data_2ATE # _model_server_result.job_id VeP6cJeYEkCDc75C0S-eFA _model_server_result.datetime_utc '2024-11-16 11:27:08' _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 2ate # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":400}' # _entry.id 2ATE # _exptl.entry_id 2ATE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 340.184 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '((2R,3S,4R,5R)-5-(5-AMINO-4-NITRO-1H-IMIDAZOL-1-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE' _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 2ATE _cell.length_a 112.495 _cell.length_b 112.495 _cell.length_c 49.796 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ATE _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_554 -x,y,-z-1 -1 0 0 0 1 0 0 0 -1 0 0 -49.796 6 'crystal symmetry operation' 6_554 x,-y,-z-1 1 0 0 0 -1 0 0 0 -1 0 0 -49.796 7 'crystal symmetry operation' 7_554 y,x,-z-1 0 1 0 1 0 0 0 0 -1 0 0 -49.796 8 'crystal symmetry operation' 8_554 -y,-x,-z-1 0 -1 0 -1 0 0 0 0 -1 0 0 -49.796 # _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 covale ? covale1 A C VAL 13 A VAL 13 1_555 A N MSE 14 A MSE 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale2 A C MSE 14 A MSE 14 1_555 A N GLY 15 A GLY 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C THR 22 A THR 22 1_555 A N MSE 23 A MSE 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale4 A C MSE 23 A MSE 23 1_555 A N GLN 24 A GLN 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale5 A C GLY 78 A GLY 78 1_555 A N MSE 79 A MSE 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.301 ? covale ? covale6 A C MSE 79 A MSE 79 1_555 A N ILE 80 A ILE 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 A C GLN 109 A GLN 109 1_555 A N MSE 110 A MSE 110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C MSE 110 A MSE 110 1_555 A N PRO 111 A PRO 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? # _chem_comp.formula 'C8 H13 N4 O9 P' _chem_comp.formula_weight 340.184 _chem_comp.id NIA _chem_comp.mon_nstd_flag . _chem_comp.name '((2R,3S,4R,5R)-5-(5-AMINO-4-NITRO-1H-IMIDAZOL-1-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '4-NITRO-5-AMINOIMIDAZOLE RIBONUCLEOTIDE;NITRO AIR' # 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 O8 P NIA sing 243 n n O8 HO8 NIA sing 244 n n P O6 NIA doub 245 n n P O7 NIA sing 246 n n P O5' NIA sing 247 n n O7 HO7 NIA sing 248 n n O5' C5' NIA sing 249 n n C5' C4' NIA sing 250 n n C5' "H5'1" NIA sing 251 n n C5' "H5'2" NIA sing 252 n n C4' C3' NIA sing 253 n n C4' O4' NIA sing 254 n n C4' H4' NIA sing 255 n n C3' O3' NIA sing 256 n n C3' C2' NIA sing 257 n n C3' H3' NIA sing 258 n n O3' H1 NIA sing 259 n n C2' O2' NIA sing 260 n n C2' C1' NIA sing 261 n n C2' H2' NIA sing 262 n n O2' H2 NIA sing 263 n n O4' C1' NIA sing 264 n n C1' N1 NIA sing 265 n n C1' H1' NIA sing 266 n n N1 C5 NIA sing 267 n y N1 C2 NIA sing 268 n y C5 N6 NIA sing 269 n n C5 C4 NIA doub 270 n y N6 HN61 NIA sing 271 n n N6 HN62 NIA sing 272 n n C4 N7 NIA sing 273 n n C4 N3 NIA sing 274 n y N7 O72 NIA doub 275 n n N7 O71 NIA sing 276 n n N3 C2 NIA doub 277 n y C2 H3 NIA sing 278 n n # _atom_sites.entry_id 2ATE _atom_sites.fract_transf_matrix[1][1] 0.008889 _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] 0.008889 _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] 0.020082 _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 NIA A 1 400 400 NIA NIA . C 3 HOH A 1 401 1 HOH HOH . C 3 HOH A 2 402 2 HOH HOH . C 3 HOH A 3 403 3 HOH HOH . C 3 HOH A 4 404 4 HOH HOH . C 3 HOH A 5 405 5 HOH HOH . C 3 HOH A 6 406 6 HOH HOH . C 3 HOH A 7 407 7 HOH HOH . C 3 HOH A 8 408 8 HOH HOH . C 3 HOH A 9 409 9 HOH HOH . C 3 HOH A 10 410 10 HOH HOH . C 3 HOH A 11 411 11 HOH HOH . C 3 HOH A 12 412 12 HOH HOH . C 3 HOH A 13 413 13 HOH HOH . C 3 HOH A 14 414 14 HOH HOH . C 3 HOH A 15 415 15 HOH HOH . C 3 HOH A 16 416 16 HOH HOH . C 3 HOH A 17 417 17 HOH HOH . C 3 HOH A 18 418 18 HOH HOH . C 3 HOH A 19 419 19 HOH HOH . C 3 HOH A 20 420 20 HOH HOH . C 3 HOH A 21 421 21 HOH HOH . C 3 HOH A 22 422 22 HOH HOH . C 3 HOH A 23 423 23 HOH HOH . C 3 HOH A 24 424 24 HOH HOH . C 3 HOH A 25 425 25 HOH HOH . C 3 HOH A 26 426 26 HOH HOH . C 3 HOH A 27 427 27 HOH HOH . C 3 HOH A 28 428 28 HOH HOH . C 3 HOH A 29 429 29 HOH HOH . C 3 HOH A 30 430 30 HOH HOH . C 3 HOH A 31 431 31 HOH HOH . C 3 HOH A 32 432 32 HOH HOH . C 3 HOH A 33 433 33 HOH HOH . C 3 HOH A 34 434 34 HOH HOH . C 3 HOH A 35 435 35 HOH HOH . C 3 HOH A 36 436 36 HOH HOH . C 3 HOH A 37 437 37 HOH HOH . C 3 HOH A 38 438 38 HOH HOH . C 3 HOH A 39 439 39 HOH HOH . C 3 HOH A 40 440 40 HOH HOH . C 3 HOH A 41 441 41 HOH HOH . C 3 HOH A 42 442 42 HOH HOH . C 3 HOH A 43 443 43 HOH HOH . C 3 HOH A 44 444 44 HOH HOH . C 3 HOH A 45 445 45 HOH HOH . C 3 HOH A 46 446 46 HOH HOH . C 3 HOH A 47 447 47 HOH HOH . C 3 HOH A 48 448 48 HOH HOH . C 3 HOH A 49 449 49 HOH HOH . C 3 HOH A 50 450 50 HOH HOH . C 3 HOH A 51 451 51 HOH HOH . C 3 HOH A 52 452 52 HOH HOH . C 3 HOH A 53 453 53 HOH HOH . C 3 HOH A 54 454 54 HOH HOH . C 3 HOH A 55 455 55 HOH HOH . C 3 HOH A 56 456 56 HOH HOH . C 3 HOH A 57 457 57 HOH HOH . C 3 HOH A 58 458 58 HOH HOH . C 3 HOH A 59 459 59 HOH HOH . C 3 HOH A 60 460 60 HOH HOH . C 3 HOH A 61 461 61 HOH HOH . C 3 HOH A 62 462 62 HOH HOH . C 3 HOH A 63 463 63 HOH HOH . C 3 HOH A 64 464 64 HOH HOH . C 3 HOH A 65 465 65 HOH HOH . C 3 HOH A 66 466 66 HOH HOH . C 3 HOH A 67 467 67 HOH HOH . C 3 HOH A 68 468 68 HOH HOH . C 3 HOH A 69 469 69 HOH HOH . C 3 HOH A 70 470 70 HOH HOH . C 3 HOH A 71 471 71 HOH HOH . C 3 HOH A 72 472 72 HOH HOH . C 3 HOH A 73 473 73 HOH HOH . C 3 HOH A 74 474 74 HOH HOH . C 3 HOH A 75 475 75 HOH HOH . C 3 HOH A 76 476 76 HOH HOH . C 3 HOH A 77 477 77 HOH HOH . C 3 HOH A 78 478 78 HOH HOH . C 3 HOH A 79 479 79 HOH HOH . C 3 HOH A 80 480 80 HOH HOH . C 3 HOH A 81 481 81 HOH HOH . C 3 HOH A 82 482 82 HOH HOH . C 3 HOH A 83 483 83 HOH HOH . C 3 HOH A 84 484 84 HOH HOH . C 3 HOH A 85 485 85 HOH HOH . C 3 HOH A 86 486 86 HOH HOH . C 3 HOH A 87 487 87 HOH HOH . C 3 HOH A 88 488 88 HOH HOH . C 3 HOH A 89 489 89 HOH HOH . C 3 HOH A 90 490 90 HOH HOH . C 3 HOH A 91 491 91 HOH HOH . C 3 HOH A 92 492 92 HOH HOH . C 3 HOH A 93 493 93 HOH HOH . C 3 HOH A 94 494 94 HOH HOH . C 3 HOH A 95 495 95 HOH HOH . C 3 HOH A 96 496 96 HOH HOH . C 3 HOH A 97 497 97 HOH HOH . C 3 HOH A 98 498 98 HOH HOH . C 3 HOH A 99 499 99 HOH HOH . C 3 HOH A 100 500 100 HOH HOH . C 3 HOH A 101 501 101 HOH HOH . C 3 HOH A 102 502 102 HOH HOH . C 3 HOH A 103 503 103 HOH HOH . C 3 HOH A 104 504 104 HOH HOH . C 3 HOH A 105 505 105 HOH HOH . C 3 HOH A 106 506 106 HOH HOH . C 3 HOH A 107 507 107 HOH HOH . C 3 HOH A 108 508 108 HOH HOH . C 3 HOH A 109 509 109 HOH HOH . C 3 HOH A 110 510 110 HOH HOH . C 3 HOH A 111 511 111 HOH HOH . C 3 HOH A 112 512 112 HOH HOH . C 3 HOH A 113 513 113 HOH HOH . C 3 HOH A 114 514 114 HOH HOH . C 3 HOH A 115 515 115 HOH HOH . C 3 HOH A 116 516 116 HOH HOH . C 3 HOH A 117 517 117 HOH HOH . C 3 HOH A 118 518 118 HOH HOH . C 3 HOH A 119 519 119 HOH HOH . C 3 HOH A 120 520 120 HOH HOH . C 3 HOH A 121 521 121 HOH HOH . C 3 HOH A 122 522 122 HOH HOH . C 3 HOH A 123 523 123 HOH HOH . C 3 HOH A 124 524 124 HOH HOH . C 3 HOH A 125 525 125 HOH HOH . C 3 HOH A 126 526 126 HOH HOH . C 3 HOH A 127 527 127 HOH HOH . C 3 HOH A 128 528 128 HOH HOH . C 3 HOH A 129 529 129 HOH HOH . C 3 HOH A 130 530 130 HOH HOH . C 3 HOH A 131 531 131 HOH HOH . C 3 HOH A 132 532 132 HOH HOH . C 3 HOH A 133 533 133 HOH HOH . C 3 HOH A 134 534 134 HOH HOH . C 3 HOH A 135 535 135 HOH HOH . C 3 HOH A 136 536 136 HOH HOH . C 3 HOH A 137 537 137 HOH HOH . C 3 HOH A 138 538 138 HOH HOH . C 3 HOH A 139 539 139 HOH HOH . C 3 HOH A 140 540 140 HOH HOH . C 3 HOH A 141 541 141 HOH HOH . C 3 HOH A 142 542 142 HOH HOH . C 3 HOH A 143 543 143 HOH HOH . C 3 HOH A 144 544 144 HOH HOH . C 3 HOH A 145 545 145 HOH HOH . C 3 HOH A 146 546 146 HOH HOH . C 3 HOH A 147 547 147 HOH HOH . C 3 HOH A 148 548 148 HOH HOH . C 3 HOH A 149 549 149 HOH HOH . C 3 HOH A 150 550 150 HOH HOH . C 3 HOH A 151 551 151 HOH HOH . C 3 HOH A 152 552 152 HOH HOH . C 3 HOH A 153 553 153 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 O O8 NIA . . . B 2 16.277 -12.941 -9.181 1 14.43 ? O8 NIA 400 A 1 HETATM 2 P P NIA . . . B 2 15.601 -11.667 -9.589 1 19.22 ? P NIA 400 A 1 HETATM 3 O O6 NIA . . . B 2 14.59 -11.16 -8.616 1 20.67 ? O6 NIA 400 A 1 HETATM 4 O O7 NIA . . . B 2 16.536 -10.585 -10.075 1 18.08 ? O7 NIA 400 A 1 HETATM 5 O O5' NIA . . . B 2 14.781 -12.14 -10.905 1 18.04 ? O5' NIA 400 A 1 HETATM 6 C C5' NIA . . . B 2 14.044 -11.149 -11.593 1 14.8 ? C5' NIA 400 A 1 HETATM 7 C C4' NIA . . . B 2 13.348 -11.78 -12.767 1 14.27 ? C4' NIA 400 A 1 HETATM 8 C C3' NIA . . . B 2 12.538 -13.077 -12.506 1 15.44 ? C3' NIA 400 A 1 HETATM 9 O O3' NIA . . . B 2 11.15 -12.861 -12.819 1 10.66 ? O3' NIA 400 A 1 HETATM 10 C C2' NIA . . . B 2 13.214 -14.092 -13.44 1 14.78 ? C2' NIA 400 A 1 HETATM 11 O O2' NIA . . . B 2 12.306 -15.067 -14.06 1 13.79 ? O2' NIA 400 A 1 HETATM 12 O O4' NIA . . . B 2 14.405 -12.071 -13.715 1 19.05 ? O4' NIA 400 A 1 HETATM 13 C C1' NIA . . . B 2 13.973 -13.175 -14.462 1 15.08 ? C1' NIA 400 A 1 HETATM 14 N N1 NIA . . . B 2 14.874 -14.073 -15.154 1 16.11 ? N1 NIA 400 A 1 HETATM 15 C C5 NIA . . . B 2 14.777 -14.288 -16.484 1 16.33 ? C5 NIA 400 A 1 HETATM 16 N N6 NIA . . . B 2 13.915 -13.641 -17.316 1 11.68 ? N6 NIA 400 A 1 HETATM 17 C C4 NIA . . . B 2 15.589 -15.36 -16.772 1 14.64 ? C4 NIA 400 A 1 HETATM 18 N N7 NIA . . . B 2 15.774 -15.971 -17.958 1 16.49 ? N7 NIA 400 A 1 HETATM 19 O O72 NIA . . . B 2 14.989 -15.749 -18.913 1 15.48 ? O72 NIA 400 A 1 HETATM 20 O O71 NIA . . . B 2 16.485 -17.004 -17.967 1 19.12 ? O71 NIA 400 A 1 HETATM 21 N N3 NIA . . . B 2 16.244 -15.741 -15.652 1 16.04 ? N3 NIA 400 A 1 HETATM 22 C C2 NIA . . . B 2 15.76 -14.958 -14.663 1 13.49 ? C2 NIA 400 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 22 #