data_3PFQ # _model_server_result.job_id gNdxp_EKc-RP5jynrlj--g _model_server_result.datetime_utc '2024-11-19 17:30:34' _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 3pfq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":800}' # _entry.id 3PFQ # _exptl.entry_id 3PFQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.196 _entity.id 4 _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 3PFQ _cell.length_a 114.27 _cell.length_b 114.27 _cell.length_c 170.84 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PFQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _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 _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 4 _struct_asym.id G _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 covale ? covale1 A C LYS 500 A LYS 499 1_555 A N TPO 501 A TPO 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C TPO 501 A TPO 500 1_555 A N PHE 502 A PHE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C LEU 641 A LEU 640 1_555 A N TPO 642 A TPO 641 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C TPO 642 A TPO 641 1_555 A N PRO 643 A PRO 642 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.343 ? covale ? covale5 A C PHE 660 A PHE 659 1_555 A N SEP 661 A SEP 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 A C SEP 661 A SEP 660 1_555 A N PHE 662 A PHE 661 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A SG CYS 116 A CYS 115 1_555 F ZN ZN . A ZN 751 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc2 A SG CYS 136 A CYS 135 1_555 E ZN ZN . A ZN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? metalc ? metalc3 A ND1 HIS 141 A HIS 140 1_555 F ZN ZN . A ZN 751 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc4 A O MET 187 A MET 186 1_555 C CA CA . A CA 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc5 A OD2 ASP 188 A ASP 187 1_555 B CA CA . A CA 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? metalc ? metalc6 A OD1 ASP 188 A ASP 187 1_555 B CA CA . A CA 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.149 ? metalc ? metalc7 A OD1 ASP 194 A ASP 193 1_555 B CA CA . A CA 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc8 A OD2 ASP 247 A ASP 246 1_555 B CA CA . A CA 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.137 ? metalc ? metalc9 A OD2 ASP 247 A ASP 246 1_555 C CA CA . A CA 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc10 A O TRP 248 A TRP 247 1_555 B CA CA . A CA 674 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc11 A OD2 ASP 249 A ASP 248 1_555 C CA CA . A CA 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc12 A OD1 ASP 249 A ASP 248 1_555 C CA CA . A CA 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc13 A OD2 ASP 249 A ASP 248 1_555 D CA CA . A CA 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.076 ? metalc ? metalc14 A OG SER 252 A SER 251 1_555 D CA CA . A CA 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.084 ? metalc ? metalc15 A O ARG 253 A ARG 252 1_555 D CA CA . A CA 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? metalc ? metalc16 A OD2 ASP 255 A ASP 254 1_555 C CA CA . A CA 675 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? # _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 3PFQ _atom_sites.fract_transf_matrix[1][1] 0.008751 _atom_sites.fract_transf_matrix[1][2] 0.005053 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010105 _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] 0.005853 _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 CA A 1 674 293 CA CA . C 2 CA A 1 675 294 CA CA . D 2 CA A 1 676 295 CA CA . E 3 ZN A 1 750 750 ZN ZN . F 3 ZN A 1 751 751 ZN ZN . G 4 ANP A 1 800 800 ANP ANP . # 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 4 -52.32 33.602 -20.012 1 169.32 ? PG ANP 800 A 1 HETATM 2 O O1G ANP . . . G 4 -51.704 33.514 -18.569 1 178.71 ? O1G ANP 800 A 1 HETATM 3 O O2G ANP . . . G 4 -53.521 32.593 -20.187 1 125.1 ? O2G ANP 800 A 1 HETATM 4 O O3G ANP . . . G 4 -52.788 34.995 -20.512 1 137.75 ? O3G ANP 800 A 1 HETATM 5 P PB ANP . . . G 4 -49.493 32.72 -20.663 1 182.86 ? PB ANP 800 A 1 HETATM 6 O O1B ANP . . . G 4 -48.464 33.666 -21.38 1 166.08 ? O1B ANP 800 A 1 HETATM 7 O O2B ANP . . . G 4 -49.291 32.692 -19.131 1 163.78 ? O2B ANP 800 A 1 HETATM 8 N N3B ANP . . . G 4 -51.099 33.179 -21.179 1 165.27 ? N3B ANP 800 A 1 HETATM 9 P PA ANP . . . G 4 -48.837 29.831 -20.408 1 176.06 ? PA ANP 800 A 1 HETATM 10 O O1A ANP . . . G 4 -47.649 29.03 -21.077 1 120.09 ? O1A ANP 800 A 1 HETATM 11 O O2A ANP . . . G 4 -48.545 30.16 -18.89 1 148.7 ? O2A ANP 800 A 1 HETATM 12 O O3A ANP . . . G 4 -49.293 31.175 -21.239 1 157.65 ? O3A ANP 800 A 1 HETATM 13 O O5' ANP . . . G 4 -50.214 29.01 -20.477 1 200.12 ? O5' ANP 800 A 1 HETATM 14 C C5' ANP . . . G 4 -51.339 29.658 -19.889 1 188.3 ? C5' ANP 800 A 1 HETATM 15 C C4' ANP . . . G 4 -52.273 28.597 -19.309 1 153.95 ? C4' ANP 800 A 1 HETATM 16 O O4' ANP . . . G 4 -52.083 27.237 -19.834 1 133.12 ? O4' ANP 800 A 1 HETATM 17 C C3' ANP . . . G 4 -52.282 28.457 -17.763 1 145.42 ? C3' ANP 800 A 1 HETATM 18 O O3' ANP . . . G 4 -53.307 29.133 -17.045 1 101.65 ? O3' ANP 800 A 1 HETATM 19 C C2' ANP . . . G 4 -52.101 26.959 -17.537 1 135.07 ? C2' ANP 800 A 1 HETATM 20 O O2' ANP . . . G 4 -53.375 26.506 -17.028 1 143.84 ? O2' ANP 800 A 1 HETATM 21 C C1' ANP . . . G 4 -51.981 26.249 -18.839 1 122.83 ? C1' ANP 800 A 1 HETATM 22 N N9 ANP . . . G 4 -50.656 25.558 -18.855 1 118.42 ? N9 ANP 800 A 1 HETATM 23 C C8 ANP . . . G 4 -49.45 26.071 -19.22 1 127.96 ? C8 ANP 800 A 1 HETATM 24 N N7 ANP . . . G 4 -48.425 25.17 -19.121 1 106.78 ? N7 ANP 800 A 1 HETATM 25 C C5 ANP . . . G 4 -48.971 24.023 -18.677 1 113.43 ? C5 ANP 800 A 1 HETATM 26 C C6 ANP . . . G 4 -48.56 22.64 -18.325 1 98.09 ? C6 ANP 800 A 1 HETATM 27 N N6 ANP . . . G 4 -47.275 22.254 -18.429 1 78.66 ? N6 ANP 800 A 1 HETATM 28 N N1 ANP . . . G 4 -49.514 21.758 -17.891 1 83.74 ? N1 ANP 800 A 1 HETATM 29 C C2 ANP . . . G 4 -50.827 22.067 -17.76 1 110.33 ? C2 ANP 800 A 1 HETATM 30 N N3 ANP . . . G 4 -51.304 23.288 -18.051 1 131.52 ? N3 ANP 800 A 1 HETATM 31 C C4 ANP . . . G 4 -50.387 24.299 -18.517 1 125.05 ? C4 ANP 800 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #