data_3V8Q # _model_server_result.job_id WqFlNW6hfD03AwHvvpfq7Q _model_server_result.datetime_utc '2024-11-28 07:02:30' _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 3v8q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 3V8Q # _exptl.entry_id 3V8Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 266.257 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-amino-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 3V8Q _cell.length_a 63.169 _cell.length_b 75.06 _cell.length_c 118.588 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3V8Q _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 63.169 0 0 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 63.169 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 H14 N6 O3' _chem_comp.formula_weight 266.257 _chem_comp.id 5N5 _chem_comp.mon_nstd_flag . _chem_comp.name "5'-amino-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 5N5 sing 1 n n N7 C5 5N5 sing 2 n y N7 C8 5N5 doub 3 n y C6 C5 5N5 doub 4 n y C6 N1 5N5 sing 5 n y C5 C4 5N5 sing 6 n y C8 N9 5N5 sing 7 n y C2' O2' 5N5 sing 8 n n C2' C3' 5N5 sing 9 n n C2' C1' 5N5 sing 10 n n N1 C2 5N5 doub 11 n y O3' C3' 5N5 sing 12 n n C3' C4' 5N5 sing 13 n n C4 N9 5N5 sing 14 n y C4 N3 5N5 doub 15 n y N9 C1' 5N5 sing 16 n n C2 N3 5N5 sing 17 n y C1' O4' 5N5 sing 18 n n C4' O4' 5N5 sing 19 n n C4' C5' 5N5 sing 20 n n C5' N5' 5N5 sing 21 n n O2' H1 5N5 sing 22 n n C2' H2 5N5 sing 23 n n C3' H3 5N5 sing 24 n n O3' H4 5N5 sing 25 n n C4' H5 5N5 sing 26 n n C5' H6 5N5 sing 27 n n C5' H7 5N5 sing 28 n n N5' H8 5N5 sing 29 n n N5' H9 5N5 sing 30 n n C1' H11 5N5 sing 31 n n C8 H12 5N5 sing 32 n n C2 H13 5N5 sing 33 n n N6 H14 5N5 sing 34 n n N6 H15 5N5 sing 35 n n # _atom_sites.entry_id 3V8Q _atom_sites.fract_transf_matrix[1][1] 0.015831 _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] 0.013323 _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] 0.008433 _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 5N5 A 1 301 1 5N5 5N5 . C 3 GOL A 1 302 1 GOL GOL . D 4 CIT A 1 303 1 CIT CIT . E 5 HOH A 1 401 1 HOH HOH . E 5 HOH A 2 402 2 HOH HOH . E 5 HOH A 3 403 4 HOH HOH . E 5 HOH A 4 404 5 HOH HOH . E 5 HOH A 5 405 6 HOH HOH . E 5 HOH A 6 406 7 HOH HOH . E 5 HOH A 7 407 8 HOH HOH . E 5 HOH A 8 408 9 HOH HOH . E 5 HOH A 9 409 10 HOH HOH . E 5 HOH A 10 410 11 HOH HOH . E 5 HOH A 11 411 12 HOH HOH . E 5 HOH A 12 412 13 HOH HOH . E 5 HOH A 13 413 14 HOH HOH . E 5 HOH A 14 414 15 HOH HOH . E 5 HOH A 15 415 16 HOH HOH . E 5 HOH A 16 416 17 HOH HOH . E 5 HOH A 17 417 18 HOH HOH . E 5 HOH A 18 418 19 HOH HOH . E 5 HOH A 19 419 20 HOH HOH . E 5 HOH A 20 420 21 HOH HOH . E 5 HOH A 21 421 22 HOH HOH . E 5 HOH A 22 422 23 HOH HOH . E 5 HOH A 23 423 24 HOH HOH . E 5 HOH A 24 424 25 HOH HOH . E 5 HOH A 25 425 26 HOH HOH . E 5 HOH A 26 426 27 HOH HOH . E 5 HOH A 27 427 28 HOH HOH . E 5 HOH A 28 428 29 HOH HOH . E 5 HOH A 29 429 30 HOH HOH . E 5 HOH A 30 430 31 HOH HOH . E 5 HOH A 31 431 32 HOH HOH . E 5 HOH A 32 432 33 HOH HOH . E 5 HOH A 33 433 34 HOH HOH . E 5 HOH A 34 434 35 HOH HOH . E 5 HOH A 35 435 36 HOH HOH . E 5 HOH A 36 436 37 HOH HOH . E 5 HOH A 37 437 38 HOH HOH . E 5 HOH A 38 438 39 HOH HOH . E 5 HOH A 39 439 40 HOH HOH . E 5 HOH A 40 440 41 HOH HOH . E 5 HOH A 41 441 43 HOH HOH . E 5 HOH A 42 442 44 HOH HOH . E 5 HOH A 43 443 45 HOH HOH . E 5 HOH A 44 444 46 HOH HOH . E 5 HOH A 45 445 47 HOH HOH . E 5 HOH A 46 446 49 HOH HOH . E 5 HOH A 47 447 50 HOH HOH . E 5 HOH A 48 448 51 HOH HOH . E 5 HOH A 49 449 52 HOH HOH . E 5 HOH A 50 450 53 HOH HOH . E 5 HOH A 51 451 54 HOH HOH . E 5 HOH A 52 452 55 HOH HOH . E 5 HOH A 53 453 56 HOH HOH . E 5 HOH A 54 454 57 HOH HOH . E 5 HOH A 55 455 58 HOH HOH . E 5 HOH A 56 456 59 HOH HOH . E 5 HOH A 57 457 60 HOH HOH . E 5 HOH A 58 458 61 HOH HOH . E 5 HOH A 59 459 63 HOH HOH . E 5 HOH A 60 460 64 HOH HOH . E 5 HOH A 61 461 65 HOH HOH . E 5 HOH A 62 462 66 HOH HOH . E 5 HOH A 63 463 67 HOH HOH . E 5 HOH A 64 464 68 HOH HOH . E 5 HOH A 65 465 70 HOH HOH . E 5 HOH A 66 466 71 HOH HOH . E 5 HOH A 67 467 72 HOH HOH . E 5 HOH A 68 468 73 HOH HOH . E 5 HOH A 69 469 74 HOH HOH . E 5 HOH A 70 470 76 HOH HOH . E 5 HOH A 71 471 77 HOH HOH . E 5 HOH A 72 472 78 HOH HOH . E 5 HOH A 73 473 79 HOH HOH . E 5 HOH A 74 474 80 HOH HOH . E 5 HOH A 75 475 81 HOH HOH . E 5 HOH A 76 476 82 HOH HOH . E 5 HOH A 77 477 83 HOH HOH . E 5 HOH A 78 478 84 HOH HOH . E 5 HOH A 79 479 85 HOH HOH . E 5 HOH A 80 480 86 HOH HOH . E 5 HOH A 81 481 87 HOH HOH . E 5 HOH A 82 482 88 HOH HOH . E 5 HOH A 83 483 89 HOH HOH . E 5 HOH A 84 484 90 HOH HOH . E 5 HOH A 85 485 91 HOH HOH . E 5 HOH A 86 486 92 HOH HOH . E 5 HOH A 87 487 93 HOH HOH . E 5 HOH A 88 488 94 HOH HOH . E 5 HOH A 89 489 95 HOH HOH . E 5 HOH A 90 490 96 HOH HOH . E 5 HOH A 91 491 98 HOH HOH . E 5 HOH A 92 492 99 HOH HOH . E 5 HOH A 93 493 100 HOH HOH . E 5 HOH A 94 494 101 HOH HOH . E 5 HOH A 95 495 102 HOH HOH . E 5 HOH A 96 496 103 HOH HOH . E 5 HOH A 97 497 104 HOH HOH . E 5 HOH A 98 498 105 HOH HOH . E 5 HOH A 99 499 106 HOH HOH . E 5 HOH A 100 500 107 HOH HOH . E 5 HOH A 101 501 108 HOH HOH . E 5 HOH A 102 502 109 HOH HOH . E 5 HOH A 103 503 110 HOH HOH . E 5 HOH A 104 504 111 HOH HOH . E 5 HOH A 105 505 112 HOH HOH . E 5 HOH A 106 506 113 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' 5N5 . . . B 2 17.812 10.407 8.243 0.8 25.68 ? O2' 5N5 301 A 1 HETATM 2 C C2' 5N5 . . . B 2 16.651 9.593 8.12 0.8 31.48 ? C2' 5N5 301 A 1 HETATM 3 C C3' 5N5 . . . B 2 15.385 10.39 8.469 0.8 32.17 ? C3' 5N5 301 A 1 HETATM 4 O O3' 5N5 . . . B 2 15.582 11.808 8.306 0.8 25.98 ? O3' 5N5 301 A 1 HETATM 5 C C4' 5N5 . . . B 2 15.178 10.032 9.937 0.8 38.57 ? C4' 5N5 301 A 1 HETATM 6 C C5' 5N5 . . . B 2 13.712 10.239 10.336 0.8 39.44 ? C5' 5N5 301 A 1 HETATM 7 N N5' 5N5 . . . B 2 13.587 10.145 11.8 0.8 42.44 ? N5' 5N5 301 A 1 HETATM 8 O O4' 5N5 . . . B 2 15.49 8.62 9.953 0.8 42.15 ? O4' 5N5 301 A 1 HETATM 9 C C1' 5N5 . . . B 2 16.716 8.489 9.182 0.8 37.24 ? C1' 5N5 301 A 1 HETATM 10 N N9 5N5 . . . B 2 16.813 7.144 8.521 0.8 42.95 ? N9 5N5 301 A 1 HETATM 11 C C8 5N5 . . . B 2 15.836 6.505 7.858 0.8 45.65 ? C8 5N5 301 A 1 HETATM 12 N N7 5N5 . . . B 2 16.288 5.33 7.411 0.8 44.57 ? N7 5N5 301 A 1 HETATM 13 C C5 5N5 . . . B 2 17.561 5.213 7.791 0.8 42.96 ? C5 5N5 301 A 1 HETATM 14 C C4 5N5 . . . B 2 17.893 6.365 8.497 0.8 42.84 ? C4 5N5 301 A 1 HETATM 15 N N3 5N5 . . . B 2 19.136 6.498 8.998 0.8 40.42 ? N3 5N5 301 A 1 HETATM 16 C C2 5N5 . . . B 2 20.037 5.539 8.81 0.8 37.77 ? C2 5N5 301 A 1 HETATM 17 N N1 5N5 . . . B 2 19.757 4.429 8.138 0.8 35.46 ? N1 5N5 301 A 1 HETATM 18 C C6 5N5 . . . B 2 18.535 4.229 7.621 0.8 40.46 ? C6 5N5 301 A 1 HETATM 19 N N6 5N5 . . . B 2 18.264 3.106 6.95 0.8 40.63 ? N6 5N5 301 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 19 #