data_6B42 # _model_server_result.job_id YUkaUrcmXaQHnYBvdwysrQ _model_server_result.datetime_utc '2024-11-05 00:20:08' _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 6b42 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6B42 # _exptl.entry_id 6B42 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.222 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _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 6B42 _cell.length_a 39.738 _cell.length_b 39.738 _cell.length_c 141.133 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6B42 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 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 N5 O6 P' _chem_comp.formula_weight 331.222 _chem_comp.id D5M _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" _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 O5' C5' D5M sing 83 n n O5' P D5M sing 84 n n C5' C4' D5M sing 85 n n C5' "H5'1" D5M sing 86 n n C5' "H5'2" D5M sing 87 n n C4' O4' D5M sing 88 n n C4' C3' D5M sing 89 n n C4' H4' D5M sing 90 n n O4' C1' D5M sing 91 n n C3' O3' D5M sing 92 n n C3' C2' D5M sing 93 n n C3' H1 D5M sing 94 n n O3' H3' D5M sing 95 n n C2' C1' D5M sing 96 n n C2' "H2'1" D5M sing 97 n n C2' "H2'2" D5M sing 98 n n C1' N9 D5M sing 99 n n C1' H1' D5M sing 100 n n N9 C8 D5M sing 101 n y N9 C4 D5M sing 102 n y C8 N7 D5M doub 103 n y C8 H8 D5M sing 104 n n N7 C5 D5M sing 105 n y C5 C6 D5M sing 106 n y C5 C4 D5M doub 107 n y C6 N6 D5M sing 108 n n C6 N1 D5M doub 109 n y N6 HN61 D5M sing 110 n n N6 HN62 D5M sing 111 n n N1 C2 D5M sing 112 n y C2 N3 D5M doub 113 n y C2 H2 D5M sing 114 n n N3 C4 D5M sing 115 n y P O1P D5M doub 116 n n P O3P D5M sing 117 n n P O2P D5M sing 118 n n O3P H3P D5M sing 119 n n O2P H2P D5M sing 120 n n # _atom_sites.entry_id 6B42 _atom_sites.fract_transf_matrix[1][1] 0.025165 _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] 0.025165 _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] 0.007086 _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 D5M A 1 201 201 D5M D5M . C 3 HOH A 1 301 82 HOH HOH . C 3 HOH A 2 302 136 HOH HOH . C 3 HOH A 3 303 137 HOH HOH . C 3 HOH A 4 304 27 HOH HOH . C 3 HOH A 5 305 142 HOH HOH . C 3 HOH A 6 306 105 HOH HOH . C 3 HOH A 7 307 4 HOH HOH . C 3 HOH A 8 308 39 HOH HOH . C 3 HOH A 9 309 58 HOH HOH . C 3 HOH A 10 310 14 HOH HOH . C 3 HOH A 11 311 47 HOH HOH . C 3 HOH A 12 312 84 HOH HOH . C 3 HOH A 13 313 69 HOH HOH . C 3 HOH A 14 314 36 HOH HOH . C 3 HOH A 15 315 60 HOH HOH . C 3 HOH A 16 316 40 HOH HOH . C 3 HOH A 17 317 8 HOH HOH . C 3 HOH A 18 318 74 HOH HOH . C 3 HOH A 19 319 71 HOH HOH . C 3 HOH A 20 320 13 HOH HOH . C 3 HOH A 21 321 83 HOH HOH . C 3 HOH A 22 322 17 HOH HOH . C 3 HOH A 23 323 146 HOH HOH . C 3 HOH A 24 324 28 HOH HOH . C 3 HOH A 25 325 110 HOH HOH . C 3 HOH A 26 326 9 HOH HOH . C 3 HOH A 27 327 57 HOH HOH . C 3 HOH A 28 328 48 HOH HOH . C 3 HOH A 29 329 127 HOH HOH . C 3 HOH A 30 330 113 HOH HOH . C 3 HOH A 31 331 70 HOH HOH . C 3 HOH A 32 332 129 HOH HOH . C 3 HOH A 33 333 49 HOH HOH . C 3 HOH A 34 334 24 HOH HOH . C 3 HOH A 35 335 53 HOH HOH . C 3 HOH A 36 336 54 HOH HOH . C 3 HOH A 37 337 55 HOH HOH . C 3 HOH A 38 338 20 HOH HOH . C 3 HOH A 39 339 30 HOH HOH . C 3 HOH A 40 340 68 HOH HOH . C 3 HOH A 41 341 15 HOH HOH . C 3 HOH A 42 342 121 HOH HOH . C 3 HOH A 43 343 43 HOH HOH . C 3 HOH A 44 344 37 HOH HOH . C 3 HOH A 45 345 33 HOH HOH . C 3 HOH A 46 346 22 HOH HOH . C 3 HOH A 47 347 46 HOH HOH . C 3 HOH A 48 348 45 HOH HOH . C 3 HOH A 49 349 10 HOH HOH . C 3 HOH A 50 350 5 HOH HOH . C 3 HOH A 51 351 6 HOH HOH . C 3 HOH A 52 352 131 HOH HOH . C 3 HOH A 53 353 112 HOH HOH . C 3 HOH A 54 354 102 HOH HOH . C 3 HOH A 55 355 35 HOH HOH . C 3 HOH A 56 356 106 HOH HOH . C 3 HOH A 57 357 89 HOH HOH . C 3 HOH A 58 358 34 HOH HOH . C 3 HOH A 59 359 72 HOH HOH . C 3 HOH A 60 360 73 HOH HOH . C 3 HOH A 61 361 97 HOH HOH . C 3 HOH A 62 362 138 HOH HOH . C 3 HOH A 63 363 94 HOH HOH . C 3 HOH A 64 364 126 HOH HOH . C 3 HOH A 65 365 108 HOH HOH . C 3 HOH A 66 366 44 HOH HOH . C 3 HOH A 67 367 149 HOH HOH . C 3 HOH A 68 368 50 HOH HOH . C 3 HOH A 69 369 21 HOH HOH . C 3 HOH A 70 370 1 HOH HOH . C 3 HOH A 71 371 18 HOH HOH . C 3 HOH A 72 372 12 HOH HOH . C 3 HOH A 73 373 56 HOH HOH . C 3 HOH A 74 374 3 HOH HOH . C 3 HOH A 75 375 51 HOH HOH . C 3 HOH A 76 376 61 HOH HOH . C 3 HOH A 77 377 32 HOH HOH . C 3 HOH A 78 378 19 HOH HOH . C 3 HOH A 79 379 11 HOH HOH . C 3 HOH A 80 380 111 HOH HOH . C 3 HOH A 81 381 75 HOH HOH . C 3 HOH A 82 382 123 HOH HOH . C 3 HOH A 83 383 78 HOH HOH . C 3 HOH A 84 384 67 HOH HOH . C 3 HOH A 85 385 93 HOH HOH . C 3 HOH A 86 386 133 HOH HOH . C 3 HOH A 87 387 16 HOH HOH . C 3 HOH A 88 388 90 HOH HOH . C 3 HOH A 89 389 80 HOH HOH . C 3 HOH A 90 390 2 HOH HOH . C 3 HOH A 91 391 41 HOH HOH . C 3 HOH A 92 392 23 HOH HOH . C 3 HOH A 93 393 26 HOH HOH . C 3 HOH A 94 394 66 HOH HOH . C 3 HOH A 95 395 59 HOH HOH . C 3 HOH A 96 396 64 HOH HOH . C 3 HOH A 97 397 25 HOH HOH . C 3 HOH A 98 398 143 HOH HOH . C 3 HOH A 99 399 65 HOH HOH . C 3 HOH A 100 400 31 HOH HOH . C 3 HOH A 101 401 116 HOH HOH . C 3 HOH A 102 402 88 HOH HOH . C 3 HOH A 103 403 100 HOH HOH . C 3 HOH A 104 404 52 HOH HOH . C 3 HOH A 105 405 141 HOH HOH . C 3 HOH A 106 406 140 HOH HOH . C 3 HOH A 107 407 38 HOH HOH . C 3 HOH A 108 408 29 HOH HOH . C 3 HOH A 109 409 7 HOH HOH . C 3 HOH A 110 410 122 HOH HOH . C 3 HOH A 111 411 120 HOH HOH . C 3 HOH A 112 412 145 HOH HOH . C 3 HOH A 113 413 79 HOH HOH . C 3 HOH A 114 414 76 HOH HOH . C 3 HOH A 115 415 62 HOH HOH . C 3 HOH A 116 416 103 HOH HOH . C 3 HOH A 117 417 144 HOH HOH . C 3 HOH A 118 418 119 HOH HOH . C 3 HOH A 119 419 77 HOH HOH . C 3 HOH A 120 420 148 HOH HOH . C 3 HOH A 121 421 125 HOH HOH . C 3 HOH A 122 422 135 HOH HOH . C 3 HOH A 123 423 139 HOH HOH . C 3 HOH A 124 424 87 HOH HOH . C 3 HOH A 125 425 118 HOH HOH . C 3 HOH A 126 426 147 HOH HOH . C 3 HOH A 127 427 86 HOH HOH . C 3 HOH A 128 428 101 HOH HOH . C 3 HOH A 129 429 132 HOH HOH . C 3 HOH A 130 430 96 HOH HOH . C 3 HOH A 131 431 114 HOH HOH . C 3 HOH A 132 432 81 HOH HOH . C 3 HOH A 133 433 115 HOH HOH . C 3 HOH A 134 434 109 HOH HOH . C 3 HOH A 135 435 42 HOH HOH . C 3 HOH A 136 436 95 HOH HOH . C 3 HOH A 137 437 98 HOH HOH . C 3 HOH A 138 438 128 HOH HOH . C 3 HOH A 139 439 63 HOH HOH . C 3 HOH A 140 440 117 HOH HOH . C 3 HOH A 141 441 85 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 O5' D5M . . . B 2 13.024 9.598 11.83 1 8.47 ? O5' D5M 201 A 1 HETATM 2 C C5' D5M . . . B 2 12.067 9.727 12.887 1 8.19 ? C5' D5M 201 A 1 HETATM 3 C C4' D5M . . . B 2 11.061 10.84 12.628 1 7.12 ? C4' D5M 201 A 1 HETATM 4 O O4' D5M . . . B 2 10.098 10.821 13.688 1 8.19 ? O4' D5M 201 A 1 HETATM 5 C C3' D5M . . . B 2 11.692 12.228 12.625 1 7.07 ? C3' D5M 201 A 1 HETATM 6 O O3' D5M . . . B 2 11.149 13.044 11.577 1 8.01 ? O3' D5M 201 A 1 HETATM 7 C C2' D5M . . . B 2 11.333 12.789 13.99 1 8.09 ? C2' D5M 201 A 1 HETATM 8 C C1' D5M . . . B 2 10.013 12.093 14.296 1 7.66 ? C1' D5M 201 A 1 HETATM 9 N N9 D5M . . . B 2 9.776 11.908 15.734 1 7.02 ? N9 D5M 201 A 1 HETATM 10 C C8 D5M . . . B 2 10.633 11.364 16.628 1 7.49 ? C8 D5M 201 A 1 HETATM 11 N N7 D5M . . . B 2 10.097 11.363 17.871 1 8.23 ? N7 D5M 201 A 1 HETATM 12 C C5 D5M . . . B 2 8.873 11.903 17.739 1 7.5 ? C5 D5M 201 A 1 HETATM 13 C C6 D5M . . . B 2 7.792 12.214 18.652 1 7.87 ? C6 D5M 201 A 1 HETATM 14 N N6 D5M . . . B 2 7.931 11.926 19.966 1 9.43 ? N6 D5M 201 A 1 HETATM 15 N N1 D5M . . . B 2 6.676 12.771 18.151 1 7.92 ? N1 D5M 201 A 1 HETATM 16 C C2 D5M . . . B 2 6.543 13.061 16.837 1 8.19 ? C2 D5M 201 A 1 HETATM 17 N N3 D5M . . . B 2 7.502 12.831 15.919 1 7.76 ? N3 D5M 201 A 1 HETATM 18 C C4 D5M . . . B 2 8.657 12.26 16.339 1 7.93 ? C4 D5M 201 A 1 HETATM 19 P P D5M . . . B 2 12.816 8.482 10.686 1 6.8 ? P D5M 201 A 1 HETATM 20 O O1P D5M . . . B 2 13.949 8.724 9.736 1 8.17 ? O1P D5M 201 A 1 HETATM 21 O O3P D5M . . . B 2 11.473 8.813 10.065 1 8.36 ? O3P D5M 201 A 1 HETATM 22 O O2P D5M . . . B 2 12.839 7.118 11.331 1 7.57 ? O2P D5M 201 A 1 HETATM 23 H "H5'1" D5M . . . B 2 12.592 9.929 13.823 1 9.83 ? "H5'1" D5M 201 A 1 HETATM 24 H "H5'2" D5M . . . B 2 11.533 8.782 13.005 1 9.83 ? "H5'2" D5M 201 A 1 HETATM 25 H H4' D5M . . . B 2 10.568 10.665 11.662 1 8.54 ? H4' D5M 201 A 1 HETATM 26 H H1 D5M . . . B 2 12.784 12.142 12.534 1 8.48 ? H1 D5M 201 A 1 HETATM 27 H H3' D5M . . . B 2 10.183 13.006 11.607 1 9.61 ? H3' D5M 201 A 1 HETATM 28 H "H2'1" D5M . . . B 2 11.205 13.873 13.949 1 9.71 ? "H2'1" D5M 201 A 1 HETATM 29 H "H2'2" D5M . . . B 2 12.093 12.536 14.732 1 9.71 ? "H2'2" D5M 201 A 1 HETATM 30 H H1' D5M . . . B 2 9.192 12.67 13.849 1 9.19 ? H1' D5M 201 A 1 HETATM 31 H H8 D5M . . . B 2 11.624 11 16.387 1 8.99 ? H8 D5M 201 A 1 HETATM 32 H HN61 D5M . . . B 2 8.779 11.491 20.301 1 11.32 ? HN61 D5M 201 A 1 HETATM 33 H HN62 D5M . . . B 2 7.173 12.115 20.607 1 11.32 ? HN62 D5M 201 A 1 HETATM 34 H H2 D5M . . . B 2 5.621 13.523 16.506 1 9.83 ? H2 D5M 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 34 #