data_3MIA # _model_server_result.job_id oNZGzDV6JrYtj2tRq86D6A _model_server_result.datetime_utc '2024-11-22 10:16:23' _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 3mia # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":352}' # _entry.id 3MIA # _exptl.entry_id 3MIA _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 3MIA _cell.length_a 134.286 _cell.length_b 134.286 _cell.length_c 97.185 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3MIA _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,H,I _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 D _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 disulf ? disulf1 C SG CYS 25 C CYS 25 1_555 C SG CYS 27 C CYS 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.82 ? disulf ? disulf2 C SG CYS 25 C CYS 25 1_555 C SG CYS 30 C CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? covale ? covale1 A C TYR 185 A TYR 185 1_555 A N TPO 186 A TPO 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C TPO 186 A TPO 186 1_555 A N ASN 187 A ASN 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OD1 ASN 154 A ASN 154 1_555 E MG MG . A MG 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc2 A OD2 ASP 167 A ASP 167 1_555 E MG MG . A MG 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc3 D O2A ANP . A ANP 352 1_555 E MG MG . A MG 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc4 B SG CYS 261 B CYS 261 1_555 G ZN ZN . C ZN 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc5 C SG CYS 22 C CYS 22 1_555 F ZN ZN . C ZN 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc6 C SG CYS 25 C CYS 25 1_555 G ZN ZN . C ZN 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc7 C SG CYS 27 C CYS 27 1_555 G ZN ZN . C ZN 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc8 C SG CYS 30 C CYS 30 1_555 G ZN ZN . C ZN 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc9 C ND1 HIS 33 C HIS 33 1_555 F ZN ZN . C ZN 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc10 C SG CYS 34 C CYS 34 1_555 F ZN ZN . C ZN 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? metalc ? metalc11 C SG CYS 37 C CYS 37 1_555 F ZN ZN . C ZN 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? # _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 3MIA _atom_sites.fract_transf_matrix[1][1] 0.007447 _atom_sites.fract_transf_matrix[1][2] 0.004299 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008599 _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] 0.01029 _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 D 4 ANP A 1 352 1 ANP ANP . E 5 MG A 1 353 1 MG MG . F 6 ZN C 1 87 1 ZN ZN . G 6 ZN C 1 88 2 ZN ZN . H 7 HOH A 1 354 2 HOH H2O . H 7 HOH A 2 355 3 HOH H2O . H 7 HOH A 3 356 4 HOH H2O . H 7 HOH A 4 357 5 HOH H2O . H 7 HOH A 5 358 6 HOH H2O . H 7 HOH A 6 359 7 HOH H2O . H 7 HOH A 7 360 8 HOH H2O . H 7 HOH A 8 361 9 HOH H2O . H 7 HOH A 9 362 11 HOH H2O . H 7 HOH A 10 363 12 HOH H2O . H 7 HOH A 11 364 13 HOH H2O . H 7 HOH A 12 365 14 HOH H2O . H 7 HOH A 13 366 15 HOH H2O . H 7 HOH A 14 367 16 HOH H2O . H 7 HOH A 15 368 17 HOH H2O . H 7 HOH A 16 369 18 HOH H2O . H 7 HOH A 17 370 19 HOH H2O . H 7 HOH A 18 371 20 HOH H2O . H 7 HOH A 19 372 22 HOH H2O . H 7 HOH A 20 373 23 HOH H2O . H 7 HOH A 21 374 24 HOH H2O . H 7 HOH A 22 375 25 HOH H2O . H 7 HOH A 23 376 26 HOH H2O . H 7 HOH A 24 377 27 HOH H2O . I 7 HOH B 1 267 1 HOH H2O . I 7 HOH B 2 268 10 HOH H2O . I 7 HOH B 3 269 21 HOH H2O . # 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 . . . D 4 58.96 15.453 33.381 1 85.03 ? PG ANP 352 A 1 HETATM 2 O O1G ANP . . . D 4 60.276 15.097 34.015 1 84.13 ? O1G ANP 352 A 1 HETATM 3 O O2G ANP . . . D 4 58.086 14.237 33.427 1 85.53 ? O2G ANP 352 A 1 HETATM 4 O O3G ANP . . . D 4 59.181 15.864 31.959 1 83.91 ? O3G ANP 352 A 1 HETATM 5 P PB ANP . . . D 4 57.034 17.354 33.432 1 72.66 ? PB ANP 352 A 1 HETATM 6 O O1B ANP . . . D 4 56.515 16.494 32.418 1 71.02 ? O1B ANP 352 A 1 HETATM 7 O O2B ANP . . . D 4 55.952 17.607 34.369 1 71.8 ? O2B ANP 352 A 1 HETATM 8 N N3B ANP . . . D 4 58.273 16.672 34.214 1 77.86 ? N3B ANP 352 A 1 HETATM 9 P PA ANP . . . D 4 58.731 19.495 33.357 1 65.78 ? PA ANP 352 A 1 HETATM 10 O O1A ANP . . . D 4 58.685 20.892 32.965 1 61.99 ? O1A ANP 352 A 1 HETATM 11 O O2A ANP . . . D 4 58.707 19.41 34.84 1 65.65 ? O2A ANP 352 A 1 HETATM 12 O O3A ANP . . . D 4 57.476 18.728 32.725 1 69.85 ? O3A ANP 352 A 1 HETATM 13 O O5' ANP . . . D 4 59.966 18.888 32.818 1 63.83 ? O5' ANP 352 A 1 HETATM 14 C C5' ANP . . . D 4 60.947 19.184 33.553 1 58.67 ? C5' ANP 352 A 1 HETATM 15 C C4' ANP . . . D 4 62.214 18.554 33.124 1 52.91 ? C4' ANP 352 A 1 HETATM 16 O O4' ANP . . . D 4 62.411 19.242 31.867 1 49.13 ? O4' ANP 352 A 1 HETATM 17 C C3' ANP . . . D 4 62.939 19.19 34.228 1 51.12 ? C3' ANP 352 A 1 HETATM 18 O O3' ANP . . . D 4 63.223 18.409 35.368 1 53.45 ? O3' ANP 352 A 1 HETATM 19 C C2' ANP . . . D 4 64.125 19.821 33.472 1 48.89 ? C2' ANP 352 A 1 HETATM 20 O O2' ANP . . . D 4 65.228 18.935 33.5 1 50.45 ? O2' ANP 352 A 1 HETATM 21 C C1' ANP . . . D 4 63.606 20.101 32.003 1 45.88 ? C1' ANP 352 A 1 HETATM 22 N N9 ANP . . . D 4 63.161 21.516 31.832 1 39.76 ? N9 ANP 352 A 1 HETATM 23 C C8 ANP . . . D 4 61.886 22.091 31.966 1 37.81 ? C8 ANP 352 A 1 HETATM 24 N N7 ANP . . . D 4 61.832 23.363 31.76 1 35.65 ? N7 ANP 352 A 1 HETATM 25 C C5 ANP . . . D 4 63.146 23.656 31.472 1 34.44 ? C5 ANP 352 A 1 HETATM 26 C C6 ANP . . . D 4 63.803 24.884 31.148 1 31.75 ? C6 ANP 352 A 1 HETATM 27 N N6 ANP . . . D 4 63.142 26.016 31.086 1 28.27 ? N6 ANP 352 A 1 HETATM 28 N N1 ANP . . . D 4 65.163 24.859 30.901 1 31.16 ? N1 ANP 352 A 1 HETATM 29 C C2 ANP . . . D 4 65.849 23.704 30.964 1 33.63 ? C2 ANP 352 A 1 HETATM 30 N N3 ANP . . . D 4 65.347 22.48 31.264 1 35.45 ? N3 ANP 352 A 1 HETATM 31 C C4 ANP . . . D 4 63.957 22.54 31.508 1 36.37 ? C4 ANP 352 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #