data_3V8N # _model_server_result.job_id 5fdLyYD2AmKOKHuLUUYkVw _model_server_result.datetime_utc '2024-11-28 06:08:28' _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 3v8n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 3V8N # _exptl.entry_id 3V8N _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 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 3V8N _cell.length_a 63.063 _cell.length_b 75.966 _cell.length_c 119.012 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3V8N _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 63.063 0 0 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 63.063 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _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 # _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 54 n n C6 N1 5NB doub 55 n y C6 C5 5NB sing 56 n y N1 C2 5NB sing 57 n y N7 C5 5NB sing 58 n y N7 C8 5NB doub 59 n y C5 C4 5NB doub 60 n y C2 N3 5NB doub 61 n y C8 BR8 5NB sing 62 n n C8 N9 5NB sing 63 n y C4 N3 5NB sing 64 n y C4 N9 5NB sing 65 n y O2' C2' 5NB sing 66 n n N9 C1' 5NB sing 67 n n C2' C1' 5NB sing 68 n n C2' C3' 5NB sing 69 n n C1' O4' 5NB sing 70 n n C3' O3' 5NB sing 71 n n C3' C4' 5NB sing 72 n n O4' C4' 5NB sing 73 n n C4' C5' 5NB sing 74 n n C5' N5' 5NB sing 75 n n O2' H1 5NB sing 76 n n C2' H2 5NB sing 77 n n C3' H3 5NB sing 78 n n O3' H4 5NB sing 79 n n C4' H5 5NB sing 80 n n C5' H6 5NB sing 81 n n C5' H7 5NB sing 82 n n N5' H8 5NB sing 83 n n N5' H9 5NB sing 84 n n C1' H11 5NB sing 85 n n C2 H12 5NB sing 86 n n N6 H13 5NB sing 87 n n N6 H14 5NB sing 88 n n # _atom_sites.entry_id 3V8N _atom_sites.fract_transf_matrix[1][1] 0.015857 _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] 0.013164 _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] 0.008403 _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 3 5CI A 1 302 2 5CI 5CI . D 4 CIT A 1 303 1 CIT CIT . E 5 HOH A 1 401 1 HOH HOH . E 5 HOH A 2 402 3 HOH HOH . E 5 HOH A 3 403 5 HOH HOH . E 5 HOH A 4 404 6 HOH HOH . E 5 HOH A 5 405 8 HOH HOH . E 5 HOH A 6 406 9 HOH HOH . E 5 HOH A 7 407 10 HOH HOH . E 5 HOH A 8 408 11 HOH HOH . E 5 HOH A 9 409 12 HOH HOH . E 5 HOH A 10 410 13 HOH HOH . E 5 HOH A 11 411 14 HOH HOH . E 5 HOH A 12 412 16 HOH HOH . E 5 HOH A 13 413 17 HOH HOH . E 5 HOH A 14 414 18 HOH HOH . E 5 HOH A 15 415 19 HOH HOH . E 5 HOH A 16 416 20 HOH HOH . E 5 HOH A 17 417 21 HOH HOH . E 5 HOH A 18 418 22 HOH HOH . E 5 HOH A 19 419 23 HOH HOH . E 5 HOH A 20 420 26 HOH HOH . E 5 HOH A 21 421 27 HOH HOH . E 5 HOH A 22 422 30 HOH HOH . E 5 HOH A 23 423 32 HOH HOH . E 5 HOH A 24 424 34 HOH HOH . E 5 HOH A 25 425 35 HOH HOH . E 5 HOH A 26 426 37 HOH HOH . E 5 HOH A 27 427 41 HOH HOH . E 5 HOH A 28 428 43 HOH HOH . E 5 HOH A 29 429 44 HOH HOH . E 5 HOH A 30 430 45 HOH HOH . E 5 HOH A 31 431 46 HOH HOH . E 5 HOH A 32 432 47 HOH HOH . E 5 HOH A 33 433 48 HOH HOH . E 5 HOH A 34 434 50 HOH HOH . E 5 HOH A 35 435 52 HOH HOH . E 5 HOH A 36 436 54 HOH HOH . E 5 HOH A 37 437 57 HOH HOH . E 5 HOH A 38 438 58 HOH HOH . E 5 HOH A 39 439 61 HOH HOH . E 5 HOH A 40 440 62 HOH HOH . E 5 HOH A 41 441 65 HOH HOH . E 5 HOH A 42 442 66 HOH HOH . E 5 HOH A 43 443 68 HOH HOH . E 5 HOH A 44 444 70 HOH HOH . E 5 HOH A 45 445 72 HOH HOH . E 5 HOH A 46 446 73 HOH HOH . E 5 HOH A 47 447 76 HOH HOH . E 5 HOH A 48 448 77 HOH HOH . E 5 HOH A 49 449 78 HOH HOH . E 5 HOH A 50 450 79 HOH HOH . E 5 HOH A 51 451 82 HOH HOH . E 5 HOH A 52 452 83 HOH HOH . E 5 HOH A 53 453 84 HOH HOH . E 5 HOH A 54 454 85 HOH HOH . E 5 HOH A 55 455 87 HOH HOH . E 5 HOH A 56 456 91 HOH HOH . E 5 HOH A 57 457 92 HOH HOH . E 5 HOH A 58 458 93 HOH HOH . E 5 HOH A 59 459 94 HOH HOH . E 5 HOH A 60 460 95 HOH HOH . E 5 HOH A 61 461 101 HOH HOH . E 5 HOH A 62 462 102 HOH HOH . E 5 HOH A 63 463 103 HOH HOH . E 5 HOH A 64 464 104 HOH HOH . E 5 HOH A 65 465 105 HOH HOH . E 5 HOH A 66 466 106 HOH HOH . E 5 HOH A 67 467 107 HOH HOH . E 5 HOH A 68 468 108 HOH HOH . E 5 HOH A 69 469 109 HOH HOH . E 5 HOH A 70 470 110 HOH HOH . E 5 HOH A 71 471 111 HOH HOH . E 5 HOH A 72 472 112 HOH HOH . E 5 HOH A 73 473 113 HOH HOH . E 5 HOH A 74 474 114 HOH HOH . E 5 HOH A 75 475 115 HOH HOH . E 5 HOH A 76 476 116 HOH HOH . E 5 HOH A 77 477 117 HOH HOH . E 5 HOH A 78 478 118 HOH HOH . E 5 HOH A 79 479 119 HOH HOH . E 5 HOH A 80 480 120 HOH HOH . E 5 HOH A 81 481 121 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 18.201 8.064 13.11 1 49.52 ? O2' 5NB 301 A 1 HETATM 2 C C2' 5NB . . . B 2 19.119 8.832 13.848 1 49.62 ? C2' 5NB 301 A 1 HETATM 3 C C3' 5NB . . . B 2 19.464 8.151 15.164 1 53.16 ? C3' 5NB 301 A 1 HETATM 4 O O3' 5NB . . . B 2 18.48 7.207 15.504 1 58.15 ? O3' 5NB 301 A 1 HETATM 5 C C4' 5NB . . . B 2 19.444 9.254 16.193 1 52.09 ? C4' 5NB 301 A 1 HETATM 6 C C5' 5NB . . . B 2 20.883 9.645 16.386 1 49.14 ? C5' 5NB 301 A 1 HETATM 7 N N5' 5NB . . . B 2 20.998 10.942 17.043 1 46.54 ? N5' 5NB 301 A 1 HETATM 8 O O4' 5NB . . . B 2 18.766 10.34 15.615 1 53.22 ? O4' 5NB 301 A 1 HETATM 9 C C1' 5NB . . . B 2 18.398 10.069 14.262 1 51.58 ? C1' 5NB 301 A 1 HETATM 10 N N9 5NB . . . B 2 18.832 11.212 13.477 1 52.26 ? N9 5NB 301 A 1 HETATM 11 C C8 5NB . . . B 2 18.028 12.141 13.033 1 51.82 ? C8 5NB 301 A 1 HETATM 12 BR BR8 5NB . . . B 2 16.191 12.122 13.32 0.6 44.81 ? BR8 5NB 301 A 1 HETATM 13 N N7 5NB . . . B 2 18.687 13.065 12.38 1 47.01 ? N7 5NB 301 A 1 HETATM 14 C C5 5NB . . . B 2 19.948 12.725 12.407 1 42.85 ? C5 5NB 301 A 1 HETATM 15 C C4 5NB . . . B 2 20.049 11.548 13.109 1 46.53 ? C4 5NB 301 A 1 HETATM 16 N N3 5NB . . . B 2 21.243 10.994 13.269 1 39.06 ? N3 5NB 301 A 1 HETATM 17 C C2 5NB . . . B 2 22.294 11.572 12.759 1 50.3 ? C2 5NB 301 A 1 HETATM 18 N N1 5NB . . . B 2 22.233 12.693 12.089 1 37.38 ? N1 5NB 301 A 1 HETATM 19 C C6 5NB . . . B 2 21.085 13.295 11.89 1 40.89 ? C6 5NB 301 A 1 HETATM 20 N N6 5NB . . . B 2 21.057 14.412 11.212 1 36.91 ? N6 5NB 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #