data_5YT3 # _model_server_result.job_id R8Gfql5IwR8KBMK2q6WadQ _model_server_result.datetime_utc '2024-11-08 09:04:37' _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 5yt3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 5YT3 # _exptl.entry_id 5YT3 _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 4 _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 5YT3 _cell.length_a 132.17 _cell.length_b 132.55 _cell.length_c 91.21 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YT3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,K,L 1 1 C,D,H,I,J,M,N 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 H N N ? 2 J N 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 ASN 157 A ASN 195 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc2 A OD2 ASP 170 A ASP 208 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc3 E O2G ANP . A ANP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc4 E O1B ANP . A ANP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc5 E O1A ANP . A ANP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.855 ? metalc ? metalc6 C OD1 ASN 157 C ASN 195 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc7 C OD2 ASP 170 C ASP 208 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.879 ? metalc ? metalc8 H O2G ANP . C ANP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc9 H O1B ANP . C ANP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc10 H O1A ANP . C ANP 401 1_555 I MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? # _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 5YT3 _atom_sites.fract_transf_matrix[1][1] 0.007566 _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] 0.007544 _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] 0.010964 _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 E 2 ANP A 1 401 1 ANP ANP . F 3 MG A 1 402 1 MG MG . G 2 ANP B 1 401 2 ANP ANP . H 2 ANP C 1 401 3 ANP ANP . I 3 MG C 1 402 2 MG MG . J 2 ANP D 1 401 4 ANP ANP . K 4 HOH A 1 501 24 HOH HOH . K 4 HOH A 2 502 12 HOH HOH . K 4 HOH A 3 503 4 HOH HOH . K 4 HOH A 4 504 23 HOH HOH . K 4 HOH A 5 505 9 HOH HOH . L 4 HOH B 1 501 25 HOH HOH . L 4 HOH B 2 502 26 HOH HOH . M 4 HOH C 1 501 6 HOH HOH . M 4 HOH C 2 502 18 HOH HOH . M 4 HOH C 3 503 1 HOH HOH . M 4 HOH C 4 504 28 HOH HOH . N 4 HOH D 1 501 21 HOH HOH . N 4 HOH D 2 502 22 HOH HOH . N 4 HOH D 3 503 29 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 . . . J 2 9.14 -33.68 7.128 1 90.14 ? PG ANP 401 D 1 HETATM 2 O O1G ANP . . . J 2 8.911 -33.906 5.646 1 87.79 ? O1G ANP 401 D 1 HETATM 3 O O2G ANP . . . J 2 8.839 -32.279 7.599 1 86.92 ? O2G ANP 401 D 1 HETATM 4 O O3G ANP . . . J 2 10.474 -34.212 7.642 1 85.82 ? O3G ANP 401 D 1 HETATM 5 P PB ANP . . . J 2 7.803 -34.813 9.555 1 89.21 ? PB ANP 401 D 1 HETATM 6 O O1B ANP . . . J 2 6.508 -35.509 9.946 1 81.22 ? O1B ANP 401 D 1 HETATM 7 O O2B ANP . . . J 2 8.152 -33.492 10.183 1 88.85 ? O2B ANP 401 D 1 HETATM 8 N N3B ANP . . . J 2 7.842 -34.612 7.827 1 85.95 ? N3B ANP 401 D 1 HETATM 9 P PA ANP . . . J 2 9.595 -37.033 9.164 1 67.99 ? PA ANP 401 D 1 HETATM 10 O O1A ANP . . . J 2 10.191 -36.636 7.808 1 46.44 ? O1A ANP 401 D 1 HETATM 11 O O2A ANP . . . J 2 8.583 -38.169 9.244 1 70.01 ? O2A ANP 401 D 1 HETATM 12 O O3A ANP . . . J 2 9.058 -35.741 9.973 1 81.32 ? O3A ANP 401 D 1 HETATM 13 O O5' ANP . . . J 2 10.669 -37.339 10.339 1 63.13 ? O5' ANP 401 D 1 HETATM 14 C C5' ANP . . . J 2 11.97 -36.732 10.38 1 56.67 ? C5' ANP 401 D 1 HETATM 15 C C4' ANP . . . J 2 13.056 -37.787 10.587 1 49.31 ? C4' ANP 401 D 1 HETATM 16 O O4' ANP . . . J 2 12.638 -38.659 11.624 1 50.86 ? O4' ANP 401 D 1 HETATM 17 C C3' ANP . . . J 2 13.289 -38.755 9.449 1 46.78 ? C3' ANP 401 D 1 HETATM 18 O O3' ANP . . . J 2 14.253 -38.178 8.591 1 50.32 ? O3' ANP 401 D 1 HETATM 19 C C2' ANP . . . J 2 13.829 -39.979 10.152 1 46.52 ? C2' ANP 401 D 1 HETATM 20 O O2' ANP . . . J 2 15.226 -39.778 10.419 1 43.21 ? O2' ANP 401 D 1 HETATM 21 C C1' ANP . . . J 2 13.089 -39.992 11.475 1 45.42 ? C1' ANP 401 D 1 HETATM 22 N N9 ANP . . . J 2 11.911 -40.895 11.427 1 44.12 ? N9 ANP 401 D 1 HETATM 23 C C8 ANP . . . J 2 10.626 -40.567 11.13 1 43.2 ? C8 ANP 401 D 1 HETATM 24 N N7 ANP . . . J 2 9.814 -41.675 11.162 1 39.86 ? N7 ANP 401 D 1 HETATM 25 C C5 ANP . . . J 2 10.587 -42.711 11.476 1 34.52 ? C5 ANP 401 D 1 HETATM 26 C C6 ANP . . . J 2 10.399 -44.133 11.666 1 34.63 ? C6 ANP 401 D 1 HETATM 27 N N6 ANP . . . J 2 9.186 -44.673 11.523 1 35.1 ? N6 ANP 401 D 1 HETATM 28 N N1 ANP . . . J 2 11.473 -44.9 11.99 1 39.54 ? N1 ANP 401 D 1 HETATM 29 C C2 ANP . . . J 2 12.705 -44.393 12.148 1 37.57 ? C2 ANP 401 D 1 HETATM 30 N N3 ANP . . . J 2 12.947 -43.074 11.975 1 39.73 ? N3 ANP 401 D 1 HETATM 31 C C4 ANP . . . J 2 11.954 -42.209 11.655 1 39.36 ? C4 ANP 401 D 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 361 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #