data_9CDF # _model_server_result.job_id wj_fRQd9msutI5nPUlY4aA _model_server_result.datetime_utc '2025-08-20 22:44:55' _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 9cdf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1102}' # _entry.id 9CDF # _exptl.entry_id 9CDF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 506.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER' _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 9CDF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9CDF _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 3 D N N ? 3 G N 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 A SG CYS 499 A CYS 499 1_555 C ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? metalc ? metalc2 A SG CYS 502 A CYS 502 1_555 C ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc3 A SG CYS 525 A CYS 525 1_555 C ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc4 D O3G ANP . A ANP 1102 1_555 E MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc5 B SG CYS 499 B CYS 499 1_555 F ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.959 ? metalc ? metalc6 B SG CYS 502 B CYS 502 1_555 F ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? metalc ? metalc7 B SG CYS 525 B CYS 525 1_555 F ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc8 G O2G ANP . B ANP 1102 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc9 G O3G ANP . B ANP 1102 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.871 ? metalc ? metalc10 G O1B ANP . B ANP 1102 1_555 H MG MG . B MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? # _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 9CDF _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 C 2 ZN A 1 1101 701 ZN ZN . D 3 ANP A 1 1102 702 ANP ANP . E 4 MG A 1 1103 703 MG MG . F 2 ZN B 1 1101 701 ZN ZN . G 3 ANP B 1 1102 702 ANP ANP . H 4 MG B 1 1103 703 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 . . . G 3 108.864 115.809 93.986 1 61.28 ? PG ANP 1102 B 1 HETATM 2 O O1G ANP . . . G 3 108.514 114.325 93.987 1 61.28 ? O1G ANP 1102 B 1 HETATM 3 O O2G ANP . . . G 3 107.658 116.737 93.833 1 61.28 ? O2G ANP 1102 B 1 HETATM 4 O O3G ANP . . . G 3 109.855 116.239 95.063 1 61.28 ? O3G ANP 1102 B 1 HETATM 5 P PB ANP . . . G 3 109.464 117.047 91.245 1 61.28 ? PB ANP 1102 B 1 HETATM 6 O O1B ANP . . . G 3 108.752 118.274 91.728 1 61.28 ? O1B ANP 1102 B 1 HETATM 7 O O2B ANP . . . G 3 110.543 117.141 90.2 1 61.28 ? O2B ANP 1102 B 1 HETATM 8 N N3B ANP . . . G 3 109.844 116.034 92.507 1 61.28 ? N3B ANP 1102 B 1 HETATM 9 P PA ANP . . . G 3 106.706 116.678 90.362 1 61.28 ? PA ANP 1102 B 1 HETATM 10 O O1A ANP . . . G 3 106.137 117.207 91.634 1 61.28 ? O1A ANP 1102 B 1 HETATM 11 O O2A ANP . . . G 3 105.928 115.693 89.515 1 61.28 ? O2A ANP 1102 B 1 HETATM 12 O O3A ANP . . . G 3 108.207 116.142 90.559 1 61.28 ? O3A ANP 1102 B 1 HETATM 13 O O5' ANP . . . G 3 107.064 117.998 89.444 1 61.28 ? O5' ANP 1102 B 1 HETATM 14 C C5' ANP . . . G 3 107.881 117.877 88.306 1 61.28 ? C5' ANP 1102 B 1 HETATM 15 C C4' ANP . . . G 3 108.397 119.22 87.856 1 61.28 ? C4' ANP 1102 B 1 HETATM 16 O O4' ANP . . . G 3 107.327 120.005 87.339 1 61.28 ? O4' ANP 1102 B 1 HETATM 17 C C3' ANP . . . G 3 108.99 120.109 88.947 1 61.28 ? C3' ANP 1102 B 1 HETATM 18 O O3' ANP . . . G 3 110.24 119.712 89.39 1 61.28 ? O3' ANP 1102 B 1 HETATM 19 C C2' ANP . . . G 3 108.917 121.459 88.257 1 61.28 ? C2' ANP 1102 B 1 HETATM 20 O O2' ANP . . . G 3 109.895 121.527 87.262 1 61.28 ? O2' ANP 1102 B 1 HETATM 21 C C1' ANP . . . G 3 107.525 121.352 87.603 1 61.28 ? C1' ANP 1102 B 1 HETATM 22 N N9 ANP . . . G 3 106.432 121.827 88.446 1 61.28 ? N9 ANP 1102 B 1 HETATM 23 C C8 ANP . . . G 3 105.355 121.147 88.946 1 61.28 ? C8 ANP 1102 B 1 HETATM 24 N N7 ANP . . . G 3 104.56 121.898 89.657 1 61.28 ? N7 ANP 1102 B 1 HETATM 25 C C5 ANP . . . G 3 105.134 123.141 89.616 1 61.28 ? C5 ANP 1102 B 1 HETATM 26 C C6 ANP . . . G 3 104.803 124.389 90.169 1 61.28 ? C6 ANP 1102 B 1 HETATM 27 N N6 ANP . . . G 3 103.72 124.592 90.927 1 61.28 ? N6 ANP 1102 B 1 HETATM 28 N N1 ANP . . . G 3 105.613 125.418 89.921 1 61.28 ? N1 ANP 1102 B 1 HETATM 29 C C2 ANP . . . G 3 106.692 125.225 89.172 1 61.28 ? C2 ANP 1102 B 1 HETATM 30 N N3 ANP . . . G 3 107.112 124.118 88.606 1 61.28 ? N3 ANP 1102 B 1 HETATM 31 C C4 ANP . . . G 3 106.296 123.108 88.866 1 61.28 ? C4 ANP 1102 B 1 HETATM 32 H HNB1 ANP . . . G 3 110.232 115.281 92.239 1 61.28 ? HNB1 ANP 1102 B 1 HETATM 33 H "H5'1" ANP . . . G 3 108.649 117.302 88.439 1 61.28 ? "H5'1" ANP 1102 B 1 HETATM 34 H "H5'2" ANP . . . G 3 107.358 117.479 87.596 1 61.28 ? "H5'2" ANP 1102 B 1 HETATM 35 H H4' ANP . . . G 3 109.052 119.062 87.158 1 61.28 ? H4' ANP 1102 B 1 HETATM 36 H H3' ANP . . . G 3 108.36 120.158 89.683 1 61.28 ? H3' ANP 1102 B 1 HETATM 37 H H2' ANP . . . G 3 108.975 122.2 88.879 1 61.28 ? H2' ANP 1102 B 1 HETATM 38 H HO2' ANP . . . G 3 109.963 122.333 87.002 1 61.28 ? HO2' ANP 1102 B 1 HETATM 39 H H1' ANP . . . G 3 107.481 121.866 86.782 1 61.28 ? H1' ANP 1102 B 1 HETATM 40 H H8 ANP . . . G 3 105.229 120.239 88.788 1 61.28 ? H8 ANP 1102 B 1 HETATM 41 H HN61 ANP . . . G 3 103.031 124.029 90.891 1 61.28 ? HN61 ANP 1102 B 1 HETATM 42 H HN62 ANP . . . G 3 103.666 125.291 91.476 1 61.28 ? HN62 ANP 1102 B 1 HETATM 43 H H2 ANP . . . G 3 107.222 125.972 89.03 1 61.28 ? H2 ANP 1102 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 43 #