data_5E3U # _model_server_result.job_id 6dto7nD6uZslfx6tcfjU3A _model_server_result.datetime_utc '2024-11-05 00:37:17' _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 5e3u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5E3U # _exptl.entry_id 5E3U _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 90 _cell.entry_id 5E3U _cell.length_a 88.134 _cell.length_b 88.134 _cell.length_c 155.757 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5E3U _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 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,F,G _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' 7_465 y-1,x+1,-z 0 1 0 1 0 0 0 0 -1 -88.134 88.134 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 metalc ? metalc1 A OD1 ASP 323 A ASP 378 1_555 C MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc2 A OD2 ASP 323 A ASP 378 1_555 C MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.891 ? metalc ? metalc3 A OD2 ASP 323 A ASP 378 1_555 D MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.853 ? metalc ? metalc4 B O2G ANP . A ANP 501 1_555 C MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc5 B O1B ANP . A ANP 501 1_555 C MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc6 B O2A ANP . A ANP 501 1_555 D MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc7 C MN MN . A MN 502 1_555 G O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc8 D MN MN . A MN 503 1_555 G O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? # _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 5E3U _atom_sites.fract_transf_matrix[1][1] 0.011346 _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] 0.011346 _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] 0.00642 _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 1 501 900 ANP ANP . C 3 MN A 1 502 351 MN MN . D 3 MN A 1 503 352 MN MN . E 4 SE4 A 1 504 1 SE4 SE4 . F 4 SE4 A 1 505 2 SE4 SE4 . G 5 HOH A 1 601 1 HOH HOH . G 5 HOH A 2 602 2 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 2.953 110.661 24.534 1 85.75 ? PG ANP 501 A 1 HETATM 2 O O1G ANP . . . B 2 2.892 111.909 23.677 1 97.77 ? O1G ANP 501 A 1 HETATM 3 O O2G ANP . . . B 2 2.84 109.399 23.715 1 89.45 ? O2G ANP 501 A 1 HETATM 4 O O3G ANP . . . B 2 2.067 110.746 25.748 1 83.55 ? O3G ANP 501 A 1 HETATM 5 P PB ANP . . . B 2 5.523 109.159 24.927 1 83.43 ? PB ANP 501 A 1 HETATM 6 O O1B ANP . . . B 2 4.852 108.238 23.915 1 71.78 ? O1B ANP 501 A 1 HETATM 7 O O2B ANP . . . B 2 6.011 108.571 26.239 1 82.65 ? O2B ANP 501 A 1 HETATM 8 N N3B ANP . . . B 2 4.535 110.557 25.25 1 81.51 ? N3B ANP 501 A 1 HETATM 9 P PA ANP . . . B 2 7.314 111.277 24.085 1 75.56 ? PA ANP 501 A 1 HETATM 10 O O1A ANP . . . B 2 8.629 111.153 23.374 1 76.5 ? O1A ANP 501 A 1 HETATM 11 O O2A ANP . . . B 2 6.245 112.184 23.529 1 72.74 ? O2A ANP 501 A 1 HETATM 12 O O3A ANP . . . B 2 6.86 109.734 24.233 1 84.48 ? O3A ANP 501 A 1 HETATM 13 O O5' ANP . . . B 2 7.613 111.805 25.552 1 72.64 ? O5' ANP 501 A 1 HETATM 14 C C5' ANP . . . B 2 7.465 113.209 25.685 1 74.36 ? C5' ANP 501 A 1 HETATM 15 C C4' ANP . . . B 2 8.551 113.839 26.558 1 78.52 ? C4' ANP 501 A 1 HETATM 16 O O4' ANP . . . B 2 9.747 113.057 26.836 1 72.07 ? O4' ANP 501 A 1 HETATM 17 C C3' ANP . . . B 2 8.99 115.133 25.881 1 77.73 ? C3' ANP 501 A 1 HETATM 18 O O3' ANP . . . B 2 8.072 116.207 26.117 1 74.2 ? O3' ANP 501 A 1 HETATM 19 C C2' ANP . . . B 2 10.365 115.365 26.464 1 77.2 ? C2' ANP 501 A 1 HETATM 20 O O2' ANP . . . B 2 10.326 116.225 27.611 1 71.49 ? O2' ANP 501 A 1 HETATM 21 C C1' ANP . . . B 2 10.88 113.938 26.739 1 77.19 ? C1' ANP 501 A 1 HETATM 22 N N9 ANP . . . B 2 11.702 113.612 25.545 1 83.64 ? N9 ANP 501 A 1 HETATM 23 C C8 ANP . . . B 2 11.42 112.665 24.643 1 85.91 ? C8 ANP 501 A 1 HETATM 24 N N7 ANP . . . B 2 12.347 112.655 23.657 1 84.97 ? N7 ANP 501 A 1 HETATM 25 C C5 ANP . . . B 2 13.239 113.613 23.904 1 81.37 ? C5 ANP 501 A 1 HETATM 26 C C6 ANP . . . B 2 14.454 114.129 23.249 1 80.24 ? C6 ANP 501 A 1 HETATM 27 N N6 ANP . . . B 2 14.909 113.572 22.101 1 86.08 ? N6 ANP 501 A 1 HETATM 28 N N1 ANP . . . B 2 15.109 115.152 23.832 1 78.51 ? N1 ANP 501 A 1 HETATM 29 C C2 ANP . . . B 2 14.677 115.715 24.973 1 84.65 ? C2 ANP 501 A 1 HETATM 30 N N3 ANP . . . B 2 13.572 115.288 25.615 1 92.63 ? N3 ANP 501 A 1 HETATM 31 C C4 ANP . . . B 2 12.814 114.255 25.143 1 87.5 ? C4 ANP 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #