data_3IDC # _model_server_result.job_id 0OgiaomJZ2DiVsnFLtmc5Q _model_server_result.datetime_utc '2024-10-13 18:19:58' _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 3idc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":450}' # _entry.id 3IDC # _exptl.entry_id 3IDC _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 99.51 _cell.angle_gamma 90 _cell.entry_id 3IDC _cell.length_a 179.272 _cell.length_b 67.434 _cell.length_c 47.325 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3IDC _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 E _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 TRP 196 A TRP 196 1_555 A N TPO 197 A TPO 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C TPO 197 A TPO 197 1_555 A N LEU 198 A LEU 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale3 A C VAL 337 A VAL 337 1_555 A N SEP 338 A SEP 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 A C SEP 338 A SEP 338 1_555 A N ILE 339 A ILE 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A OD1 ASN 171 A ASN 171 1_555 C MN MN . A MN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc2 A OD1 ASP 184 A ASP 184 1_555 D MN MN . A MN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc3 C MN MN . A MN 401 1_555 E O2A ANP . A ANP 450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc4 D MN MN . A MN 402 1_555 E O2B ANP . A ANP 450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc5 D MN MN . A MN 402 1_555 E O1G ANP . A ANP 450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? # _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 3IDC _atom_sites.fract_transf_matrix[1][1] 0.005578 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000934 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014829 _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] 0.021425 _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 C 3 MN A 1 401 401 MN MN2 . D 3 MN A 1 402 402 MN MN2 . E 4 ANP A 1 450 400 ANP ANP . F 5 HOH A 1 501 401 HOH WAT . F 5 HOH A 2 502 402 HOH WAT . F 5 HOH A 3 503 403 HOH WAT . F 5 HOH A 4 504 404 HOH WAT . F 5 HOH A 5 505 405 HOH WAT . F 5 HOH A 6 506 406 HOH WAT . F 5 HOH A 7 507 407 HOH WAT . F 5 HOH A 8 508 408 HOH WAT . F 5 HOH A 9 509 409 HOH WAT . F 5 HOH A 10 510 410 HOH WAT . F 5 HOH A 11 511 411 HOH WAT . F 5 HOH A 12 512 412 HOH WAT . F 5 HOH A 13 513 413 HOH WAT . F 5 HOH A 14 514 414 HOH WAT . F 5 HOH A 15 515 415 HOH WAT . F 5 HOH A 16 516 416 HOH WAT . F 5 HOH A 17 517 417 HOH WAT . F 5 HOH A 18 518 418 HOH WAT . F 5 HOH A 19 519 419 HOH WAT . F 5 HOH A 20 520 420 HOH WAT . F 5 HOH A 21 521 421 HOH WAT . F 5 HOH A 22 522 422 HOH WAT . F 5 HOH A 23 523 423 HOH WAT . F 5 HOH A 24 524 424 HOH WAT . F 5 HOH A 25 525 425 HOH WAT . F 5 HOH A 26 526 426 HOH WAT . F 5 HOH A 27 527 427 HOH WAT . F 5 HOH A 28 528 428 HOH WAT . F 5 HOH A 29 529 429 HOH WAT . F 5 HOH A 30 530 430 HOH WAT . F 5 HOH A 31 531 431 HOH WAT . F 5 HOH A 32 532 432 HOH WAT . F 5 HOH A 33 533 433 HOH WAT . F 5 HOH A 34 534 434 HOH WAT . F 5 HOH A 35 535 435 HOH WAT . F 5 HOH A 36 536 436 HOH WAT . F 5 HOH A 37 537 437 HOH WAT . F 5 HOH A 38 538 438 HOH WAT . F 5 HOH A 39 539 439 HOH WAT . F 5 HOH A 40 540 440 HOH WAT . F 5 HOH A 41 541 441 HOH WAT . F 5 HOH A 42 542 442 HOH WAT . F 5 HOH A 43 543 443 HOH WAT . # 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 . . . E 4 68.737 -1.033 9.189 1 54.31 ? PG ANP 450 A 1 HETATM 2 O O1G ANP . . . E 4 68.256 -2.006 8.114 1 55.39 ? O1G ANP 450 A 1 HETATM 3 O O2G ANP . . . E 4 67.562 -0.24 9.687 1 52.24 ? O2G ANP 450 A 1 HETATM 4 O O3G ANP . . . E 4 69.341 -1.82 10.347 1 50.1 ? O3G ANP 450 A 1 HETATM 5 P PB ANP . . . E 4 69.295 0.986 7.389 1 54.62 ? PB ANP 450 A 1 HETATM 6 O O1B ANP . . . E 4 70.289 1.023 6.287 1 55.3 ? O1B ANP 450 A 1 HETATM 7 O O2B ANP . . . E 4 67.982 0.533 6.853 1 57.85 ? O2B ANP 450 A 1 HETATM 8 N N3B ANP . . . E 4 69.858 -0.019 8.56 1 54.75 ? N3B ANP 450 A 1 HETATM 9 P PA ANP . . . E 4 67.702 3.081 8.114 1 50.16 ? PA ANP 450 A 1 HETATM 10 O O1A ANP . . . E 4 67.008 3.241 6.828 1 46.3 ? O1A ANP 450 A 1 HETATM 11 O O2A ANP . . . E 4 66.85 2.261 9.025 1 47.76 ? O2A ANP 450 A 1 HETATM 12 O O3A ANP . . . E 4 69.187 2.45 7.983 1 52.83 ? O3A ANP 450 A 1 HETATM 13 O O5' ANP . . . E 4 67.961 4.507 8.77 1 50.84 ? O5' ANP 450 A 1 HETATM 14 C C5' ANP . . . E 4 68.698 4.559 9.997 1 48.84 ? C5' ANP 450 A 1 HETATM 15 C C4' ANP . . . E 4 68.009 5.426 10.999 1 49.31 ? C4' ANP 450 A 1 HETATM 16 O O4' ANP . . . E 4 67.888 6.755 10.443 1 50.85 ? O4' ANP 450 A 1 HETATM 17 C C3' ANP . . . E 4 66.584 5.048 11.362 1 48.58 ? C3' ANP 450 A 1 HETATM 18 O O3' ANP . . . E 4 66.537 3.989 12.316 1 46.19 ? O3' ANP 450 A 1 HETATM 19 C C2' ANP . . . E 4 66.049 6.371 11.904 1 48.5 ? C2' ANP 450 A 1 HETATM 20 O O2' ANP . . . E 4 66.436 6.647 13.234 1 47.87 ? O2' ANP 450 A 1 HETATM 21 C C1' ANP . . . E 4 66.727 7.375 10.966 1 50.28 ? C1' ANP 450 A 1 HETATM 22 N N9 ANP . . . E 4 65.871 7.795 9.855 1 50.78 ? N9 ANP 450 A 1 HETATM 23 C C8 ANP . . . E 4 65.582 7.138 8.683 1 50.69 ? C8 ANP 450 A 1 HETATM 24 N N7 ANP . . . E 4 64.707 7.76 7.934 1 53.21 ? N7 ANP 450 A 1 HETATM 25 C C5 ANP . . . E 4 64.413 8.911 8.649 1 51.91 ? C5 ANP 450 A 1 HETATM 26 C C6 ANP . . . E 4 63.535 9.977 8.4 1 54.2 ? C6 ANP 450 A 1 HETATM 27 N N6 ANP . . . E 4 62.751 10.059 7.319 1 55.06 ? N6 ANP 450 A 1 HETATM 28 N N1 ANP . . . E 4 63.482 10.969 9.316 1 55.33 ? N1 ANP 450 A 1 HETATM 29 C C2 ANP . . . E 4 64.267 10.88 10.403 1 53.97 ? C2 ANP 450 A 1 HETATM 30 N N3 ANP . . . E 4 65.127 9.928 10.747 1 49.94 ? N3 ANP 450 A 1 HETATM 31 C C4 ANP . . . E 4 65.146 8.959 9.82 1 50.94 ? C4 ANP 450 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #