data_3V7Y # _model_server_result.job_id tSwYhF5Au1l_QQWFf5ltfw _model_server_result.datetime_utc '2024-11-08 22:30:08' _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 3v7y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 3V7Y # _exptl.entry_id 3V7Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 304.305 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-deoxy-5'-(prop-2-yn-1-ylamino)adenosine" _entity.pdbx_number_of_molecules 2 _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 3V7Y _cell.length_a 62.812 _cell.length_b 75.675 _cell.length_c 118.619 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3V7Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 62.812 0 0 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 62.812 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D N N # _chem_comp.formula 'C13 H16 N6 O3' _chem_comp.formula_weight 304.305 _chem_comp.id A3N _chem_comp.mon_nstd_flag . _chem_comp.name "5'-deoxy-5'-(prop-2-yn-1-ylamino)adenosine" _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 N6 C1 A3N sing 1 n n N4 C2 A3N sing 2 n y N4 C5 A3N doub 3 n y C1 C2 A3N doub 4 n y C1 N1 A3N sing 5 n y C2 C3 A3N sing 6 n y C5 N3 A3N sing 7 n y C7 O3 A3N sing 8 n n C7 C8 A3N sing 9 n n C7 C6 A3N sing 10 n n N1 C4 A3N doub 11 n y O2 C8 A3N sing 12 n n C8 C9 A3N sing 13 n n C3 N3 A3N sing 14 n y C3 N2 A3N doub 15 n y N3 C6 A3N sing 16 n n C4 N2 A3N sing 17 n y C6 O1 A3N sing 18 n n C9 O1 A3N sing 19 n n C9 C10 A3N sing 20 n n C10 N5 A3N sing 21 n n N5 C11 A3N sing 22 n n C11 C12 A3N sing 23 n n C12 C13 A3N trip 24 n n C13 H1 A3N sing 25 n n C11 H2 A3N sing 26 n n C11 H3 A3N sing 27 n n N5 H4 A3N sing 28 n n C10 H6 A3N sing 29 n n C10 H7 A3N sing 30 n n C9 H8 A3N sing 31 n n C8 H9 A3N sing 32 n n O2 H10 A3N sing 33 n n C7 H11 A3N sing 34 n n O3 H12 A3N sing 35 n n C6 H13 A3N sing 36 n n C5 H14 A3N sing 37 n n C4 H15 A3N sing 38 n n N6 H16 A3N sing 39 n n N6 H17 A3N sing 40 n n # _atom_sites.entry_id 3V7Y _atom_sites.fract_transf_matrix[1][1] 0.015921 _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] 0.013214 _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] 0.00843 _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 CIT A 1 301 1 CIT CIT . C 3 A3N A 1 302 1 A3N A3N . D 3 A3N A 1 303 2 A3N A3N . E 4 HOH A 1 401 1 HOH HOH . E 4 HOH A 2 402 2 HOH HOH . E 4 HOH A 3 403 3 HOH HOH . E 4 HOH A 4 404 4 HOH HOH . E 4 HOH A 5 405 5 HOH HOH . E 4 HOH A 6 406 6 HOH HOH . E 4 HOH A 7 407 7 HOH HOH . E 4 HOH A 8 408 8 HOH HOH . E 4 HOH A 9 409 9 HOH HOH . E 4 HOH A 10 410 11 HOH HOH . E 4 HOH A 11 411 12 HOH HOH . E 4 HOH A 12 412 13 HOH HOH . E 4 HOH A 13 413 14 HOH HOH . E 4 HOH A 14 414 15 HOH HOH . E 4 HOH A 15 415 16 HOH HOH . E 4 HOH A 16 416 17 HOH HOH . E 4 HOH A 17 417 18 HOH HOH . E 4 HOH A 18 418 19 HOH HOH . E 4 HOH A 19 419 20 HOH HOH . E 4 HOH A 20 420 21 HOH HOH . E 4 HOH A 21 421 22 HOH HOH . E 4 HOH A 22 422 23 HOH HOH . E 4 HOH A 23 423 24 HOH HOH . E 4 HOH A 24 424 25 HOH HOH . E 4 HOH A 25 425 26 HOH HOH . E 4 HOH A 26 426 27 HOH HOH . E 4 HOH A 27 427 28 HOH HOH . E 4 HOH A 28 428 29 HOH HOH . E 4 HOH A 29 429 30 HOH HOH . E 4 HOH A 30 430 31 HOH HOH . E 4 HOH A 31 431 32 HOH HOH . E 4 HOH A 32 432 33 HOH HOH . E 4 HOH A 33 433 34 HOH HOH . E 4 HOH A 34 434 35 HOH HOH . E 4 HOH A 35 435 37 HOH HOH . E 4 HOH A 36 436 38 HOH HOH . E 4 HOH A 37 437 39 HOH HOH . E 4 HOH A 38 438 40 HOH HOH . E 4 HOH A 39 439 41 HOH HOH . E 4 HOH A 40 440 42 HOH HOH . E 4 HOH A 41 441 43 HOH HOH . E 4 HOH A 42 442 44 HOH HOH . E 4 HOH A 43 443 45 HOH HOH . E 4 HOH A 44 444 46 HOH HOH . E 4 HOH A 45 445 47 HOH HOH . E 4 HOH A 46 446 48 HOH HOH . E 4 HOH A 47 447 49 HOH HOH . E 4 HOH A 48 448 50 HOH HOH . E 4 HOH A 49 449 51 HOH HOH . E 4 HOH A 50 450 52 HOH HOH . E 4 HOH A 51 451 53 HOH HOH . E 4 HOH A 52 452 55 HOH HOH . E 4 HOH A 53 453 57 HOH HOH . E 4 HOH A 54 454 58 HOH HOH . E 4 HOH A 55 455 59 HOH HOH . E 4 HOH A 56 456 60 HOH HOH . E 4 HOH A 57 457 61 HOH HOH . E 4 HOH A 58 458 62 HOH HOH . E 4 HOH A 59 459 63 HOH HOH . E 4 HOH A 60 460 66 HOH HOH . E 4 HOH A 61 461 68 HOH HOH . E 4 HOH A 62 462 69 HOH HOH . E 4 HOH A 63 463 70 HOH HOH . E 4 HOH A 64 464 72 HOH HOH . E 4 HOH A 65 465 73 HOH HOH . E 4 HOH A 66 466 74 HOH HOH . E 4 HOH A 67 467 75 HOH HOH . E 4 HOH A 68 468 77 HOH HOH . E 4 HOH A 69 469 82 HOH HOH . E 4 HOH A 70 470 83 HOH HOH . E 4 HOH A 71 471 84 HOH HOH . E 4 HOH A 72 472 88 HOH HOH . E 4 HOH A 73 473 89 HOH HOH . E 4 HOH A 74 474 90 HOH HOH . E 4 HOH A 75 475 91 HOH HOH . E 4 HOH A 76 476 92 HOH HOH . E 4 HOH A 77 477 93 HOH HOH . E 4 HOH A 78 478 94 HOH HOH . E 4 HOH A 79 479 97 HOH HOH . E 4 HOH A 80 480 98 HOH HOH . E 4 HOH A 81 481 99 HOH HOH . E 4 HOH A 82 482 100 HOH HOH . E 4 HOH A 83 483 105 HOH HOH . E 4 HOH A 84 484 106 HOH HOH . E 4 HOH A 85 485 108 HOH HOH . E 4 HOH A 86 486 111 HOH HOH . E 4 HOH A 87 487 113 HOH HOH . E 4 HOH A 88 488 116 HOH HOH . E 4 HOH A 89 489 117 HOH HOH . E 4 HOH A 90 490 118 HOH HOH . E 4 HOH A 91 491 125 HOH HOH . E 4 HOH A 92 492 126 HOH HOH . E 4 HOH A 93 493 127 HOH HOH . E 4 HOH A 94 494 128 HOH HOH . E 4 HOH A 95 495 129 HOH HOH . E 4 HOH A 96 496 130 HOH HOH . E 4 HOH A 97 497 131 HOH HOH . E 4 HOH A 98 498 132 HOH HOH . E 4 HOH A 99 499 133 HOH HOH . E 4 HOH A 100 500 134 HOH HOH . E 4 HOH A 101 501 135 HOH HOH . E 4 HOH A 102 502 136 HOH HOH . E 4 HOH A 103 503 137 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 C C13 A3N . . . D 3 13.199 5.911 10.873 0.4 75.69 ? C13 A3N 303 A 1 HETATM 2 C C12 A3N . . . D 3 13.972 6.035 11.738 0.5 75.56 ? C12 A3N 303 A 1 HETATM 3 C C11 A3N . . . D 3 14.917 6.195 12.843 0.5 74.88 ? C11 A3N 303 A 1 HETATM 4 N N5 A3N . . . D 3 16.305 6.266 12.398 0.7 72.87 ? N5 A3N 303 A 1 HETATM 5 C C10 A3N . . . D 3 16.857 7.526 12.873 1 72.62 ? C10 A3N 303 A 1 HETATM 6 C C9 A3N . . . D 3 18.182 7.316 13.555 1 70.77 ? C9 A3N 303 A 1 HETATM 7 O O1 A3N . . . D 3 19.043 8.235 12.951 1 68.32 ? O1 A3N 303 A 1 HETATM 8 C C8 A3N . . . D 3 18.106 7.772 14.98 1 69.5 ? C8 A3N 303 A 1 HETATM 9 O O2 A3N . . . D 3 19.322 7.379 15.575 1 68.85 ? O2 A3N 303 A 1 HETATM 10 C C7 A3N . . . D 3 18.126 9.239 14.836 1 67.89 ? C7 A3N 303 A 1 HETATM 11 O O3 A3N . . . D 3 18.663 9.779 16.012 1 67.57 ? O3 A3N 303 A 1 HETATM 12 C C6 A3N . . . D 3 19.195 9.364 13.821 1 67.22 ? C6 A3N 303 A 1 HETATM 13 N N3 A3N . . . D 3 19.176 10.677 13.139 1 64.76 ? N3 A3N 303 A 1 HETATM 14 C C5 A3N . . . D 3 18.232 11.503 12.772 1 59.02 ? C5 A3N 303 A 1 HETATM 15 N N4 A3N . . . D 3 18.824 12.539 12.234 1 59.82 ? N4 A3N 303 A 1 HETATM 16 C C2 A3N . . . D 3 20.133 12.35 12.262 1 64.23 ? C2 A3N 303 A 1 HETATM 17 C C3 A3N . . . D 3 20.339 11.193 12.847 1 65.84 ? C3 A3N 303 A 1 HETATM 18 N N2 A3N . . . D 3 21.56 10.711 13.037 1 53.15 ? N2 A3N 303 A 1 HETATM 19 C C4 A3N . . . D 3 22.631 11.432 12.622 1 52.89 ? C4 A3N 303 A 1 HETATM 20 N N1 A3N . . . D 3 22.44 12.579 12.037 1 58.78 ? N1 A3N 303 A 1 HETATM 21 C C1 A3N . . . D 3 21.181 13.057 11.845 1 62.75 ? C1 A3N 303 A 1 HETATM 22 N N6 A3N . . . D 3 20.976 14.219 11.256 1 52.53 ? N6 A3N 303 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #