data_3DZ2 # _model_server_result.job_id 3xf4JKjzN9pkNY1rYxYj9w _model_server_result.datetime_utc '2024-11-22 10:36:24' _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 3dz2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":368}' # _entry.id 3DZ2 # _exptl.entry_id 3DZ2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 351.404 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-[(3-aminopropyl)(methyl)amino]-5'-deoxy-8-methyladenosine" _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 105.56 _cell.angle_gamma 90 _cell.entry_id 3DZ2 _cell.length_a 100.088 _cell.length_b 50.745 _cell.length_c 69.039 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DZ2 _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 1.408 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C15 H25 N7 O3' _chem_comp.formula_weight 351.404 _chem_comp.id A8M _chem_comp.mon_nstd_flag . _chem_comp.name "5'-[(3-aminopropyl)(methyl)amino]-5'-deoxy-8-methyladenosine" _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 C2 A8M sing 1 n n C2 C4 A8M sing 2 n n C4 C5 A8M sing 3 n n C5 N2 A8M sing 4 n n N2 C6 A8M sing 5 n n N2 C5' A8M sing 6 n n C5' C4' A8M sing 7 n n C4' O4' A8M sing 8 n n C4' C3' A8M sing 9 n n O4' C1' A8M sing 10 n n C1' N5 A8M sing 11 n n C1' C2' A8M sing 12 n n N5 C11 A8M sing 13 n y N5 C7 A8M sing 14 n y C11 N4 A8M doub 15 n y C11 C12 A8M sing 16 n y N4 C10 A8M sing 17 n y C10 N3 A8M doub 18 n y N3 C9 A8M sing 19 n y C9 N7 A8M sing 20 n n C9 C12 A8M doub 21 n y C12 N6 A8M sing 22 n y N6 C7 A8M doub 23 n y C7 C8 A8M sing 24 n n C2' O2' A8M sing 25 n n C2' C3' A8M sing 26 n n C3' O3' A8M sing 27 n n N1 HN1 A8M sing 28 n n N1 HN1A A8M sing 29 n n C2 H2 A8M sing 30 n n C2 H2A A8M sing 31 n n C4 H4 A8M sing 32 n n C4 H4A A8M sing 33 n n C5 H5 A8M sing 34 n n C5 H5A A8M sing 35 n n C6 H6 A8M sing 36 n n C6 H6A A8M sing 37 n n C6 H6B A8M sing 38 n n C5' H5' A8M sing 39 n n C5' "H5'A" A8M sing 40 n n C4' H4' A8M sing 41 n n C1' H1' A8M sing 42 n n C10 H10 A8M sing 43 n n N7 HN7 A8M sing 44 n n N7 HN7A A8M sing 45 n n C2' H2' A8M sing 46 n n O2' HO2' A8M sing 47 n n C3' H3' A8M sing 48 n n O3' HO3' A8M sing 49 n n C8 H8 A8M sing 50 n n C8 H8A A8M sing 51 n n C8 H8B A8M sing 52 n n # _atom_sites.entry_id 3DZ2 _atom_sites.fract_transf_matrix[1][1] 0.009991 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002783 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019706 _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] 0.015036 _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 A8M A 1 368 368 A8M A8M . E 5 HOH B 1 351 1 HOH HOH . E 5 HOH B 2 352 2 HOH HOH . E 5 HOH B 3 353 5 HOH HOH . E 5 HOH B 4 354 10 HOH HOH . E 5 HOH B 5 355 18 HOH HOH . E 5 HOH B 6 356 20 HOH HOH . E 5 HOH B 7 357 25 HOH HOH . E 5 HOH B 8 359 34 HOH HOH . E 5 HOH B 9 360 35 HOH HOH . E 5 HOH B 10 361 41 HOH HOH . E 5 HOH B 11 362 43 HOH HOH . E 5 HOH B 12 363 45 HOH HOH . E 5 HOH B 13 364 48 HOH HOH . E 5 HOH B 14 365 51 HOH HOH . E 5 HOH B 15 366 52 HOH HOH . E 5 HOH B 16 367 60 HOH HOH . E 5 HOH B 17 368 67 HOH HOH . E 5 HOH B 18 369 69 HOH HOH . E 5 HOH B 19 370 76 HOH HOH . E 5 HOH B 20 371 77 HOH HOH . E 5 HOH B 21 372 80 HOH HOH . E 5 HOH B 22 373 86 HOH HOH . E 5 HOH B 23 374 87 HOH HOH . E 5 HOH B 24 375 89 HOH HOH . E 5 HOH B 25 376 101 HOH HOH . E 5 HOH B 26 378 108 HOH HOH . E 5 HOH B 27 379 110 HOH HOH . E 5 HOH B 28 380 112 HOH HOH . E 5 HOH B 29 381 113 HOH HOH . E 5 HOH B 30 382 119 HOH HOH . E 5 HOH B 31 383 121 HOH HOH . E 5 HOH B 32 384 127 HOH HOH . E 5 HOH B 33 385 133 HOH HOH . E 5 HOH B 34 386 136 HOH HOH . E 5 HOH B 35 387 139 HOH HOH . E 5 HOH B 36 388 147 HOH HOH . E 5 HOH B 37 389 153 HOH HOH . E 5 HOH B 38 390 158 HOH HOH . E 5 HOH B 39 391 159 HOH HOH . E 5 HOH B 40 392 165 HOH HOH . E 5 HOH B 41 393 175 HOH HOH . E 5 HOH B 42 394 191 HOH HOH . E 5 HOH B 43 395 196 HOH HOH . E 5 HOH B 44 396 198 HOH HOH . E 5 HOH B 45 397 199 HOH HOH . E 5 HOH B 46 398 207 HOH HOH . E 5 HOH B 47 399 208 HOH HOH . E 5 HOH B 48 400 209 HOH HOH . E 5 HOH B 49 401 210 HOH HOH . F 5 HOH A 1 369 26 HOH HOH . F 5 HOH A 2 370 107 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 6 HOH HOH . F 5 HOH A 6 374 7 HOH HOH . F 5 HOH A 7 375 8 HOH HOH . F 5 HOH A 8 376 9 HOH HOH . F 5 HOH A 9 377 11 HOH HOH . F 5 HOH A 10 378 12 HOH HOH . F 5 HOH A 11 379 13 HOH HOH . F 5 HOH A 12 380 14 HOH HOH . F 5 HOH A 13 381 15 HOH HOH . F 5 HOH A 14 382 16 HOH HOH . F 5 HOH A 15 383 17 HOH HOH . F 5 HOH A 16 384 19 HOH HOH . F 5 HOH A 17 385 21 HOH HOH . F 5 HOH A 18 386 22 HOH HOH . F 5 HOH A 19 387 23 HOH HOH . F 5 HOH A 20 388 24 HOH HOH . F 5 HOH A 21 389 27 HOH HOH . F 5 HOH A 22 390 38 HOH HOH . F 5 HOH A 23 391 29 HOH HOH . F 5 HOH A 24 392 30 HOH HOH . F 5 HOH A 25 393 31 HOH HOH . F 5 HOH A 26 394 32 HOH HOH . F 5 HOH A 27 395 33 HOH HOH . F 5 HOH A 28 396 36 HOH HOH . F 5 HOH A 29 397 37 HOH HOH . F 5 HOH A 30 398 39 HOH HOH . F 5 HOH A 31 399 40 HOH HOH . F 5 HOH A 32 400 42 HOH HOH . F 5 HOH A 33 401 44 HOH HOH . F 5 HOH A 34 402 46 HOH HOH . F 5 HOH A 35 403 47 HOH HOH . F 5 HOH A 36 404 49 HOH HOH . F 5 HOH A 37 405 50 HOH HOH . F 5 HOH A 38 406 53 HOH HOH . F 5 HOH A 39 407 54 HOH HOH . F 5 HOH A 40 408 55 HOH HOH . F 5 HOH A 41 409 56 HOH HOH . F 5 HOH A 42 410 57 HOH HOH . F 5 HOH A 43 411 58 HOH HOH . F 5 HOH A 44 412 59 HOH HOH . F 5 HOH A 45 413 61 HOH HOH . F 5 HOH A 46 414 62 HOH HOH . F 5 HOH A 47 415 63 HOH HOH . F 5 HOH A 48 416 64 HOH HOH . F 5 HOH A 49 417 65 HOH HOH . F 5 HOH A 50 418 66 HOH HOH . F 5 HOH A 51 419 68 HOH HOH . F 5 HOH A 52 420 70 HOH HOH . F 5 HOH A 53 421 71 HOH HOH . F 5 HOH A 54 422 72 HOH HOH . F 5 HOH A 55 423 73 HOH HOH . F 5 HOH A 56 424 74 HOH HOH . F 5 HOH A 57 425 75 HOH HOH . F 5 HOH A 58 426 78 HOH HOH . F 5 HOH A 59 427 79 HOH HOH . F 5 HOH A 60 428 81 HOH HOH . F 5 HOH A 61 429 82 HOH HOH . F 5 HOH A 62 430 83 HOH HOH . F 5 HOH A 63 431 84 HOH HOH . F 5 HOH A 64 432 85 HOH HOH . F 5 HOH A 65 433 88 HOH HOH . F 5 HOH A 66 434 90 HOH HOH . F 5 HOH A 67 435 91 HOH HOH . F 5 HOH A 68 436 92 HOH HOH . F 5 HOH A 69 437 93 HOH HOH . F 5 HOH A 70 438 94 HOH HOH . F 5 HOH A 71 439 95 HOH HOH . F 5 HOH A 72 440 96 HOH HOH . F 5 HOH A 73 441 97 HOH HOH . F 5 HOH A 74 442 98 HOH HOH . F 5 HOH A 75 443 99 HOH HOH . F 5 HOH A 76 444 100 HOH HOH . F 5 HOH A 77 445 102 HOH HOH . F 5 HOH A 78 446 103 HOH HOH . F 5 HOH A 79 447 104 HOH HOH . F 5 HOH A 80 448 105 HOH HOH . F 5 HOH A 81 449 106 HOH HOH . F 5 HOH A 82 450 109 HOH HOH . F 5 HOH A 83 451 111 HOH HOH . F 5 HOH A 84 452 114 HOH HOH . F 5 HOH A 85 453 115 HOH HOH . F 5 HOH A 86 454 116 HOH HOH . F 5 HOH A 87 455 117 HOH HOH . F 5 HOH A 88 456 118 HOH HOH . F 5 HOH A 89 457 120 HOH HOH . F 5 HOH A 90 458 122 HOH HOH . F 5 HOH A 91 459 123 HOH HOH . F 5 HOH A 92 460 124 HOH HOH . F 5 HOH A 93 461 125 HOH HOH . F 5 HOH A 94 462 126 HOH HOH . F 5 HOH A 95 463 128 HOH HOH . F 5 HOH A 96 464 129 HOH HOH . F 5 HOH A 97 465 130 HOH HOH . F 5 HOH A 98 466 131 HOH HOH . F 5 HOH A 99 467 132 HOH HOH . F 5 HOH A 100 468 134 HOH HOH . F 5 HOH A 101 469 135 HOH HOH . F 5 HOH A 102 470 137 HOH HOH . F 5 HOH A 103 471 138 HOH HOH . F 5 HOH A 104 472 140 HOH HOH . F 5 HOH A 105 473 141 HOH HOH . F 5 HOH A 106 474 142 HOH HOH . F 5 HOH A 107 475 143 HOH HOH . F 5 HOH A 108 476 144 HOH HOH . F 5 HOH A 109 477 145 HOH HOH . F 5 HOH A 110 478 146 HOH HOH . F 5 HOH A 111 479 148 HOH HOH . F 5 HOH A 112 480 149 HOH HOH . F 5 HOH A 113 481 150 HOH HOH . F 5 HOH A 114 482 151 HOH HOH . F 5 HOH A 115 483 152 HOH HOH . F 5 HOH A 116 484 154 HOH HOH . F 5 HOH A 117 485 155 HOH HOH . F 5 HOH A 118 486 156 HOH HOH . F 5 HOH A 119 487 157 HOH HOH . F 5 HOH A 120 488 160 HOH HOH . F 5 HOH A 121 489 161 HOH HOH . F 5 HOH A 122 490 162 HOH HOH . F 5 HOH A 123 491 163 HOH HOH . F 5 HOH A 124 492 164 HOH HOH . F 5 HOH A 125 493 166 HOH HOH . F 5 HOH A 126 494 167 HOH HOH . F 5 HOH A 127 495 168 HOH HOH . F 5 HOH A 128 496 169 HOH HOH . F 5 HOH A 129 497 170 HOH HOH . F 5 HOH A 130 498 171 HOH HOH . F 5 HOH A 131 499 172 HOH HOH . F 5 HOH A 132 500 173 HOH HOH . F 5 HOH A 133 501 174 HOH HOH . F 5 HOH A 134 502 176 HOH HOH . F 5 HOH A 135 503 177 HOH HOH . F 5 HOH A 136 504 178 HOH HOH . F 5 HOH A 137 505 179 HOH HOH . F 5 HOH A 138 506 180 HOH HOH . F 5 HOH A 139 507 181 HOH HOH . F 5 HOH A 140 508 182 HOH HOH . F 5 HOH A 141 509 183 HOH HOH . F 5 HOH A 142 510 184 HOH HOH . F 5 HOH A 143 511 185 HOH HOH . F 5 HOH A 144 512 186 HOH HOH . F 5 HOH A 145 513 187 HOH HOH . F 5 HOH A 146 514 188 HOH HOH . F 5 HOH A 147 515 189 HOH HOH . F 5 HOH A 148 516 190 HOH HOH . F 5 HOH A 149 517 192 HOH HOH . F 5 HOH A 150 518 193 HOH HOH . F 5 HOH A 151 519 194 HOH HOH . F 5 HOH A 152 520 195 HOH HOH . F 5 HOH A 153 521 197 HOH HOH . F 5 HOH A 154 522 200 HOH HOH . F 5 HOH A 155 523 201 HOH HOH . F 5 HOH A 156 524 202 HOH HOH . F 5 HOH A 157 525 203 HOH HOH . F 5 HOH A 158 526 204 HOH HOH . F 5 HOH A 159 527 205 HOH HOH . F 5 HOH A 160 528 206 HOH HOH . F 5 HOH A 161 529 211 HOH HOH . F 5 HOH A 162 530 212 HOH HOH . F 5 HOH A 163 531 213 HOH HOH . F 5 HOH A 164 532 214 HOH HOH . F 5 HOH A 165 533 215 HOH HOH . F 5 HOH A 166 534 216 HOH HOH . F 5 HOH A 167 535 217 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 A8M . . . D 4 -68.691 -5.857 10.961 1 52.76 ? N1 A8M 368 A 1 HETATM 2 C C2 A8M . . . D 4 -69.263 -5.246 9.825 1 49.17 ? C2 A8M 368 A 1 HETATM 3 C C4 A8M . . . D 4 -68.191 -4.685 8.914 1 44.75 ? C4 A8M 368 A 1 HETATM 4 C C5 A8M . . . D 4 -68.789 -4.029 7.709 1 42.24 ? C5 A8M 368 A 1 HETATM 5 N N2 A8M . . . D 4 -67.932 -4.042 6.576 1 40.73 ? N2 A8M 368 A 1 HETATM 6 C C6 A8M . . . D 4 -67.422 -5.421 6.37 1 38.26 ? C6 A8M 368 A 1 HETATM 7 C C5' A8M . . . D 4 -66.841 -3.144 6.755 1 38.71 ? C5' A8M 368 A 1 HETATM 8 C C4' A8M . . . D 4 -65.924 -3.12 5.542 1 36.51 ? C4' A8M 368 A 1 HETATM 9 O O4' A8M . . . D 4 -66.592 -2.726 4.286 1 36.1 ? O4' A8M 368 A 1 HETATM 10 C C1' A8M . . . D 4 -66.181 -1.431 4.106 1 35.84 ? C1' A8M 368 A 1 HETATM 11 N N5 A8M . . . D 4 -67.438 -0.52 3.825 1 37.1 ? N5 A8M 368 A 1 HETATM 12 C C11 A8M . . . D 4 -68.565 -0.569 4.665 1 39.02 ? C11 A8M 368 A 1 HETATM 13 N N4 A8M . . . D 4 -68.773 -1.332 5.771 1 39.87 ? N4 A8M 368 A 1 HETATM 14 C C10 A8M . . . D 4 -69.984 -1.102 6.321 1 42.88 ? C10 A8M 368 A 1 HETATM 15 N N3 A8M . . . D 4 -70.947 -0.247 5.913 1 43.98 ? N3 A8M 368 A 1 HETATM 16 C C9 A8M . . . D 4 -70.715 0.509 4.799 1 42 ? C9 A8M 368 A 1 HETATM 17 N N7 A8M . . . D 4 -71.666 1.357 4.39 1 42.34 ? N7 A8M 368 A 1 HETATM 18 C C12 A8M . . . D 4 -69.469 0.356 4.125 1 39.99 ? C12 A8M 368 A 1 HETATM 19 N N6 A8M . . . D 4 -68.947 0.962 2.998 1 38.08 ? N6 A8M 368 A 1 HETATM 20 C C7 A8M . . . D 4 -67.761 0.421 2.858 1 38.61 ? C7 A8M 368 A 1 HETATM 21 C C2' A8M . . . D 4 -65.386 -0.92 5.092 1 35.82 ? C2' A8M 368 A 1 HETATM 22 O O2' A8M . . . D 4 -64.492 0.139 4.854 1 34.57 ? O2' A8M 368 A 1 HETATM 23 C C3' A8M . . . D 4 -64.749 -2.173 5.64 1 36.52 ? C3' A8M 368 A 1 HETATM 24 O O3' A8M . . . D 4 -63.692 -2.581 4.763 1 34.69 ? O3' A8M 368 A 1 HETATM 25 C C8 A8M . . . D 4 -66.776 0.74 1.775 1 37.55 ? C8 A8M 368 A 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 634 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #