data_7DH1 # _model_server_result.job_id UljDLHNFlo8s93qbkRRwRg _model_server_result.datetime_utc '2024-12-19 10:49:21' _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 7dh1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 7DH1 # _exptl.entry_id 7DH1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.225 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description 2,3-dihydroxanthosine _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 120 _cell.entry_id 7DH1 _cell.length_a 118.776 _cell.length_b 118.776 _cell.length_c 39.54 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DH1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall 'P 61' _symmetry.space_group_name_H-M 'P 61' # _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,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A ND1 HIS 56 A HIS 80 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc2 A SG CYS 86 A CYS 110 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc3 A SG CYS 89 A CYS 113 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc4 C ZN ZN . A ZN 201 1_555 D O2 4UO . A 4UO 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc5 B ND1 HIS 56 D HIS 80 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc6 B SG CYS 86 D CYS 110 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc7 B SG CYS 89 D CYS 113 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc8 E ZN ZN . D ZN 201 1_555 F O2 4UO . D 4UO 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? # _chem_comp.formula 'C10 H12 N4 O6' _chem_comp.formula_weight 284.225 _chem_comp.id 4UO _chem_comp.mon_nstd_flag . _chem_comp.name 2,3-dihydroxanthosine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Xanthosine # 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 N7 C8 4UO doub 1 n y N7 C5 4UO sing 2 n y C8 N9 4UO sing 3 n y O6 C6 4UO doub 4 n n C5 C6 4UO sing 5 n n C5 C4 4UO doub 6 n y C6 N1 4UO sing 7 n n N9 C4 4UO sing 8 n y N9 C1' 4UO sing 9 n n C4 N3 4UO sing 10 n n C1' C2' 4UO sing 11 n n C1' O4' 4UO sing 12 n n O2' C2' 4UO sing 13 n n N1 C2 4UO sing 14 n n C2' C3' 4UO sing 15 n n O4' C4' 4UO sing 16 n n N3 C2 4UO sing 17 n n C2 O2 4UO doub 18 n n C3' C4' 4UO sing 19 n n C3' O3' 4UO sing 20 n n C4' C5' 4UO sing 21 n n O5' C5' 4UO sing 22 n n N1 H1 4UO sing 23 n n N3 H2 4UO sing 24 n n C8 H3 4UO sing 25 n n C1' H4 4UO sing 26 n n C4' H5 4UO sing 27 n n C5' H6 4UO sing 28 n n C5' H7 4UO sing 29 n n O5' H8 4UO sing 30 n n C3' H9 4UO sing 31 n n O3' H10 4UO sing 32 n n C2' H11 4UO sing 33 n n O2' H12 4UO sing 34 n n # _atom_sites.entry_id 7DH1 _atom_sites.fract_transf_matrix[1][1] 0.008419 _atom_sites.fract_transf_matrix[1][2] 0.004861 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009722 _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] 0.025291 _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 C 2 ZN A 1 201 2 ZN ZN . D 3 4UO A 1 202 1 4UO 4UO . E 2 ZN D 1 201 1 ZN ZN . F 3 4UO D 1 202 2 4UO 4UO . G 4 HOH A 1 301 189 HOH HOH . G 4 HOH A 2 302 120 HOH HOH . G 4 HOH A 3 303 38 HOH HOH . G 4 HOH A 4 304 35 HOH HOH . G 4 HOH A 5 305 2 HOH HOH . G 4 HOH A 6 306 110 HOH HOH . G 4 HOH A 7 307 104 HOH HOH . G 4 HOH A 8 308 83 HOH HOH . G 4 HOH A 9 309 93 HOH HOH . G 4 HOH A 10 310 10 HOH HOH . G 4 HOH A 11 311 176 HOH HOH . G 4 HOH A 12 312 47 HOH HOH . G 4 HOH A 13 313 81 HOH HOH . G 4 HOH A 14 314 49 HOH HOH . G 4 HOH A 15 315 9 HOH HOH . G 4 HOH A 16 316 108 HOH HOH . G 4 HOH A 17 317 63 HOH HOH . G 4 HOH A 18 318 54 HOH HOH . G 4 HOH A 19 319 78 HOH HOH . G 4 HOH A 20 320 64 HOH HOH . G 4 HOH A 21 321 153 HOH HOH . G 4 HOH A 22 322 150 HOH HOH . G 4 HOH A 23 323 194 HOH HOH . G 4 HOH A 24 324 198 HOH HOH . G 4 HOH A 25 325 48 HOH HOH . G 4 HOH A 26 326 119 HOH HOH . G 4 HOH A 27 327 74 HOH HOH . G 4 HOH A 28 328 30 HOH HOH . G 4 HOH A 29 329 102 HOH HOH . G 4 HOH A 30 330 61 HOH HOH . G 4 HOH A 31 331 55 HOH HOH . G 4 HOH A 32 332 15 HOH HOH . G 4 HOH A 33 333 44 HOH HOH . G 4 HOH A 34 334 97 HOH HOH . G 4 HOH A 35 335 59 HOH HOH . G 4 HOH A 36 336 25 HOH HOH . G 4 HOH A 37 337 115 HOH HOH . G 4 HOH A 38 338 28 HOH HOH . G 4 HOH A 39 339 181 HOH HOH . G 4 HOH A 40 340 87 HOH HOH . G 4 HOH A 41 341 33 HOH HOH . G 4 HOH A 42 342 154 HOH HOH . G 4 HOH A 43 343 60 HOH HOH . G 4 HOH A 44 344 21 HOH HOH . G 4 HOH A 45 345 84 HOH HOH . G 4 HOH A 46 346 16 HOH HOH . G 4 HOH A 47 347 167 HOH HOH . G 4 HOH A 48 348 23 HOH HOH . G 4 HOH A 49 349 121 HOH HOH . G 4 HOH A 50 350 163 HOH HOH . G 4 HOH A 51 351 123 HOH HOH . G 4 HOH A 52 352 56 HOH HOH . G 4 HOH A 53 353 105 HOH HOH . G 4 HOH A 54 354 172 HOH HOH . G 4 HOH A 55 355 6 HOH HOH . G 4 HOH A 56 356 171 HOH HOH . G 4 HOH A 57 357 103 HOH HOH . G 4 HOH A 58 358 18 HOH HOH . G 4 HOH A 59 359 156 HOH HOH . G 4 HOH A 60 360 192 HOH HOH . G 4 HOH A 61 361 24 HOH HOH . G 4 HOH A 62 362 27 HOH HOH . G 4 HOH A 63 363 85 HOH HOH . G 4 HOH A 64 364 66 HOH HOH . G 4 HOH A 65 365 126 HOH HOH . G 4 HOH A 66 366 12 HOH HOH . G 4 HOH A 67 367 52 HOH HOH . G 4 HOH A 68 368 134 HOH HOH . G 4 HOH A 69 369 118 HOH HOH . G 4 HOH A 70 370 136 HOH HOH . G 4 HOH A 71 371 166 HOH HOH . G 4 HOH A 72 372 183 HOH HOH . G 4 HOH A 73 373 179 HOH HOH . G 4 HOH A 74 374 71 HOH HOH . G 4 HOH A 75 375 116 HOH HOH . G 4 HOH A 76 376 139 HOH HOH . G 4 HOH A 77 377 68 HOH HOH . G 4 HOH A 78 378 73 HOH HOH . G 4 HOH A 79 379 79 HOH HOH . G 4 HOH A 80 380 164 HOH HOH . G 4 HOH A 81 381 137 HOH HOH . G 4 HOH A 82 382 99 HOH HOH . H 4 HOH D 1 301 92 HOH HOH . H 4 HOH D 2 302 196 HOH HOH . H 4 HOH D 3 303 31 HOH HOH . H 4 HOH D 4 304 175 HOH HOH . H 4 HOH D 5 305 77 HOH HOH . H 4 HOH D 6 306 186 HOH HOH . H 4 HOH D 7 307 46 HOH HOH . H 4 HOH D 8 308 96 HOH HOH . H 4 HOH D 9 309 62 HOH HOH . H 4 HOH D 10 310 128 HOH HOH . H 4 HOH D 11 311 188 HOH HOH . H 4 HOH D 12 312 129 HOH HOH . H 4 HOH D 13 313 147 HOH HOH . H 4 HOH D 14 314 177 HOH HOH . H 4 HOH D 15 315 91 HOH HOH . H 4 HOH D 16 316 39 HOH HOH . H 4 HOH D 17 317 131 HOH HOH . H 4 HOH D 18 318 51 HOH HOH . H 4 HOH D 19 319 57 HOH HOH . H 4 HOH D 20 320 1 HOH HOH . H 4 HOH D 21 321 182 HOH HOH . H 4 HOH D 22 322 13 HOH HOH . H 4 HOH D 23 323 80 HOH HOH . H 4 HOH D 24 324 162 HOH HOH . H 4 HOH D 25 325 174 HOH HOH . H 4 HOH D 26 326 26 HOH HOH . H 4 HOH D 27 327 193 HOH HOH . H 4 HOH D 28 328 40 HOH HOH . H 4 HOH D 29 329 95 HOH HOH . H 4 HOH D 30 330 43 HOH HOH . H 4 HOH D 31 331 178 HOH HOH . H 4 HOH D 32 332 5 HOH HOH . H 4 HOH D 33 333 145 HOH HOH . H 4 HOH D 34 334 70 HOH HOH . H 4 HOH D 35 335 36 HOH HOH . H 4 HOH D 36 336 65 HOH HOH . H 4 HOH D 37 337 7 HOH HOH . H 4 HOH D 38 338 161 HOH HOH . H 4 HOH D 39 339 20 HOH HOH . H 4 HOH D 40 340 76 HOH HOH . H 4 HOH D 41 341 109 HOH HOH . H 4 HOH D 42 342 4 HOH HOH . H 4 HOH D 43 343 41 HOH HOH . H 4 HOH D 44 344 19 HOH HOH . H 4 HOH D 45 345 53 HOH HOH . H 4 HOH D 46 346 82 HOH HOH . H 4 HOH D 47 347 151 HOH HOH . H 4 HOH D 48 348 42 HOH HOH . H 4 HOH D 49 349 113 HOH HOH . H 4 HOH D 50 350 3 HOH HOH . H 4 HOH D 51 351 67 HOH HOH . H 4 HOH D 52 352 29 HOH HOH . H 4 HOH D 53 353 37 HOH HOH . H 4 HOH D 54 354 90 HOH HOH . H 4 HOH D 55 355 86 HOH HOH . H 4 HOH D 56 356 94 HOH HOH . H 4 HOH D 57 357 50 HOH HOH . H 4 HOH D 58 358 98 HOH HOH . H 4 HOH D 59 359 187 HOH HOH . H 4 HOH D 60 360 165 HOH HOH . H 4 HOH D 61 361 149 HOH HOH . H 4 HOH D 62 362 75 HOH HOH . H 4 HOH D 63 363 14 HOH HOH . H 4 HOH D 64 364 100 HOH HOH . H 4 HOH D 65 365 45 HOH HOH . H 4 HOH D 66 366 157 HOH HOH . H 4 HOH D 67 367 141 HOH HOH . H 4 HOH D 68 368 58 HOH HOH . H 4 HOH D 69 369 195 HOH HOH . H 4 HOH D 70 370 112 HOH HOH . H 4 HOH D 71 371 8 HOH HOH . H 4 HOH D 72 372 142 HOH HOH . H 4 HOH D 73 373 170 HOH HOH . H 4 HOH D 74 374 11 HOH HOH . H 4 HOH D 75 375 132 HOH HOH . H 4 HOH D 76 376 17 HOH HOH . H 4 HOH D 77 377 159 HOH HOH . H 4 HOH D 78 378 122 HOH HOH . H 4 HOH D 79 379 197 HOH HOH . H 4 HOH D 80 380 155 HOH HOH . H 4 HOH D 81 381 173 HOH HOH . H 4 HOH D 82 382 32 HOH HOH . H 4 HOH D 83 383 114 HOH HOH . H 4 HOH D 84 384 106 HOH HOH . H 4 HOH D 85 385 130 HOH HOH . H 4 HOH D 86 386 101 HOH HOH . H 4 HOH D 87 387 117 HOH HOH . H 4 HOH D 88 388 89 HOH HOH . H 4 HOH D 89 389 133 HOH HOH . H 4 HOH D 90 390 107 HOH HOH . H 4 HOH D 91 391 88 HOH HOH . H 4 HOH D 92 392 152 HOH HOH . H 4 HOH D 93 393 146 HOH HOH . H 4 HOH D 94 394 144 HOH HOH . H 4 HOH D 95 395 124 HOH HOH . H 4 HOH D 96 396 191 HOH HOH . H 4 HOH D 97 397 135 HOH HOH . H 4 HOH D 98 398 69 HOH HOH . H 4 HOH D 99 399 72 HOH HOH . H 4 HOH D 100 400 184 HOH HOH . H 4 HOH D 101 401 138 HOH HOH . H 4 HOH D 102 402 160 HOH HOH . H 4 HOH D 103 403 140 HOH HOH . H 4 HOH D 104 404 148 HOH HOH . H 4 HOH D 105 405 169 HOH HOH . H 4 HOH D 106 406 190 HOH HOH . H 4 HOH D 107 407 125 HOH HOH . H 4 HOH D 108 408 185 HOH HOH . H 4 HOH D 109 409 158 HOH HOH . H 4 HOH D 110 410 127 HOH HOH . H 4 HOH D 111 411 34 HOH HOH . H 4 HOH D 112 412 168 HOH HOH . H 4 HOH D 113 413 111 HOH HOH . H 4 HOH D 114 414 143 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 O6 4UO . . . D 3 23.002 -34.786 -2.228 1 26.44 ? O6 4UO 202 A 1 HETATM 2 C C6 4UO . . . D 3 21.932 -34.495 -2.667 1 29.15 ? C6 4UO 202 A 1 HETATM 3 N N1 4UO . . . D 3 20.768 -34.356 -1.834 1 29.23 ? N1 4UO 202 A 1 HETATM 4 C C2 4UO . . . D 3 19.465 -34.067 -2.406 1 34.27 ? C2 4UO 202 A 1 HETATM 5 O O2 4UO . . . D 3 18.474 -34.014 -1.727 1 30.59 ? O2 4UO 202 A 1 HETATM 6 N N3 4UO . . . D 3 19.369 -33.768 -3.836 1 32.43 ? N3 4UO 202 A 1 HETATM 7 C C4 4UO . . . D 3 20.556 -33.9 -4.69 1 27.32 ? C4 4UO 202 A 1 HETATM 8 C C5 4UO . . . D 3 21.777 -34.287 -4.152 1 27.46 ? C5 4UO 202 A 1 HETATM 9 N N7 4UO . . . D 3 22.647 -34.409 -5.122 1 27.26 ? N7 4UO 202 A 1 HETATM 10 C C8 4UO . . . D 3 22.024 -34.054 -6.28 1 30.71 ? C8 4UO 202 A 1 HETATM 11 N N9 4UO . . . D 3 20.723 -33.782 -5.989 1 32.13 ? N9 4UO 202 A 1 HETATM 12 C C1' 4UO . . . D 3 19.747 -33.418 -6.994 1 32.46 ? C1' 4UO 202 A 1 HETATM 13 O O4' 4UO . . . D 3 19.516 -32.009 -6.942 1 33.97 ? O4' 4UO 202 A 1 HETATM 14 C C4' 4UO . . . D 3 18.158 -31.752 -7.421 1 33.09 ? C4' 4UO 202 A 1 HETATM 15 C C5' 4UO . . . D 3 17.398 -30.853 -6.465 1 35.61 ? C5' 4UO 202 A 1 HETATM 16 O O5' 4UO . . . D 3 17.038 -31.517 -5.253 1 39.36 ? O5' 4UO 202 A 1 HETATM 17 C C3' 4UO . . . D 3 17.548 -33.14 -7.692 1 29.71 ? C3' 4UO 202 A 1 HETATM 18 O O3' 4UO . . . D 3 17.879 -33.472 -9.034 1 32.12 ? O3' 4UO 202 A 1 HETATM 19 C C2' 4UO . . . D 3 18.377 -34.046 -6.798 1 29.88 ? C2' 4UO 202 A 1 HETATM 20 O O2' 4UO . . . D 3 18.399 -35.405 -7.183 1 29.67 ? O2' 4UO 202 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #