data_5LPV # _model_server_result.job_id ydaddlpfP5XS89MA2MXawQ _model_server_result.datetime_utc '2025-07-26 00:35:18' _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 5lpv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1200}' # _entry.id 5LPV # _exptl.entry_id 5LPV _exptl.method 'X-RAY DIFFRACTION' # _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 120 _cell.entry_id 5LPV _cell.length_a 115.63 _cell.length_b 115.63 _cell.length_c 49.64 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LPV _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details 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 # _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 covale ? covale1 A C ASP 174 A ASP 1038 1_555 A N TPO 175 A TPO 1039 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C TPO 175 A TPO 1039 1_555 A N HIS 176 A HIS 1040 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C LEU 177 A LEU 1041 1_555 A N SEP 178 A SEP 1042 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 A C SEP 178 A SEP 1042 1_555 A N VAL 179 A VAL 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 A C VAL 179 A VAL 1043 1_555 A N SEP 180 A SEP 1044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 A C SEP 180 A SEP 1044 1_555 A N THR 181 A THR 1045 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OD1 ASN 150 A ASN 1014 1_555 C MN MN . A MN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc2 A OD2 ASP 163 A ASP 1027 1_555 C MN MN . A MN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc3 A OD1 ASP 163 A ASP 1027 1_555 D MN MN . A MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc4 A OD2 ASP 163 A ASP 1027 1_555 D MN MN . A MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc5 B N3B ANP . A ANP 1200 1_555 C MN MN . A MN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? metalc ? metalc6 B O2A ANP . A ANP 1200 1_555 C MN MN . A MN 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.87 ? metalc ? metalc7 B O1B ANP . A ANP 1200 1_555 D MN MN . A MN 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? # _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 5LPV _atom_sites.fract_transf_matrix[1][1] 0.008648 _atom_sites.fract_transf_matrix[1][2] 0.004993 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009986 _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] 0.020145 _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 1200 1200 ANP ANP . C 3 MN A 1 1201 1201 MN MN . D 3 MN A 1 1202 1202 MN MN . E 4 HOH A 1 1301 7 HOH HOH . E 4 HOH A 2 1302 5 HOH HOH . E 4 HOH A 3 1303 10 HOH HOH . E 4 HOH A 4 1304 11 HOH HOH . E 4 HOH A 5 1305 2 HOH HOH . E 4 HOH A 6 1306 4 HOH HOH . E 4 HOH A 7 1307 12 HOH HOH . E 4 HOH A 8 1308 9 HOH HOH . E 4 HOH A 9 1309 1 HOH HOH . E 4 HOH A 10 1310 6 HOH HOH . E 4 HOH A 11 1311 8 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 . . . B 2 42.867 32.393 19.152 1 207.37 ? PG ANP 1200 A 1 HETATM 2 O O1G ANP . . . B 2 43.13 33.579 18.279 1 206.71 ? O1G ANP 1200 A 1 HETATM 3 O O2G ANP . . . B 2 43.625 31.153 18.536 1 68.36 ? O2G ANP 1200 A 1 HETATM 4 O O3G ANP . . . B 2 43.437 32.663 20.604 1 87.75 ? O3G ANP 1200 A 1 HETATM 5 P PB ANP . . . B 2 40.223 33.367 18.85 1 219.09 ? PB ANP 1200 A 1 HETATM 6 O O1B ANP . . . B 2 39.966 33.363 17.314 1 90.4 ? O1B ANP 1200 A 1 HETATM 7 O O2B ANP . . . B 2 40.881 34.65 19.242 1 217.53 ? O2B ANP 1200 A 1 HETATM 8 N N3B ANP . . . B 2 41.202 32.057 19.247 1 211.73 ? N3B ANP 1200 A 1 HETATM 9 P PA ANP . . . B 2 37.994 31.958 19.708 1 94.52 ? PA ANP 1200 A 1 HETATM 10 O O1A ANP . . . B 2 36.949 31.874 18.659 1 64.37 ? O1A ANP 1200 A 1 HETATM 11 O O2A ANP . . . B 2 38.969 30.777 19.73 1 96.54 ? O2A ANP 1200 A 1 HETATM 12 O O3A ANP . . . B 2 38.848 33.295 19.588 1 113.14 ? O3A ANP 1200 A 1 HETATM 13 O O5' ANP . . . B 2 37.269 32.115 21.101 1 66.15 ? O5' ANP 1200 A 1 HETATM 14 C C5' ANP . . . B 2 37.998 32.556 22.262 1 58.84 ? C5' ANP 1200 A 1 HETATM 15 C C4' ANP . . . B 2 37.4 31.896 23.478 1 65.36 ? C4' ANP 1200 A 1 HETATM 16 O O4' ANP . . . B 2 36.042 32.353 23.654 1 72.64 ? O4' ANP 1200 A 1 HETATM 17 C C3' ANP . . . B 2 37.297 30.378 23.409 1 69.88 ? C3' ANP 1200 A 1 HETATM 18 O O3' ANP . . . B 2 38.51 29.756 23.819 1 74.75 ? O3' ANP 1200 A 1 HETATM 19 C C2' ANP . . . B 2 36.138 30.088 24.364 1 76.1 ? C2' ANP 1200 A 1 HETATM 20 O O2' ANP . . . B 2 36.551 30.03 25.725 1 87.58 ? O2' ANP 1200 A 1 HETATM 21 C C1' ANP . . . B 2 35.225 31.296 24.126 1 70.7 ? C1' ANP 1200 A 1 HETATM 22 N N9 ANP . . . B 2 34.183 31.043 23.138 1 64.02 ? N9 ANP 1200 A 1 HETATM 23 C C8 ANP . . . B 2 34.241 31.282 21.79 1 62.22 ? C8 ANP 1200 A 1 HETATM 24 N N7 ANP . . . B 2 33.155 30.939 21.139 1 54.92 ? N7 ANP 1200 A 1 HETATM 25 C C5 ANP . . . B 2 32.327 30.43 22.128 1 50.91 ? C5 ANP 1200 A 1 HETATM 26 C C6 ANP . . . B 2 31.025 29.894 22.091 1 56.42 ? C6 ANP 1200 A 1 HETATM 27 N N6 ANP . . . B 2 30.302 29.778 20.976 1 58.64 ? N6 ANP 1200 A 1 HETATM 28 N N1 ANP . . . B 2 30.485 29.476 23.26 1 52.95 ? N1 ANP 1200 A 1 HETATM 29 C C2 ANP . . . B 2 31.206 29.591 24.38 1 61.74 ? C2 ANP 1200 A 1 HETATM 30 N N3 ANP . . . B 2 32.44 30.079 24.536 1 67.73 ? N3 ANP 1200 A 1 HETATM 31 C C4 ANP . . . B 2 32.948 30.484 23.364 1 57.35 ? C4 ANP 1200 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #