data_3DZ6 # _model_server_result.job_id jou1UPJH88bbHPD9mw6oGg _model_server_result.datetime_utc '2024-11-16 20:55:59' _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 3dz6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":368}' # _entry.id 3DZ6 # _exptl.entry_id 3DZ6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 393.441 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-{[4-(aminooxy)butyl](methyl)amino}-5'-deoxy-8-ethenyladenosine" _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 105.34 _cell.angle_gamma 90 _cell.entry_id 3DZ6 _cell.length_a 94.434 _cell.length_b 50.041 _cell.length_c 70.408 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DZ6 _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 D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id C _struct_conn.ptnr1_label_comp_id PYR _struct_conn.ptnr1_label_seq_id 1 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id PYR _struct_conn.ptnr1_auth_seq_id 68 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id N _struct_conn.ptnr2_label_comp_id SER _struct_conn.ptnr2_label_seq_id 2 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id SER _struct_conn.ptnr2_auth_seq_id 69 _struct_conn.ptnr2_symmetry 1_555 _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 1.33 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C17 H27 N7 O4' _chem_comp.formula_weight 393.441 _chem_comp.id M8E _chem_comp.mon_nstd_flag . _chem_comp.name "5'-{[4-(aminooxy)butyl](methyl)amino}-5'-deoxy-8-ethenyladenosine" _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 N1 O1 M8E sing 218 n n O1 C4 M8E sing 219 n n C6 C7 M8E sing 220 n n C6 C5 M8E sing 221 n n C7 N2 M8E sing 222 n n N2 C8 M8E sing 223 n n N2 C5' M8E sing 224 n n C5' C4' M8E sing 225 n n C4' O4' M8E sing 226 n n C4' C3' M8E sing 227 n n O4' C1' M8E sing 228 n n C1' N6 M8E sing 229 n n C1' C2' M8E sing 230 n n N6 C13 M8E sing 231 n y N6 C12 M8E sing 232 n y C13 N3 M8E doub 233 n y C13 C11 M8E sing 234 n y N3 C9 M8E sing 235 n y C9 N4 M8E doub 236 n y N4 C10 M8E sing 237 n y C10 N7 M8E sing 238 n n C10 C11 M8E doub 239 n y C11 N5 M8E sing 240 n y N5 C12 M8E doub 241 n y C12 C14 M8E sing 242 n n C2' O2' M8E sing 243 n n C2' C3' M8E sing 244 n n C3' O3' M8E sing 245 n n C5 C4 M8E sing 246 n n C15 C14 M8E doub 247 n n N1 HN1 M8E sing 248 n n N1 HN1A M8E sing 249 n n C6 H6 M8E sing 250 n n C6 H6A M8E sing 251 n n C7 H7 M8E sing 252 n n C7 H7A M8E sing 253 n n C8 H8 M8E sing 254 n n C8 H8A M8E sing 255 n n C8 H8B M8E sing 256 n n C5' H5' M8E sing 257 n n C5' "H5'A" M8E sing 258 n n C4' H4' M8E sing 259 n n C1' H1' M8E sing 260 n n C9 H9 M8E sing 261 n n N7 HN7 M8E sing 262 n n N7 HN7A M8E sing 263 n n C2' H2' M8E sing 264 n n O2' HO2' M8E sing 265 n n C3' H3' M8E sing 266 n n O3' HO3' M8E sing 267 n n C5 H5 M8E sing 268 n n C5 H5A M8E sing 269 n n C4 H4 M8E sing 270 n n C4 H4A M8E sing 271 n n C15 H15 M8E sing 272 n n C15 H15A M8E sing 273 n n C14 H14 M8E sing 274 n n # _atom_sites.entry_id 3DZ6 _atom_sites.fract_transf_matrix[1][1] 0.010589 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002904 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019984 _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] 0.014727 _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 PUT B 1 350 350 PUT PUT . D 4 M8E A 1 368 368 M8E M8E . E 5 HOH B 1 351 11 HOH HOH . E 5 HOH B 2 352 17 HOH HOH . E 5 HOH B 3 353 26 HOH HOH . E 5 HOH B 4 354 30 HOH HOH . E 5 HOH B 5 355 33 HOH HOH . E 5 HOH B 6 356 37 HOH HOH . E 5 HOH B 7 357 38 HOH HOH . E 5 HOH B 8 358 40 HOH HOH . E 5 HOH B 9 359 41 HOH HOH . E 5 HOH B 10 360 43 HOH HOH . E 5 HOH B 11 361 47 HOH HOH . E 5 HOH B 12 362 50 HOH HOH . E 5 HOH B 13 363 61 HOH HOH . E 5 HOH B 14 364 63 HOH HOH . E 5 HOH B 15 365 67 HOH HOH . E 5 HOH B 16 366 68 HOH HOH . E 5 HOH B 17 367 80 HOH HOH . E 5 HOH B 18 368 86 HOH HOH . E 5 HOH B 19 369 94 HOH HOH . E 5 HOH B 20 370 95 HOH HOH . E 5 HOH B 21 371 97 HOH HOH . E 5 HOH B 22 372 98 HOH HOH . E 5 HOH B 23 373 99 HOH HOH . E 5 HOH B 24 374 109 HOH HOH . E 5 HOH B 25 375 110 HOH HOH . E 5 HOH B 26 376 112 HOH HOH . E 5 HOH B 27 377 121 HOH HOH . E 5 HOH B 28 378 122 HOH HOH . E 5 HOH B 29 379 123 HOH HOH . E 5 HOH B 30 380 127 HOH HOH . E 5 HOH B 31 381 128 HOH HOH . F 5 HOH A 1 369 1 HOH HOH . F 5 HOH A 2 370 2 HOH HOH . F 5 HOH A 3 371 3 HOH HOH . F 5 HOH A 4 372 4 HOH HOH . F 5 HOH A 5 373 5 HOH HOH . F 5 HOH A 6 374 6 HOH HOH . F 5 HOH A 7 375 7 HOH HOH . F 5 HOH A 8 376 8 HOH HOH . F 5 HOH A 9 377 9 HOH HOH . F 5 HOH A 10 378 10 HOH HOH . F 5 HOH A 11 379 12 HOH HOH . F 5 HOH A 12 380 13 HOH HOH . F 5 HOH A 13 381 14 HOH HOH . F 5 HOH A 14 382 15 HOH HOH . F 5 HOH A 15 383 16 HOH HOH . F 5 HOH A 16 384 18 HOH HOH . F 5 HOH A 17 385 19 HOH HOH . F 5 HOH A 18 386 20 HOH HOH . F 5 HOH A 19 387 21 HOH HOH . F 5 HOH A 20 388 22 HOH HOH . F 5 HOH A 21 389 23 HOH HOH . F 5 HOH A 22 390 24 HOH HOH . F 5 HOH A 23 391 25 HOH HOH . F 5 HOH A 24 392 27 HOH HOH . F 5 HOH A 25 393 28 HOH HOH . F 5 HOH A 26 394 29 HOH HOH . F 5 HOH A 27 395 31 HOH HOH . F 5 HOH A 28 396 32 HOH HOH . F 5 HOH A 29 397 34 HOH HOH . F 5 HOH A 30 398 35 HOH HOH . F 5 HOH A 31 399 36 HOH HOH . F 5 HOH A 32 400 39 HOH HOH . F 5 HOH A 33 401 42 HOH HOH . F 5 HOH A 34 402 44 HOH HOH . F 5 HOH A 35 403 45 HOH HOH . F 5 HOH A 36 404 46 HOH HOH . F 5 HOH A 37 405 48 HOH HOH . F 5 HOH A 38 406 49 HOH HOH . F 5 HOH A 39 407 51 HOH HOH . F 5 HOH A 40 408 52 HOH HOH . F 5 HOH A 41 409 53 HOH HOH . F 5 HOH A 42 410 54 HOH HOH . F 5 HOH A 43 411 55 HOH HOH . F 5 HOH A 44 412 56 HOH HOH . F 5 HOH A 45 413 57 HOH HOH . F 5 HOH A 46 414 58 HOH HOH . F 5 HOH A 47 415 59 HOH HOH . F 5 HOH A 48 416 60 HOH HOH . F 5 HOH A 49 417 62 HOH HOH . F 5 HOH A 50 418 64 HOH HOH . F 5 HOH A 51 419 65 HOH HOH . F 5 HOH A 52 420 66 HOH HOH . F 5 HOH A 53 421 69 HOH HOH . F 5 HOH A 54 422 70 HOH HOH . F 5 HOH A 55 423 71 HOH HOH . F 5 HOH A 56 424 72 HOH HOH . F 5 HOH A 57 425 73 HOH HOH . F 5 HOH A 58 426 74 HOH HOH . F 5 HOH A 59 427 75 HOH HOH . F 5 HOH A 60 428 76 HOH HOH . F 5 HOH A 61 429 77 HOH HOH . F 5 HOH A 62 430 78 HOH HOH . F 5 HOH A 63 431 79 HOH HOH . F 5 HOH A 64 432 81 HOH HOH . F 5 HOH A 65 433 82 HOH HOH . F 5 HOH A 66 434 83 HOH HOH . F 5 HOH A 67 435 84 HOH HOH . F 5 HOH A 68 436 85 HOH HOH . F 5 HOH A 69 437 87 HOH HOH . F 5 HOH A 70 438 88 HOH HOH . F 5 HOH A 71 439 89 HOH HOH . F 5 HOH A 72 440 90 HOH HOH . F 5 HOH A 73 441 91 HOH HOH . F 5 HOH A 74 442 92 HOH HOH . F 5 HOH A 75 443 93 HOH HOH . F 5 HOH A 76 444 96 HOH HOH . F 5 HOH A 77 445 100 HOH HOH . F 5 HOH A 78 446 101 HOH HOH . F 5 HOH A 79 447 102 HOH HOH . F 5 HOH A 80 448 103 HOH HOH . F 5 HOH A 81 449 104 HOH HOH . F 5 HOH A 82 450 105 HOH HOH . F 5 HOH A 83 451 106 HOH HOH . F 5 HOH A 84 452 107 HOH HOH . F 5 HOH A 85 453 108 HOH HOH . F 5 HOH A 86 454 111 HOH HOH . F 5 HOH A 87 455 113 HOH HOH . F 5 HOH A 88 456 114 HOH HOH . F 5 HOH A 89 457 115 HOH HOH . F 5 HOH A 90 458 116 HOH HOH . F 5 HOH A 91 459 117 HOH HOH . F 5 HOH A 92 460 118 HOH HOH . F 5 HOH A 93 461 119 HOH HOH . F 5 HOH A 94 462 120 HOH HOH . F 5 HOH A 95 463 124 HOH HOH . F 5 HOH A 96 464 125 HOH HOH . F 5 HOH A 97 465 126 HOH HOH . F 5 HOH A 98 466 129 HOH HOH . F 5 HOH A 99 467 130 HOH HOH . F 5 HOH A 100 468 131 HOH HOH . F 5 HOH A 101 469 132 HOH HOH . F 5 HOH A 102 470 133 HOH HOH . F 5 HOH A 103 471 134 HOH HOH . F 5 HOH A 104 472 135 HOH HOH . F 5 HOH A 105 473 136 HOH HOH . F 5 HOH A 106 474 137 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 N N1 M8E . . . D 4 -22.185 -5.882 10.147 1 57.22 ? N1 M8E 368 A 1 HETATM 2 O O1 M8E . . . D 4 -20.972 -6.721 9.947 1 57.46 ? O1 M8E 368 A 1 HETATM 3 C C6 M8E . . . D 4 -18.461 -7.632 8.901 1 43.53 ? C6 M8E 368 A 1 HETATM 4 C C7 M8E . . . D 4 -17.251 -8.684 8.642 1 36.11 ? C7 M8E 368 A 1 HETATM 5 N N2 M8E . . . D 4 -16.701 -8.478 7.27 1 32.18 ? N2 M8E 368 A 1 HETATM 6 C C8 M8E . . . D 4 -16.596 -9.829 6.6 1 28.17 ? C8 M8E 368 A 1 HETATM 7 C C5' M8E . . . D 4 -15.354 -7.823 7.387 1 26.02 ? C5' M8E 368 A 1 HETATM 8 C C4' M8E . . . D 4 -14.661 -7.556 6.057 1 25.29 ? C4' M8E 368 A 1 HETATM 9 O O4' M8E . . . D 4 -15.63 -6.985 5.1 1 22.97 ? O4' M8E 368 A 1 HETATM 10 C C1' M8E . . . D 4 -15.156 -5.704 4.67 1 25.67 ? C1' M8E 368 A 1 HETATM 11 N N6 M8E . . . D 4 -16.37 -4.879 4.414 1 26.82 ? N6 M8E 368 A 1 HETATM 12 C C13 M8E . . . D 4 -17.479 -4.809 5.219 1 28.09 ? C13 M8E 368 A 1 HETATM 13 N N3 M8E . . . D 4 -17.697 -5.461 6.39 1 27.84 ? N3 M8E 368 A 1 HETATM 14 C C9 M8E . . . D 4 -18.907 -5.147 6.909 1 32.44 ? C9 M8E 368 A 1 HETATM 15 N N4 M8E . . . D 4 -19.859 -4.305 6.408 1 32.03 ? N4 M8E 368 A 1 HETATM 16 C C10 M8E . . . D 4 -19.598 -3.67 5.225 1 31.23 ? C10 M8E 368 A 1 HETATM 17 N N7 M8E . . . D 4 -20.529 -2.839 4.725 1 31.06 ? N7 M8E 368 A 1 HETATM 18 C C11 M8E . . . D 4 -18.351 -3.92 4.585 1 28.88 ? C11 M8E 368 A 1 HETATM 19 N N5 M8E . . . D 4 -17.805 -3.447 3.42 1 28.6 ? N5 M8E 368 A 1 HETATM 20 C C12 M8E . . . D 4 -16.645 -4.025 3.35 1 27.95 ? C12 M8E 368 A 1 HETATM 21 C C2' M8E . . . D 4 -14.234 -5.246 5.822 1 23.68 ? C2' M8E 368 A 1 HETATM 22 O O2' M8E . . . D 4 -13.386 -4.165 5.493 1 24.85 ? O2' M8E 368 A 1 HETATM 23 C C3' M8E . . . D 4 -13.535 -6.553 6.193 1 22.02 ? C3' M8E 368 A 1 HETATM 24 O O3' M8E . . . D 4 -12.554 -6.863 5.234 1 23.21 ? O3' M8E 368 A 1 HETATM 25 C C5 M8E . . . D 4 -19.773 -8.168 8.342 1 48.38 ? C5 M8E 368 A 1 HETATM 26 C C4 M8E . . . D 4 -20.909 -7.158 8.581 1 53.44 ? C4 M8E 368 A 1 HETATM 27 C C15 M8E . . . D 4 -14.689 -3.184 2.2 1 31.63 ? C15 M8E 368 A 1 HETATM 28 C C14 M8E . . . D 4 -15.642 -3.826 2.241 1 28.67 ? C14 M8E 368 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #