 251.43 ? C8 ANP 1401 A 1 HETATM 24 N N7 ANP . . . B 2 98.904 93.403 59.246 1 248.03 ? N7 ANP 1401 A 1 HETATM 25 C C5 ANP . . . B 2 97.712 93.258 59.902 1 244.95 ? C5 ANP 1401 A 1 HETATM 26 C C6 ANP . . . B 2 97.362 93.286 61.26 1 240.26 ? C6 ANP 1401 A 1 HETATM 27 N N6 ANP . . . B 2 98.261 93.485 62.233 1 235.91 ? N6 ANP 1401 A 1 HETATM 28 N N1 ANP . . . B 2 96.079 93.107 61.582 1 240.78 ? N1 ANP 1401 A 1 HETATM 29 C C2 ANP . . . B 2 95.189 92.913 60.613 1 242.59 ? C2 ANP 1401 A 1 HETATM 30 N N3 ANP . . . B 2 95.394 92.861 59.31 1 244.55 ? N3 ANP 1401 A 1 HETATM 31 C C4 ANP . . . B 2 96.677 93.043 59.005 1 246.8 ? C4 ANP 1401 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #