data_5KIY # _model_server_result.job_id cL4Onc7u09Z2YgFeCPr3GA _model_server_result.datetime_utc '2025-02-18 17:01:15' _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 5kiy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":800}' # _entry.id 5KIY # _exptl.entry_id 5KIY _exptl.method 'X-RAY DIFFRACTION' # _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 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 120 _cell.entry_id 5KIY _cell.length_a 144.998 _cell.length_b 144.998 _cell.length_c 119.817 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KIY _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 6 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_555 y,-x+y,z 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 0 6 'crystal symmetry operation' 6_555 x-y,x,z 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 A OG1 THR 252 A THR 252 1_555 D MG MG . A MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc2 C O3G ANP . A ANP 800 1_555 D MG MG . A MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc3 C O2B ANP . A ANP 800 1_555 D MG MG . A MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc4 D MG MG . A MG 801 1_555 E O HOH . A HOH 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.861 ? metalc ? metalc5 D MG MG . A MG 801 1_555 E O HOH . A HOH 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc6 D MG MG . A MG 801 1_555 E O HOH . A HOH 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? # _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 5KIY _atom_sites.fract_transf_matrix[1][1] 0.006897 _atom_sites.fract_transf_matrix[1][2] 0.003982 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007964 _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] 0.008346 _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 3 ANP A 1 800 800 ANP ANP . D 4 MG A 1 801 801 MG MG . E 5 HOH A 1 901 14 HOH HOH . E 5 HOH A 2 902 6 HOH HOH . E 5 HOH A 3 903 19 HOH HOH . E 5 HOH A 4 904 802 HOH HOH . E 5 HOH A 5 905 804 HOH HOH . E 5 HOH A 6 906 16 HOH HOH . E 5 HOH A 7 907 4 HOH HOH . E 5 HOH A 8 908 17 HOH HOH . E 5 HOH A 9 909 15 HOH HOH . E 5 HOH A 10 910 11 HOH HOH . E 5 HOH A 11 911 10 HOH HOH . E 5 HOH A 12 912 3 HOH HOH . E 5 HOH A 13 913 9 HOH HOH . E 5 HOH A 14 914 803 HOH HOH . E 5 HOH A 15 915 7 HOH HOH . E 5 HOH A 16 916 8 HOH HOH . E 5 HOH A 17 917 13 HOH HOH . E 5 HOH A 18 918 2 HOH HOH . E 5 HOH A 19 919 1 HOH HOH . E 5 HOH A 20 920 12 HOH HOH . E 5 HOH A 21 921 18 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 . . . C 3 13.015 26.738 20.005 1 87.23 ? PG ANP 800 A 1 HETATM 2 O O1G ANP . . . C 3 11.896 26.89 19.051 1 93.26 ? O1G ANP 800 A 1 HETATM 3 O O2G ANP . . . C 3 14.048 25.758 19.585 1 90.68 ? O2G ANP 800 A 1 HETATM 4 O O3G ANP . . . C 3 12.502 26.77 21.402 1 99.82 ? O3G ANP 800 A 1 HETATM 5 P PB ANP . . . C 3 13.527 29.646 20.253 1 81.77 ? PB ANP 800 A 1 HETATM 6 O O1B ANP . . . C 3 12.633 29.996 19.12 1 83.79 ? O1B ANP 800 A 1 HETATM 7 O O2B ANP . . . C 3 12.99 29.69 21.649 1 93.47 ? O2B ANP 800 A 1 HETATM 8 N N3B ANP . . . C 3 14.107 28.074 20.012 1 87.79 ? N3B ANP 800 A 1 HETATM 9 P PA ANP . . . C 3 15.737 30.985 21.391 1 85.88 ? PA ANP 800 A 1 HETATM 10 O O1A ANP . . . C 3 15.244 32.255 22.01 1 91.38 ? O1A ANP 800 A 1 HETATM 11 O O2A ANP . . . C 3 15.968 29.741 22.14 1 83.41 ? O2A ANP 800 A 1 HETATM 12 O O3A ANP . . . C 3 14.753 30.652 20.15 1 93.67 ? O3A ANP 800 A 1 HETATM 13 O O5' ANP . . . C 3 17.01 31.309 20.53 1 78.58 ? O5' ANP 800 A 1 HETATM 14 C C5' ANP . . . C 3 18.323 30.962 20.837 1 81.89 ? C5' ANP 800 A 1 HETATM 15 C C4' ANP . . . C 3 19.233 32.184 20.753 1 81.68 ? C4' ANP 800 A 1 HETATM 16 O O4' ANP . . . C 3 19.511 32.645 19.414 1 81.9 ? O4' ANP 800 A 1 HETATM 17 C C3' ANP . . . C 3 18.661 33.386 21.461 1 90.61 ? C3' ANP 800 A 1 HETATM 18 O O3' ANP . . . C 3 18.781 33.255 22.867 1 94.53 ? O3' ANP 800 A 1 HETATM 19 C C2' ANP . . . C 3 19.531 34.446 20.848 1 90.67 ? C2' ANP 800 A 1 HETATM 20 O O2' ANP . . . C 3 20.807 34.3 21.414 1 91.8 ? O2' ANP 800 A 1 HETATM 21 C C1' ANP . . . C 3 19.583 34.062 19.377 1 81.84 ? C1' ANP 800 A 1 HETATM 22 N N9 ANP . . . C 3 18.384 34.613 18.741 1 79.63 ? N9 ANP 800 A 1 HETATM 23 C C8 ANP . . . C 3 17.31 33.93 18.336 1 83.22 ? C8 ANP 800 A 1 HETATM 24 N N7 ANP . . . C 3 16.365 34.752 17.848 1 84.61 ? N7 ANP 800 A 1 HETATM 25 C C5 ANP . . . C 3 16.83 35.978 17.972 1 80.79 ? C5 ANP 800 A 1 HETATM 26 C C6 ANP . . . C 3 16.315 37.296 17.651 1 82.16 ? C6 ANP 800 A 1 HETATM 27 N N6 ANP . . . C 3 15.102 37.384 17.106 1 90.9 ? N6 ANP 800 A 1 HETATM 28 N N1 ANP . . . C 3 17.081 38.36 17.931 1 86.09 ? N1 ANP 800 A 1 HETATM 29 C C2 ANP . . . C 3 18.298 38.216 18.502 1 84.59 ? C2 ANP 800 A 1 HETATM 30 N N3 ANP . . . C 3 18.835 37.029 18.83 1 88.78 ? N3 ANP 800 A 1 HETATM 31 C C4 ANP . . . C 3 18.149 35.895 18.577 1 82.08 ? C4 ANP 800 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #