data_5E3T # _model_server_result.job_id H-5DArP8p5RMo9DNZGWabw _model_server_result.datetime_utc '2025-03-06 09:02:08' _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 5e3t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5E3T # _exptl.entry_id 5E3T _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 5E3T _cell.length_a 87.928 _cell.length_b 87.928 _cell.length_c 156.462 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5E3T _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 _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 -87.928 87.928 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc2 A OD2 ASP 323 A ASP 378 1_555 C MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.717 ? metalc ? metalc3 A OD2 ASP 323 A ASP 378 1_555 D MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc4 B O1G ANP . A ANP 501 1_555 C MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc5 B O1B ANP . A ANP 501 1_555 C MN MN . A MN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc6 B O3G ANP . A ANP 501 1_555 D MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? metalc ? metalc7 B O2A ANP . A ANP 501 1_555 D MN MN . A MN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? metalc ? metalc8 C MN MN . A MN 502 1_555 E O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc9 D MN MN . A MN 503 1_555 E O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.854 ? # _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 5E3T _atom_sites.fract_transf_matrix[1][1] 0.011373 _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] 0.011373 _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] 0.006391 _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 HOH A 1 601 1 HOH HOH . E 4 HOH A 2 602 3 HOH HOH . E 4 HOH A 3 603 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 2.688 110.73 24.34 1 121.75 ? PG ANP 501 A 1 HETATM 2 O O1G ANP . . . B 2 2.547 109.555 23.41 1 127.74 ? O1G ANP 501 A 1 HETATM 3 O O2G ANP . . . B 2 1.539 110.854 25.342 1 119.83 ? O2G ANP 501 A 1 HETATM 4 O O3G ANP . . . B 2 2.989 112 23.577 1 129.61 ? O3G ANP 501 A 1 HETATM 5 P PB ANP . . . B 2 5.114 108.965 24.886 1 96.27 ? PB ANP 501 A 1 HETATM 6 O O1B ANP . . . B 2 4.508 108.218 23.729 1 87.55 ? O1B ANP 501 A 1 HETATM 7 O O2B ANP . . . B 2 5.494 108.162 26.12 1 93.52 ? O2B ANP 501 A 1 HETATM 8 N N3B ANP . . . B 2 4.144 110.379 25.245 1 92.56 ? N3B ANP 501 A 1 HETATM 9 P PA ANP . . . B 2 7.162 110.888 24.135 1 89.82 ? PA ANP 501 A 1 HETATM 10 O O1A ANP . . . B 2 8.413 110.725 23.318 1 85.51 ? O1A ANP 501 A 1 HETATM 11 O O2A ANP . . . B 2 6.081 111.82 23.641 1 79.86 ? O2A ANP 501 A 1 HETATM 12 O O3A ANP . . . B 2 6.602 109.407 24.446 1 103.12 ? O3A ANP 501 A 1 HETATM 13 O O5' ANP . . . B 2 7.712 111.424 25.539 1 85.27 ? O5' ANP 501 A 1 HETATM 14 C C5' ANP . . . B 2 8.013 112.807 25.414 1 88.72 ? C5' ANP 501 A 1 HETATM 15 C C4' ANP . . . B 2 8.743 113.471 26.576 1 87.73 ? C4' ANP 501 A 1 HETATM 16 O O4' ANP . . . B 2 9.945 112.801 27.035 1 80.75 ? O4' ANP 501 A 1 HETATM 17 C C3' ANP . . . B 2 9.123 114.854 26.027 1 90.1 ? C3' ANP 501 A 1 HETATM 18 O O3' ANP . . . B 2 8.271 115.935 26.438 1 86.76 ? O3' ANP 501 A 1 HETATM 19 C C2' ANP . . . B 2 10.562 115.035 26.44 1 87.19 ? C2' ANP 501 A 1 HETATM 20 O O2' ANP . . . B 2 10.658 115.979 27.49 1 80.87 ? O2' ANP 501 A 1 HETATM 21 C C1' ANP . . . B 2 11.081 113.628 26.774 1 88.41 ? C1' ANP 501 A 1 HETATM 22 N N9 ANP . . . B 2 11.813 113.229 25.525 1 103.24 ? N9 ANP 501 A 1 HETATM 23 C C8 ANP . . . B 2 11.449 112.311 24.6 1 102.54 ? C8 ANP 501 A 1 HETATM 24 N N7 ANP . . . B 2 12.347 112.269 23.576 1 95.03 ? N7 ANP 501 A 1 HETATM 25 C C5 ANP . . . B 2 13.304 113.179 23.826 1 93.84 ? C5 ANP 501 A 1 HETATM 26 C C6 ANP . . . B 2 14.535 113.673 23.169 1 96.54 ? C6 ANP 501 A 1 HETATM 27 N N6 ANP . . . B 2 14.976 113.159 21.997 1 109.99 ? N6 ANP 501 A 1 HETATM 28 N N1 ANP . . . B 2 15.227 114.656 23.775 1 93.14 ? N1 ANP 501 A 1 HETATM 29 C C2 ANP . . . B 2 14.833 115.2 24.934 1 93.89 ? C2 ANP 501 A 1 HETATM 30 N N3 ANP . . . B 2 13.733 114.802 25.578 1 95.96 ? N3 ANP 501 A 1 HETATM 31 C C4 ANP . . . B 2 12.94 113.817 25.092 1 99.7 ? C4 ANP 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #