data_7DM5 # _model_server_result.job_id l2Vmm96Jb-rCQWqstbFSYQ _model_server_result.datetime_utc '2024-11-15 15:29:55' _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 7dm5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":202}' # _entry.id 7DM5 # _exptl.entry_id 7DM5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.225 _entity.id 3 _entity.src_method syn _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 7DM5 _cell.length_a 118.566 _cell.length_b 118.566 _cell.length_c 39.405 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DM5 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc2 A SG CYS 86 A CYS 110 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc3 A SG CYS 89 A CYS 113 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc4 C ZN ZN . A ZN 201 1_555 D O2 4UO . A 4UO 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc5 B ND1 HIS 56 D HIS 80 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc6 B SG CYS 86 D CYS 110 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc7 B SG CYS 89 D CYS 113 1_555 E ZN ZN . D ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc8 E ZN ZN . D ZN 201 1_555 F O2 4UO . D 4UO 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? # _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 7DM5 _atom_sites.fract_transf_matrix[1][1] 0.008434 _atom_sites.fract_transf_matrix[1][2] 0.004869 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009739 _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] 0.025377 _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 1 301 200 HOH HOH . G 4 HOH A 2 302 75 HOH HOH . G 4 HOH A 3 303 4 HOH HOH . G 4 HOH A 4 304 124 HOH HOH . G 4 HOH A 5 305 178 HOH HOH . G 4 HOH A 6 306 77 HOH HOH . G 4 HOH A 7 307 42 HOH HOH . G 4 HOH A 8 308 126 HOH HOH . G 4 HOH A 9 309 199 HOH HOH . G 4 HOH A 10 310 28 HOH HOH . G 4 HOH A 11 311 145 HOH HOH . G 4 HOH A 12 312 128 HOH HOH . G 4 HOH A 13 313 55 HOH HOH . G 4 HOH A 14 314 87 HOH HOH . G 4 HOH A 15 315 3 HOH HOH . G 4 HOH A 16 316 62 HOH HOH . G 4 HOH A 17 317 89 HOH HOH . G 4 HOH A 18 318 113 HOH HOH . G 4 HOH A 19 319 95 HOH HOH . G 4 HOH A 20 320 44 HOH HOH . G 4 HOH A 21 321 101 HOH HOH . G 4 HOH A 22 322 53 HOH HOH . G 4 HOH A 23 323 56 HOH HOH . G 4 HOH A 24 324 21 HOH HOH . G 4 HOH A 25 325 54 HOH HOH . G 4 HOH A 26 326 9 HOH HOH . G 4 HOH A 27 327 7 HOH HOH . G 4 HOH A 28 328 40 HOH HOH . G 4 HOH A 29 329 111 HOH HOH . G 4 HOH A 30 330 47 HOH HOH . G 4 HOH A 31 331 34 HOH HOH . G 4 HOH A 32 332 51 HOH HOH . G 4 HOH A 33 333 52 HOH HOH . G 4 HOH A 34 334 181 HOH HOH . G 4 HOH A 35 335 73 HOH HOH . G 4 HOH A 36 336 63 HOH HOH . G 4 HOH A 37 337 10 HOH HOH . G 4 HOH A 38 338 105 HOH HOH . G 4 HOH A 39 339 24 HOH HOH . G 4 HOH A 40 340 172 HOH HOH . G 4 HOH A 41 341 82 HOH HOH . G 4 HOH A 42 342 81 HOH HOH . G 4 HOH A 43 343 70 HOH HOH . G 4 HOH A 44 344 103 HOH HOH . G 4 HOH A 45 345 16 HOH HOH . G 4 HOH A 46 346 192 HOH HOH . G 4 HOH A 47 347 41 HOH HOH . G 4 HOH A 48 348 115 HOH HOH . G 4 HOH A 49 349 79 HOH HOH . G 4 HOH A 50 350 48 HOH HOH . G 4 HOH A 51 351 6 HOH HOH . G 4 HOH A 52 352 92 HOH HOH . G 4 HOH A 53 353 116 HOH HOH . G 4 HOH A 54 354 146 HOH HOH . G 4 HOH A 55 355 67 HOH HOH . G 4 HOH A 56 356 106 HOH HOH . G 4 HOH A 57 357 168 HOH HOH . G 4 HOH A 58 358 119 HOH HOH . G 4 HOH A 59 359 18 HOH HOH . G 4 HOH A 60 360 43 HOH HOH . G 4 HOH A 61 361 99 HOH HOH . G 4 HOH A 62 362 107 HOH HOH . G 4 HOH A 63 363 36 HOH HOH . G 4 HOH A 64 364 129 HOH HOH . G 4 HOH A 65 365 161 HOH HOH . G 4 HOH A 66 366 156 HOH HOH . G 4 HOH A 67 367 68 HOH HOH . G 4 HOH A 68 368 88 HOH HOH . G 4 HOH A 69 369 57 HOH HOH . G 4 HOH A 70 370 30 HOH HOH . G 4 HOH A 71 371 197 HOH HOH . G 4 HOH A 72 372 29 HOH HOH . G 4 HOH A 73 373 78 HOH HOH . G 4 HOH A 74 374 96 HOH HOH . G 4 HOH A 75 375 149 HOH HOH . G 4 HOH A 76 376 191 HOH HOH . G 4 HOH A 77 377 83 HOH HOH . G 4 HOH A 78 378 165 HOH HOH . G 4 HOH A 79 379 127 HOH HOH . G 4 HOH A 80 380 155 HOH HOH . G 4 HOH A 81 381 167 HOH HOH . G 4 HOH A 82 382 31 HOH HOH . G 4 HOH A 83 383 152 HOH HOH . G 4 HOH A 84 384 114 HOH HOH . G 4 HOH A 85 385 144 HOH HOH . G 4 HOH A 86 386 133 HOH HOH . G 4 HOH A 87 387 150 HOH HOH . G 4 HOH A 88 388 94 HOH HOH . G 4 HOH A 89 389 134 HOH HOH . G 4 HOH A 90 390 189 HOH HOH . G 4 HOH A 91 391 164 HOH HOH . G 4 HOH A 92 392 170 HOH HOH . G 4 HOH A 93 393 97 HOH HOH . G 4 HOH A 94 394 117 HOH HOH . G 4 HOH A 95 395 108 HOH HOH . G 4 HOH A 96 396 120 HOH HOH . G 4 HOH A 97 397 179 HOH HOH . G 4 HOH A 98 398 182 HOH HOH . G 4 HOH A 99 399 102 HOH HOH . G 4 HOH A 100 400 123 HOH HOH . H 4 HOH D 1 301 33 HOH HOH . H 4 HOH D 2 302 72 HOH HOH . H 4 HOH D 3 303 71 HOH HOH . H 4 HOH D 4 304 66 HOH HOH . H 4 HOH D 5 305 27 HOH HOH . H 4 HOH D 6 306 135 HOH HOH . H 4 HOH D 7 307 74 HOH HOH . H 4 HOH D 8 308 84 HOH HOH . H 4 HOH D 9 309 198 HOH HOH . H 4 HOH D 10 310 1 HOH HOH . H 4 HOH D 11 311 25 HOH HOH . H 4 HOH D 12 312 203 HOH HOH . H 4 HOH D 13 313 38 HOH HOH . H 4 HOH D 14 314 76 HOH HOH . H 4 HOH D 15 315 32 HOH HOH . H 4 HOH D 16 316 19 HOH HOH . H 4 HOH D 17 317 186 HOH HOH . H 4 HOH D 18 318 5 HOH HOH . H 4 HOH D 19 319 85 HOH HOH . H 4 HOH D 20 320 148 HOH HOH . H 4 HOH D 21 321 110 HOH HOH . H 4 HOH D 22 322 46 HOH HOH . H 4 HOH D 23 323 20 HOH HOH . H 4 HOH D 24 324 14 HOH HOH . H 4 HOH D 25 325 2 HOH HOH . H 4 HOH D 26 326 39 HOH HOH . H 4 HOH D 27 327 69 HOH HOH . H 4 HOH D 28 328 195 HOH HOH . H 4 HOH D 29 329 98 HOH HOH . H 4 HOH D 30 330 61 HOH HOH . H 4 HOH D 31 331 13 HOH HOH . H 4 HOH D 32 332 64 HOH HOH . H 4 HOH D 33 333 59 HOH HOH . H 4 HOH D 34 334 171 HOH HOH . H 4 HOH D 35 335 158 HOH HOH . H 4 HOH D 36 336 8 HOH HOH . H 4 HOH D 37 337 65 HOH HOH . H 4 HOH D 38 338 173 HOH HOH . H 4 HOH D 39 339 49 HOH HOH . H 4 HOH D 40 340 202 HOH HOH . H 4 HOH D 41 341 100 HOH HOH . H 4 HOH D 42 342 151 HOH HOH . H 4 HOH D 43 343 125 HOH HOH . H 4 HOH D 44 344 136 HOH HOH . H 4 HOH D 45 345 50 HOH HOH . H 4 HOH D 46 346 58 HOH HOH . H 4 HOH D 47 347 17 HOH HOH . H 4 HOH D 48 348 86 HOH HOH . H 4 HOH D 49 349 26 HOH HOH . H 4 HOH D 50 350 12 HOH HOH . H 4 HOH D 51 351 80 HOH HOH . H 4 HOH D 52 352 141 HOH HOH . H 4 HOH D 53 353 37 HOH HOH . H 4 HOH D 54 354 11 HOH HOH . H 4 HOH D 55 355 15 HOH HOH . H 4 HOH D 56 356 22 HOH HOH . H 4 HOH D 57 357 160 HOH HOH . H 4 HOH D 58 358 153 HOH HOH . H 4 HOH D 59 359 206 HOH HOH . H 4 HOH D 60 360 184 HOH HOH . H 4 HOH D 61 361 180 HOH HOH . H 4 HOH D 62 362 159 HOH HOH . H 4 HOH D 63 363 121 HOH HOH . H 4 HOH D 64 364 60 HOH HOH . H 4 HOH D 65 365 196 HOH HOH . H 4 HOH D 66 366 190 HOH HOH . H 4 HOH D 67 367 93 HOH HOH . H 4 HOH D 68 368 91 HOH HOH . H 4 HOH D 69 369 163 HOH HOH . H 4 HOH D 70 370 169 HOH HOH . H 4 HOH D 71 371 147 HOH HOH . H 4 HOH D 72 372 142 HOH HOH . H 4 HOH D 73 373 112 HOH HOH . H 4 HOH D 74 374 204 HOH HOH . H 4 HOH D 75 375 45 HOH HOH . H 4 HOH D 76 376 132 HOH HOH . H 4 HOH D 77 377 90 HOH HOH . H 4 HOH D 78 378 166 HOH HOH . H 4 HOH D 79 379 122 HOH HOH . H 4 HOH D 80 380 109 HOH HOH . H 4 HOH D 81 381 131 HOH HOH . H 4 HOH D 82 382 137 HOH HOH . H 4 HOH D 83 383 138 HOH HOH . H 4 HOH D 84 384 139 HOH HOH . H 4 HOH D 85 385 177 HOH HOH . H 4 HOH D 86 386 140 HOH HOH . H 4 HOH D 87 387 118 HOH HOH . H 4 HOH D 88 388 193 HOH HOH . H 4 HOH D 89 389 130 HOH HOH . H 4 HOH D 90 390 154 HOH HOH . H 4 HOH D 91 391 104 HOH HOH . H 4 HOH D 92 392 162 HOH HOH . H 4 HOH D 93 393 194 HOH HOH . H 4 HOH D 94 394 143 HOH HOH . H 4 HOH D 95 395 174 HOH HOH . H 4 HOH D 96 396 35 HOH HOH . H 4 HOH D 97 397 188 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 22.917 34.739 2.127 1 12.68 ? O6 4UO 202 A 1 HETATM 2 C C6 4UO . . . D 3 21.862 34.444 2.586 1 12.95 ? C6 4UO 202 A 1 HETATM 3 N N1 4UO . . . D 3 20.713 34.324 1.729 1 13.48 ? N1 4UO 202 A 1 HETATM 4 C C2 4UO . . . D 3 19.433 33.974 2.301 1 18.18 ? C2 4UO 202 A 1 HETATM 5 O O2 4UO . . . D 3 18.482 33.869 1.599 1 15.43 ? O2 4UO 202 A 1 HETATM 6 N N3 4UO . . . D 3 19.311 33.737 3.753 1 20.56 ? N3 4UO 202 A 1 HETATM 7 C C4 4UO . . . D 3 20.51 33.868 4.644 1 15.54 ? C4 4UO 202 A 1 HETATM 8 C C5 4UO . . . D 3 21.723 34.206 4.095 1 13.68 ? C5 4UO 202 A 1 HETATM 9 N N7 4UO . . . D 3 22.621 34.263 5.072 1 16.88 ? N7 4UO 202 A 1 HETATM 10 C C8 4UO . . . D 3 21.993 33.964 6.232 1 22.2 ? C8 4UO 202 A 1 HETATM 11 N N9 4UO . . . D 3 20.693 33.719 5.965 1 17.8 ? N9 4UO 202 A 1 HETATM 12 C C1' 4UO . . . D 3 19.705 33.36 6.99 1 24.36 ? C1' 4UO 202 A 1 HETATM 13 O O4' 4UO . . . D 3 19.43 31.979 6.905 1 29.17 ? O4' 4UO 202 A 1 HETATM 14 C C4' 4UO . . . D 3 18.083 31.731 7.402 1 25.05 ? C4' 4UO 202 A 1 HETATM 15 C C5' 4UO . . . D 3 17.33 30.886 6.404 1 22.88 ? C5' 4UO 202 A 1 HETATM 16 O O5' 4UO . . . D 3 17.09 31.592 5.191 1 22.58 ? O5' 4UO 202 A 1 HETATM 17 C C3' 4UO . . . D 3 17.473 33.107 7.686 1 21.39 ? C3' 4UO 202 A 1 HETATM 18 O O3' 4UO . . . D 3 17.632 33.413 9.071 1 26.79 ? O3' 4UO 202 A 1 HETATM 19 C C2' 4UO . . . D 3 18.352 34.043 6.857 1 20.75 ? C2' 4UO 202 A 1 HETATM 20 O O2' 4UO . . . D 3 18.39 35.378 7.313 1 18.39 ? O2' 4UO 202 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #