data_6RG6 # _model_server_result.job_id '_TA-2YCIhdT5mpc1tXHnGw' _model_server_result.datetime_utc '2024-11-25 00:31:19' _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 6rg6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 6RG6 # _exptl.entry_id 6RG6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 438.4 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[3-(6-azanyl-9~{H}-purin-8-yl)prop-2-ynoxymethyl]oxolane-3,4-diol _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 6RG6 _cell.length_a 62.91 _cell.length_b 75.235 _cell.length_c 118.6 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RG6 _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D 1 1 A,B,C,D 1 2 A,B,C,D 1 3 A,B,C,D 1 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 62.91 0 0 3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 62.91 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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C18 H18 N10 O4' _chem_comp.formula_weight 438.4 _chem_comp.id K3B _chem_comp.mon_nstd_flag . _chem_comp.name (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[3-(6-azanyl-9~{H}-purin-8-yl)prop-2-ynoxymethyl]oxolane-3,4-diol _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 K3B sing 193 n n N7 C8 K3B doub 194 n y N7 C5 K3B sing 195 n y C6 C5 K3B doub 196 n y C6 N1 K3B sing 197 n y O2' C2' K3B sing 198 n n C8 N9 K3B sing 199 n y C5 C4 K3B sing 200 n y C2' C3' K3B sing 201 n n C2' C1' K3B sing 202 n n N1 C2 K3B doub 203 n y N9 C4 K3B sing 204 n y N9 C1' K3B sing 205 n n C4 N3 K3B doub 206 n y C3' O3' K3B sing 207 n n C3' C4' K3B sing 208 n n C2 N3 K3B sing 209 n y C1' O4' K3B sing 210 n n O4' C4' K3B sing 211 n n C4' C5' K3B sing 212 n n C5' O5' K3B sing 213 n n NBB CAY K3B sing 214 n n O5' CAP K3B sing 215 n n CAY NAX K3B doub 216 n y CAY CAZ K3B sing 217 n y NBA CAZ K3B sing 218 n y NBA CAS K3B doub 219 n y NAX CAW K3B sing 220 n y CAZ CAU K3B doub 221 n y CAS CAR K3B sing 222 n n CAS NAT K3B sing 223 n y CAP CAQ K3B sing 224 n n CAR CAQ K3B trip 225 n n CAW NAV K3B doub 226 n y CAU NAT K3B sing 227 n y CAU NAV K3B sing 228 n y C2 H1 K3B sing 229 n n C1' H2 K3B sing 230 n n C2' H3 K3B sing 231 n n C3' H4 K3B sing 232 n n C4' H5 K3B sing 233 n n C5' H6 K3B sing 234 n n C5' H7 K3B sing 235 n n C8 H8 K3B sing 236 n n CAP H9 K3B sing 237 n n CAP H10 K3B sing 238 n n CAW H11 K3B sing 239 n n N6 H12 K3B sing 240 n n N6 H13 K3B sing 241 n n NAT H14 K3B sing 242 n n NBB H16 K3B sing 243 n n NBB H17 K3B sing 244 n n O2' H18 K3B sing 245 n n O3' H19 K3B sing 246 n n # _atom_sites.entry_id 6RG6 _atom_sites.fract_transf_matrix[1][1] 0.015896 _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] 0.013292 _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] 0.008432 _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 CIT A 1 301 1 CIT CIT . C 3 K3B A 1 302 1 K3B PDB . D 4 HOH A 1 401 66 HOH HOH . D 4 HOH A 2 402 23 HOH HOH . D 4 HOH A 3 403 13 HOH HOH . D 4 HOH A 4 404 2 HOH HOH . D 4 HOH A 5 405 10 HOH HOH . D 4 HOH A 6 406 19 HOH HOH . D 4 HOH A 7 407 27 HOH HOH . D 4 HOH A 8 408 1 HOH HOH . D 4 HOH A 9 409 8 HOH HOH . D 4 HOH A 10 410 12 HOH HOH . D 4 HOH A 11 411 5 HOH HOH . D 4 HOH A 12 412 4 HOH HOH . D 4 HOH A 13 413 11 HOH HOH . D 4 HOH A 14 414 38 HOH HOH . D 4 HOH A 15 415 39 HOH HOH . D 4 HOH A 16 416 14 HOH HOH . D 4 HOH A 17 417 30 HOH HOH . D 4 HOH A 18 418 56 HOH HOH . D 4 HOH A 19 419 41 HOH HOH . D 4 HOH A 20 420 7 HOH HOH . D 4 HOH A 21 421 15 HOH HOH . D 4 HOH A 22 422 28 HOH HOH . D 4 HOH A 23 423 50 HOH HOH . D 4 HOH A 24 424 6 HOH HOH . D 4 HOH A 25 425 84 HOH HOH . D 4 HOH A 26 426 26 HOH HOH . D 4 HOH A 27 427 18 HOH HOH . D 4 HOH A 28 428 21 HOH HOH . D 4 HOH A 29 429 20 HOH HOH . D 4 HOH A 30 430 67 HOH HOH . D 4 HOH A 31 431 9 HOH HOH . D 4 HOH A 32 432 49 HOH HOH . D 4 HOH A 33 433 82 HOH HOH . D 4 HOH A 34 434 55 HOH HOH . D 4 HOH A 35 435 42 HOH HOH . D 4 HOH A 36 436 3 HOH HOH . D 4 HOH A 37 437 75 HOH HOH . D 4 HOH A 38 438 17 HOH HOH . D 4 HOH A 39 439 29 HOH HOH . D 4 HOH A 40 440 80 HOH HOH . D 4 HOH A 41 441 60 HOH HOH . D 4 HOH A 42 442 45 HOH HOH . D 4 HOH A 43 443 81 HOH HOH . D 4 HOH A 44 444 83 HOH HOH . D 4 HOH A 45 445 62 HOH HOH . D 4 HOH A 46 446 24 HOH HOH . D 4 HOH A 47 447 47 HOH HOH . D 4 HOH A 48 448 69 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 C C2 K3B . . . C 3 20.076 6.098 8.761 1 39.07 ? C2 K3B 302 A 1 HETATM 2 C C4 K3B . . . C 3 17.839 6.526 8.298 1 39.61 ? C4 K3B 302 A 1 HETATM 3 C C5 K3B . . . C 3 17.707 5.307 7.646 1 39.97 ? C5 K3B 302 A 1 HETATM 4 C C6 K3B . . . C 3 18.797 4.457 7.548 1 37.15 ? C6 K3B 302 A 1 HETATM 5 N N9 K3B . . . C 3 16.653 7.125 8.243 1 39.62 ? N9 K3B 302 A 1 HETATM 6 C C1' K3B . . . C 3 16.29 8.438 8.79 1 41.54 ? C1' K3B 302 A 1 HETATM 7 C C2' K3B . . . C 3 16.306 9.638 7.841 1 41.92 ? C2' K3B 302 A 1 HETATM 8 C C3' K3B . . . C 3 15.446 10.675 8.608 1 42.55 ? C3' K3B 302 A 1 HETATM 9 C C4' K3B . . . C 3 14.901 9.874 9.804 1 42.62 ? C4' K3B 302 A 1 HETATM 10 C C5' K3B . . . C 3 13.545 10.274 10.339 1 42.27 ? C5' K3B 302 A 1 HETATM 11 C C8 K3B . . . C 3 15.814 6.324 7.584 1 39.86 ? C8 K3B 302 A 1 HETATM 12 C CAP K3B . . . C 3 14.147 10.903 12.668 1 39.87 ? CAP K3B 302 A 1 HETATM 13 C CAQ K3B . . . C 3 15.609 11.005 12.68 1 37.85 ? CAQ K3B 302 A 1 HETATM 14 C CAR K3B . . . C 3 16.817 11.121 12.676 1 34.31 ? CAR K3B 302 A 1 HETATM 15 C CAS K3B . . . C 3 18.235 11.28 12.659 1 30.92 ? CAS K3B 302 A 1 HETATM 16 C CAU K3B . . . C 3 20.338 10.899 12.942 1 28.79 ? CAU K3B 302 A 1 HETATM 17 C CAW K3B . . . C 3 22.648 11.113 12.931 1 28 ? CAW K3B 302 A 1 HETATM 18 C CAY K3B . . . C 3 21.304 12.877 11.988 1 26.77 ? CAY K3B 302 A 1 HETATM 19 C CAZ K3B . . . C 3 20.184 12.128 12.317 1 28.61 ? CAZ K3B 302 A 1 HETATM 20 N N1 K3B . . . C 3 20.008 4.858 8.114 1 37.05 ? N1 K3B 302 A 1 HETATM 21 N N3 K3B . . . C 3 19.015 6.887 8.835 1 39.8 ? N3 K3B 302 A 1 HETATM 22 N N6 K3B . . . C 3 18.689 3.286 6.926 1 36.69 ? N6 K3B 302 A 1 HETATM 23 N N7 K3B . . . C 3 16.453 5.214 7.219 1 40.04 ? N7 K3B 302 A 1 HETATM 24 N NAT K3B . . . C 3 19.12 10.406 13.138 1 29.44 ? NAT K3B 302 A 1 HETATM 25 N NAV K3B . . . C 3 21.559 10.426 13.232 1 28.27 ? NAV K3B 302 A 1 HETATM 26 N NAX K3B . . . C 3 22.563 12.362 12.3 1 26.37 ? NAX K3B 302 A 1 HETATM 27 N NBA K3B . . . C 3 18.882 12.332 12.158 1 29.36 ? NBA K3B 302 A 1 HETATM 28 N NBB K3B . . . C 3 21.181 14.058 11.389 1 26.68 ? NBB K3B 302 A 1 HETATM 29 O O2' K3B . . . C 3 17.623 10.063 7.565 1 42.68 ? O2' K3B 302 A 1 HETATM 30 O O3' K3B . . . C 3 16.278 11.733 9.078 1 43.97 ? O3' K3B 302 A 1 HETATM 31 O O4' K3B . . . C 3 15.053 8.493 9.441 1 42.41 ? O4' K3B 302 A 1 HETATM 32 O O5' K3B . . . C 3 13.409 10.054 11.744 1 42.27 ? O5' K3B 302 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #