data_3V8R # _model_server_result.job_id tvd5R8a3UbQDfRn4bILwDw _model_server_result.datetime_utc '2024-11-28 06:27:31' _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 3v8r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 3V8R # _exptl.entry_id 3V8R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 345.153 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-amino-8-bromo-5'-deoxyadenosine" _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 3V8R _cell.length_a 62.718 _cell.length_b 77.135 _cell.length_c 118.358 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3V8R _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 62.718 0 0 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 62.718 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 ? 2 B N N ? 2 C N N # _chem_comp.formula 'C10 H13 Br N6 O3' _chem_comp.formula_weight 345.153 _chem_comp.id 5NB _chem_comp.mon_nstd_flag . _chem_comp.name "5'-amino-8-bromo-5'-deoxyadenosine" _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 C6 5NB sing 1 n n C6 N1 5NB doub 2 n y C6 C5 5NB sing 3 n y N1 C2 5NB sing 4 n y N7 C5 5NB sing 5 n y N7 C8 5NB doub 6 n y C5 C4 5NB doub 7 n y C2 N3 5NB doub 8 n y C8 BR8 5NB sing 9 n n C8 N9 5NB sing 10 n y C4 N3 5NB sing 11 n y C4 N9 5NB sing 12 n y O2' C2' 5NB sing 13 n n N9 C1' 5NB sing 14 n n C2' C1' 5NB sing 15 n n C2' C3' 5NB sing 16 n n C1' O4' 5NB sing 17 n n C3' O3' 5NB sing 18 n n C3' C4' 5NB sing 19 n n O4' C4' 5NB sing 20 n n C4' C5' 5NB sing 21 n n C5' N5' 5NB sing 22 n n O2' H1 5NB sing 23 n n C2' H2 5NB sing 24 n n C3' H3 5NB sing 25 n n O3' H4 5NB sing 26 n n C4' H5 5NB sing 27 n n C5' H6 5NB sing 28 n n C5' H7 5NB sing 29 n n N5' H8 5NB sing 30 n n N5' H9 5NB sing 31 n n C1' H11 5NB sing 32 n n C2 H12 5NB sing 33 n n N6 H13 5NB sing 34 n n N6 H14 5NB sing 35 n n # _atom_sites.entry_id 3V8R _atom_sites.fract_transf_matrix[1][1] 0.015944 _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] 0.012964 _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] 0.008449 _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 5NB A 1 301 1 5NB 5NB . C 2 5NB A 1 302 2 5NB 5NB . D 3 CIT A 1 303 1 CIT CIT . 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 11 HOH HOH . E 4 HOH A 10 410 12 HOH HOH . E 4 HOH A 11 411 13 HOH HOH . E 4 HOH A 12 412 14 HOH HOH . E 4 HOH A 13 413 15 HOH HOH . E 4 HOH A 14 414 16 HOH HOH . E 4 HOH A 15 415 17 HOH HOH . E 4 HOH A 16 416 18 HOH HOH . E 4 HOH A 17 417 19 HOH HOH . E 4 HOH A 18 418 20 HOH HOH . E 4 HOH A 19 419 22 HOH HOH . E 4 HOH A 20 420 23 HOH HOH . E 4 HOH A 21 421 24 HOH HOH . E 4 HOH A 22 422 25 HOH HOH . E 4 HOH A 23 423 26 HOH HOH . E 4 HOH A 24 424 27 HOH HOH . E 4 HOH A 25 425 29 HOH HOH . E 4 HOH A 26 426 30 HOH HOH . E 4 HOH A 27 427 31 HOH HOH . E 4 HOH A 28 428 32 HOH HOH . E 4 HOH A 29 429 33 HOH HOH . E 4 HOH A 30 430 36 HOH HOH . E 4 HOH A 31 431 38 HOH HOH . E 4 HOH A 32 432 39 HOH HOH . E 4 HOH A 33 433 42 HOH HOH . E 4 HOH A 34 434 43 HOH HOH . E 4 HOH A 35 435 45 HOH HOH . E 4 HOH A 36 436 46 HOH HOH . E 4 HOH A 37 437 47 HOH HOH . E 4 HOH A 38 438 49 HOH HOH . E 4 HOH A 39 439 50 HOH HOH . E 4 HOH A 40 440 51 HOH HOH . E 4 HOH A 41 441 52 HOH HOH . E 4 HOH A 42 442 53 HOH HOH . E 4 HOH A 43 443 55 HOH HOH . E 4 HOH A 44 444 56 HOH HOH . E 4 HOH A 45 445 57 HOH HOH . E 4 HOH A 46 446 58 HOH HOH . E 4 HOH A 47 447 59 HOH HOH . E 4 HOH A 48 448 60 HOH HOH . E 4 HOH A 49 449 61 HOH HOH . E 4 HOH A 50 450 62 HOH HOH . E 4 HOH A 51 451 63 HOH HOH . E 4 HOH A 52 452 64 HOH HOH . E 4 HOH A 53 453 65 HOH HOH . E 4 HOH A 54 454 68 HOH HOH . E 4 HOH A 55 455 69 HOH HOH . E 4 HOH A 56 456 71 HOH HOH . E 4 HOH A 57 457 73 HOH HOH . E 4 HOH A 58 458 75 HOH HOH . E 4 HOH A 59 459 76 HOH HOH . E 4 HOH A 60 460 77 HOH HOH . E 4 HOH A 61 461 78 HOH HOH . E 4 HOH A 62 462 79 HOH HOH . E 4 HOH A 63 463 80 HOH HOH . E 4 HOH A 64 464 81 HOH HOH . E 4 HOH A 65 465 82 HOH HOH . E 4 HOH A 66 466 83 HOH HOH . E 4 HOH A 67 467 84 HOH HOH . E 4 HOH A 68 468 88 HOH HOH . E 4 HOH A 69 469 91 HOH HOH . E 4 HOH A 70 470 95 HOH HOH . E 4 HOH A 71 471 96 HOH HOH . E 4 HOH A 72 472 97 HOH HOH . E 4 HOH A 73 473 98 HOH HOH . E 4 HOH A 74 474 99 HOH HOH . E 4 HOH A 75 475 101 HOH HOH . E 4 HOH A 76 476 102 HOH HOH . E 4 HOH A 77 477 103 HOH HOH . E 4 HOH A 78 478 104 HOH HOH . E 4 HOH A 79 479 105 HOH HOH . E 4 HOH A 80 480 106 HOH HOH . E 4 HOH A 81 481 107 HOH HOH . E 4 HOH A 82 482 108 HOH HOH . E 4 HOH A 83 483 109 HOH HOH . E 4 HOH A 84 484 110 HOH HOH . E 4 HOH A 85 485 112 HOH HOH . E 4 HOH A 86 486 113 HOH HOH . E 4 HOH A 87 487 114 HOH HOH . E 4 HOH A 88 488 115 HOH HOH . E 4 HOH A 89 489 116 HOH HOH . E 4 HOH A 90 490 117 HOH HOH . E 4 HOH A 91 491 118 HOH HOH . E 4 HOH A 92 492 120 HOH HOH . E 4 HOH A 93 493 121 HOH HOH . E 4 HOH A 94 494 122 HOH HOH . E 4 HOH A 95 495 123 HOH HOH . E 4 HOH A 96 496 124 HOH HOH . E 4 HOH A 97 497 125 HOH HOH . E 4 HOH A 98 498 126 HOH HOH . E 4 HOH A 99 499 127 HOH HOH . E 4 HOH A 100 500 128 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 O2' 5NB . . . B 2 17.748 8.309 12.775 1 44.94 ? O2' 5NB 301 A 1 HETATM 2 C C2' 5NB . . . B 2 18.658 8.959 13.676 1 41.95 ? C2' 5NB 301 A 1 HETATM 3 C C3' 5NB . . . B 2 18.804 8.17 14.959 1 47.71 ? C3' 5NB 301 A 1 HETATM 4 O O3' 5NB . . . B 2 17.546 7.57 15.293 1 49.92 ? O3' 5NB 301 A 1 HETATM 5 C C4' 5NB . . . B 2 19.123 9.252 16.004 1 49.87 ? C4' 5NB 301 A 1 HETATM 6 C C5' 5NB . . . B 2 20.632 9.484 16.257 1 51.56 ? C5' 5NB 301 A 1 HETATM 7 N N5' 5NB . . . B 2 20.816 10.796 16.908 1 52.69 ? N5' 5NB 301 A 1 HETATM 8 O O4' 5NB . . . B 2 18.548 10.479 15.496 1 48.71 ? O4' 5NB 301 A 1 HETATM 9 C C1' 5NB . . . B 2 18.015 10.234 14.187 1 40.9 ? C1' 5NB 301 A 1 HETATM 10 N N9 5NB . . . B 2 18.479 11.334 13.36 1 40.61 ? N9 5NB 301 A 1 HETATM 11 C C8 5NB . . . B 2 17.689 12.222 12.8 1 42.24 ? C8 5NB 301 A 1 HETATM 12 BR BR8 5NB . . . B 2 15.823 12.159 13.004 0.75 43.52 ? BR8 5NB 301 A 1 HETATM 13 N N7 5NB . . . B 2 18.379 13.116 12.108 1 43.82 ? N7 5NB 301 A 1 HETATM 14 C C5 5NB . . . B 2 19.667 12.792 12.241 1 41.09 ? C5 5NB 301 A 1 HETATM 15 C C4 5NB . . . B 2 19.735 11.653 13.046 1 40.69 ? C4 5NB 301 A 1 HETATM 16 N N3 5NB . . . B 2 20.936 11.099 13.337 1 38.87 ? N3 5NB 301 A 1 HETATM 17 C C2 5NB . . . B 2 22.044 11.646 12.859 1 40.65 ? C2 5NB 301 A 1 HETATM 18 N N1 5NB . . . B 2 22.018 12.732 12.084 1 43.47 ? N1 5NB 301 A 1 HETATM 19 C C6 5NB . . . B 2 20.858 13.335 11.744 1 41.34 ? C6 5NB 301 A 1 HETATM 20 N N6 5NB . . . B 2 20.852 14.42 10.959 1 38.42 ? N6 5NB 301 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #