data_3S8B # _model_server_result.job_id auCE4Wpz9OIcFtTVMMarzw _model_server_result.datetime_utc '2024-12-03 10:57:49' _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 3s8b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":890}' # _entry.id 3S8B # _exptl.entry_id 3S8B _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 90 _cell.entry_id 3S8B _cell.length_a 107.869 _cell.length_b 117.567 _cell.length_c 64.967 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S8B _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 _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # 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_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 117.567 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 C O3A ANP . A ANP 890 1_555 D MG MG . A MG 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc2 C O1G ANP . A ANP 890 1_555 D MG MG . A MG 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc3 C O2A ANP . A ANP 890 1_555 D MG MG . A MG 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.913 ? metalc ? metalc4 C O1B ANP . A ANP 890 1_555 D MG MG . A MG 891 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? # _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 3S8B _atom_sites.fract_transf_matrix[1][1] 0.009271 _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] 0.008506 _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] 0.015392 _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 CDP A 1 889 1 CDP CDP . C 3 ANP A 1 890 1 ANP ANP . D 4 MG A 1 891 1 MG MG . E 5 HOH A 1 892 1 HOH HOH . E 5 HOH A 2 893 2 HOH HOH . E 5 HOH A 3 894 4 HOH HOH . E 5 HOH A 4 895 5 HOH HOH . E 5 HOH A 5 896 6 HOH HOH . E 5 HOH A 6 897 9 HOH HOH . E 5 HOH A 7 898 10 HOH HOH . E 5 HOH A 8 899 11 HOH HOH . E 5 HOH A 9 900 12 HOH HOH . E 5 HOH A 10 901 13 HOH HOH . E 5 HOH A 11 902 14 HOH HOH . E 5 HOH A 12 903 16 HOH HOH . E 5 HOH A 13 904 18 HOH HOH . E 5 HOH A 14 905 19 HOH HOH . E 5 HOH A 15 906 20 HOH HOH . E 5 HOH A 16 907 21 HOH HOH . E 5 HOH A 17 908 22 HOH HOH . E 5 HOH A 18 909 23 HOH HOH . E 5 HOH A 19 910 25 HOH HOH . E 5 HOH A 20 911 26 HOH HOH . E 5 HOH A 21 912 27 HOH HOH . E 5 HOH A 22 913 35 HOH HOH . E 5 HOH A 23 914 37 HOH HOH . E 5 HOH A 24 915 39 HOH HOH . E 5 HOH A 25 916 42 HOH HOH . E 5 HOH A 26 917 43 HOH HOH . E 5 HOH A 27 918 45 HOH HOH . E 5 HOH A 28 919 47 HOH HOH . E 5 HOH A 29 920 48 HOH HOH . E 5 HOH A 30 921 49 HOH HOH . E 5 HOH A 31 922 51 HOH HOH . E 5 HOH A 32 923 52 HOH HOH . E 5 HOH A 33 924 57 HOH HOH . E 5 HOH A 34 925 58 HOH HOH . E 5 HOH A 35 926 59 HOH HOH . E 5 HOH A 36 927 60 HOH HOH . E 5 HOH A 37 928 61 HOH HOH . E 5 HOH A 38 929 63 HOH HOH . E 5 HOH A 39 930 65 HOH HOH . E 5 HOH A 40 931 67 HOH HOH . E 5 HOH A 41 932 68 HOH HOH . E 5 HOH A 42 933 71 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 -12.242 44.631 26.008 1 49.44 ? PG ANP 890 A 1 HETATM 2 O O1G ANP . . . C 3 -10.746 44.845 26.014 1 50.26 ? O1G ANP 890 A 1 HETATM 3 O O2G ANP . . . C 3 -12.708 43.614 24.992 1 48.96 ? O2G ANP 890 A 1 HETATM 4 O O3G ANP . . . C 3 -12.826 44.5 27.397 1 49.9 ? O3G ANP 890 A 1 HETATM 5 P PB ANP . . . C 3 -12.433 47.606 26.139 1 49.7 ? PB ANP 890 A 1 HETATM 6 O O1B ANP . . . C 3 -12.904 47.643 27.57 1 50.67 ? O1B ANP 890 A 1 HETATM 7 O O2B ANP . . . C 3 -12.853 48.68 25.172 1 51.06 ? O2B ANP 890 A 1 HETATM 8 N N3B ANP . . . C 3 -12.91 46.109 25.402 1 49.41 ? N3B ANP 890 A 1 HETATM 9 P PA ANP . . . C 3 -9.803 48.167 25.175 1 49.14 ? PA ANP 890 A 1 HETATM 10 O O1A ANP . . . C 3 -10.092 49.571 24.713 1 47.86 ? O1A ANP 890 A 1 HETATM 11 O O2A ANP . . . C 3 -8.502 47.866 25.848 1 49.82 ? O2A ANP 890 A 1 HETATM 12 O O3A ANP . . . C 3 -10.841 47.687 26.308 1 50.14 ? O3A ANP 890 A 1 HETATM 13 O O5' ANP . . . C 3 -9.973 47.092 23.989 1 48.51 ? O5' ANP 890 A 1 HETATM 14 C C5' ANP . . . C 3 -8.815 46.505 23.393 1 48.06 ? C5' ANP 890 A 1 HETATM 15 C C4' ANP . . . C 3 -8.674 47.243 22.08 1 47.98 ? C4' ANP 890 A 1 HETATM 16 O O4' ANP . . . C 3 -9.454 46.593 21.085 1 48.19 ? O4' ANP 890 A 1 HETATM 17 C C3' ANP . . . C 3 -7.324 47.45 21.413 1 48.14 ? C3' ANP 890 A 1 HETATM 18 O O3' ANP . . . C 3 -6.548 46.246 21.363 1 47.2 ? O3' ANP 890 A 1 HETATM 19 C C2' ANP . . . C 3 -7.787 47.809 20.01 1 49.03 ? C2' ANP 890 A 1 HETATM 20 O O2' ANP . . . C 3 -7.071 47.05 19.032 1 52.58 ? O2' ANP 890 A 1 HETATM 21 C C1' ANP . . . C 3 -9.251 47.395 19.932 1 48.15 ? C1' ANP 890 A 1 HETATM 22 N N9 ANP . . . C 3 -10.161 48.573 20.037 1 47.02 ? N9 ANP 890 A 1 HETATM 23 C C8 ANP . . . C 3 -10.949 48.879 21.094 1 45.97 ? C8 ANP 890 A 1 HETATM 24 N N7 ANP . . . C 3 -11.662 50.009 20.883 1 45.55 ? N7 ANP 890 A 1 HETATM 25 C C5 ANP . . . C 3 -11.339 50.446 19.655 1 45.95 ? C5 ANP 890 A 1 HETATM 26 C C6 ANP . . . C 3 -11.724 51.595 18.8 1 45.53 ? C6 ANP 890 A 1 HETATM 27 N N6 ANP . . . C 3 -12.628 52.508 19.236 1 45.08 ? N6 ANP 890 A 1 HETATM 28 N N1 ANP . . . C 3 -11.144 51.691 17.577 1 45.15 ? N1 ANP 890 A 1 HETATM 29 C C2 ANP . . . C 3 -10.245 50.786 17.137 1 45.39 ? C2 ANP 890 A 1 HETATM 30 N N3 ANP . . . C 3 -9.846 49.718 17.853 1 45.71 ? N3 ANP 890 A 1 HETATM 31 C C4 ANP . . . C 3 -10.348 49.501 19.097 1 46.56 ? C4 ANP 890 A 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #