data_7YW2 # _model_server_result.job_id AMClLhRdJYIpBZjlTCJB-w _model_server_result.datetime_utc '2024-11-15 06:30:02' _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 7yw2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 7YW2 # _exptl.entry_id 7YW2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 639.296 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate' _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 120 _cell.entry_id 7YW2 _cell.length_a 65.585 _cell.length_b 65.585 _cell.length_c 148.459 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YW2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _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 # _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 'C15 H24 N5 O17 P3' _chem_comp.formula_weight 639.296 _chem_comp.id HQG _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate' _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 N1A C2A HQG doub 198 n y N1A C6A HQG sing 199 n y C2A N3A HQG sing 200 n y N6A C6A HQG sing 201 n n N3A C4A HQG doub 202 n y C6A C5A HQG doub 203 n y C4A C5A HQG sing 204 n y C4A N9A HQG sing 205 n y C5A N7A HQG sing 206 n y O4B C1B HQG sing 207 n n O4B C4B HQG sing 208 n n N9A C1B HQG sing 209 n n N9A C8A HQG sing 210 n y N7A C8A HQG doub 211 n y C1B C2B HQG sing 212 n n C4B C5B HQG sing 213 n n C4B C3B HQG sing 214 n n C5B O5B HQG sing 215 n n O3B C3B HQG sing 216 n n O5B PA HQG sing 217 n n C2B C3B HQG sing 218 n n C2B O2B HQG sing 219 n n O2A PA HQG doub 220 n n PA O1A HQG sing 221 n n PA O3 HQG sing 222 n n O3 PN HQG sing 223 n n O2N PN HQG doub 224 n n PN O1N HQG sing 225 n n PN O5D HQG sing 226 n n O5D C5D HQG sing 227 n n C5D C4D HQG sing 228 n n O4D C4D HQG sing 229 n n O4D C1D HQG sing 230 n n C4D C3D HQG sing 231 n n O1Z PZ HQG doub 232 n n C1D C2D HQG sing 233 n n C1D O4Z HQG sing 234 n n C2D C3D HQG sing 235 n n C2D O2D HQG sing 236 n n C3D O3D HQG sing 237 n n O4Z PZ HQG sing 238 n n PZ O2Z HQG sing 239 n n PZ O3Z HQG sing 240 n n C1B H1 HQG sing 241 n n C1D H2 HQG sing 242 n n C2A H3 HQG sing 243 n n C2B H4 HQG sing 244 n n C2D H5 HQG sing 245 n n C3B H6 HQG sing 246 n n C3D H7 HQG sing 247 n n C4B H8 HQG sing 248 n n C4D H9 HQG sing 249 n n C5B H10 HQG sing 250 n n C5B H11 HQG sing 251 n n C5D H12 HQG sing 252 n n C5D H13 HQG sing 253 n n C8A H14 HQG sing 254 n n N6A H15 HQG sing 255 n n N6A H16 HQG sing 256 n n O1A H17 HQG sing 257 n n O1N H18 HQG sing 258 n n O2B H19 HQG sing 259 n n O2D H20 HQG sing 260 n n O2Z H21 HQG sing 261 n n O3B H22 HQG sing 262 n n O3D H23 HQG sing 263 n n O3Z H24 HQG sing 264 n n # _atom_sites.entry_id 7YW2 _atom_sites.fract_transf_matrix[1][1] 0.015247 _atom_sites.fract_transf_matrix[1][2] 0.008803 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017606 _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] 0.006736 _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 HQG A 1 300 300 HQG HQG . C 3 GOL A 1 301 301 GOL LIG . D 4 PO4 A 1 302 302 PO4 PO4 . E 5 EPE A 1 303 303 EPE EPE . F 3 GOL A 1 304 304 GOL LIG . G 3 GOL A 1 305 305 GOL LIG . H 6 GLY A 1 306 306 GLY GLY . I 6 GLY A 1 307 307 GLY GLY . J 6 GLY A 1 308 308 GLY GLY . K 6 GLY A 1 309 309 GLY GLY . L 6 GLY A 1 310 310 GLY GLY . M 6 GLY A 1 311 311 GLY GLY . N 3 GOL A 1 312 312 GOL LIG . O 7 SOR A 1 313 313 SOR SOR . P 7 SOR A 1 314 314 SOR SOR . Q 6 GLY A 1 315 315 GLY GLY . R 6 GLY A 1 316 316 GLY GLY . S 6 GLY A 1 317 317 GLY GLY . T 6 GLY A 1 318 318 GLY GLY . U 8 HOH A 1 401 77 HOH HOH . U 8 HOH A 2 402 30 HOH HOH . U 8 HOH A 3 403 10 HOH HOH . U 8 HOH A 4 404 54 HOH HOH . U 8 HOH A 5 405 43 HOH HOH . U 8 HOH A 6 406 22 HOH HOH . U 8 HOH A 7 407 93 HOH HOH . U 8 HOH A 8 408 33 HOH HOH . U 8 HOH A 9 409 23 HOH HOH . U 8 HOH A 10 410 59 HOH HOH . U 8 HOH A 11 411 56 HOH HOH . U 8 HOH A 12 412 81 HOH HOH . U 8 HOH A 13 413 9 HOH HOH . U 8 HOH A 14 414 46 HOH HOH . U 8 HOH A 15 415 21 HOH HOH . U 8 HOH A 16 416 2 HOH HOH . U 8 HOH A 17 417 40 HOH HOH . U 8 HOH A 18 418 7 HOH HOH . U 8 HOH A 19 419 26 HOH HOH . U 8 HOH A 20 420 89 HOH HOH . U 8 HOH A 21 421 3 HOH HOH . U 8 HOH A 22 422 34 HOH HOH . U 8 HOH A 23 423 19 HOH HOH . U 8 HOH A 24 424 11 HOH HOH . U 8 HOH A 25 425 70 HOH HOH . U 8 HOH A 26 426 47 HOH HOH . U 8 HOH A 27 427 88 HOH HOH . U 8 HOH A 28 428 4 HOH HOH . U 8 HOH A 29 429 51 HOH HOH . U 8 HOH A 30 430 82 HOH HOH . U 8 HOH A 31 431 5 HOH HOH . U 8 HOH A 32 432 41 HOH HOH . U 8 HOH A 33 433 53 HOH HOH . U 8 HOH A 34 434 28 HOH HOH . U 8 HOH A 35 435 29 HOH HOH . U 8 HOH A 36 436 1 HOH HOH . U 8 HOH A 37 437 24 HOH HOH . U 8 HOH A 38 438 58 HOH HOH . U 8 HOH A 39 439 61 HOH HOH . U 8 HOH A 40 440 13 HOH HOH . U 8 HOH A 41 441 12 HOH HOH . U 8 HOH A 42 442 69 HOH HOH . U 8 HOH A 43 443 16 HOH HOH . U 8 HOH A 44 444 38 HOH HOH . U 8 HOH A 45 445 25 HOH HOH . U 8 HOH A 46 446 37 HOH HOH . U 8 HOH A 47 447 8 HOH HOH . U 8 HOH A 48 448 6 HOH HOH . U 8 HOH A 49 449 20 HOH HOH . U 8 HOH A 50 450 49 HOH HOH . U 8 HOH A 51 451 52 HOH HOH . U 8 HOH A 52 452 73 HOH HOH . U 8 HOH A 53 453 45 HOH HOH . U 8 HOH A 54 454 36 HOH HOH . U 8 HOH A 55 455 71 HOH HOH . U 8 HOH A 56 456 17 HOH HOH . U 8 HOH A 57 457 35 HOH HOH . U 8 HOH A 58 458 62 HOH HOH . U 8 HOH A 59 459 72 HOH HOH . U 8 HOH A 60 460 14 HOH HOH . U 8 HOH A 61 461 63 HOH HOH . U 8 HOH A 62 462 44 HOH HOH . U 8 HOH A 63 463 84 HOH HOH . U 8 HOH A 64 464 90 HOH HOH . U 8 HOH A 65 465 87 HOH HOH . U 8 HOH A 66 466 83 HOH HOH . U 8 HOH A 67 467 15 HOH HOH . U 8 HOH A 68 468 32 HOH HOH . U 8 HOH A 69 469 92 HOH HOH . U 8 HOH A 70 470 55 HOH HOH . U 8 HOH A 71 471 86 HOH HOH . U 8 HOH A 72 472 42 HOH HOH . U 8 HOH A 73 473 67 HOH HOH . U 8 HOH A 74 474 66 HOH HOH . U 8 HOH A 75 475 78 HOH HOH . U 8 HOH A 76 476 74 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 C1B HQG . . . B 2 -30.284 -9.619 13.934 1 51.21 ? C1B HQG 300 A 1 HETATM 2 C C1D HQG . . . B 2 -27.51 -2.617 22.577 1 46.29 ? C1D HQG 300 A 1 HETATM 3 C C2A HQG . . . B 2 -31.563 -13.079 11.544 0.83 56.3 ? C2A HQG 300 A 1 HETATM 4 C C2B HQG . . . B 2 -30.042 -8.371 14.338 1 50.42 ? C2B HQG 300 A 1 HETATM 5 C C2D HQG . . . B 2 -27.349 -1.739 21.264 0.35 47.47 ? C2D HQG 300 A 1 HETATM 6 C C3B HQG . . . B 2 -29.326 -8.622 15.68 0.97 49.14 ? C3B HQG 300 A 1 HETATM 7 C C3D HQG . . . B 2 -28.207 -2.15 20.463 1 46.84 ? C3D HQG 300 A 1 HETATM 8 C C4A HQG . . . B 2 -31.609 -10.877 12.332 0.74 54.3 ? C4A HQG 300 A 1 HETATM 9 C C4B HQG . . . B 2 -30.029 -9.93 16.252 0.92 49.27 ? C4B HQG 300 A 1 HETATM 10 C C4D HQG . . . B 2 -29.412 -2.801 21.401 0.78 45.32 ? C4D HQG 300 A 1 HETATM 11 C C5A HQG . . . B 2 -32.65 -10.619 11.531 1 56.03 ? C5A HQG 300 A 1 HETATM 12 C C5B HQG . . . B 2 -30.894 -9.567 17.471 0.82 48.91 ? C5B HQG 300 A 1 HETATM 13 C C5D HQG . . . B 2 -30.191 -3.787 20.542 1 45.51 ? C5D HQG 300 A 1 HETATM 14 C C6A HQG . . . B 2 -33.157 -11.604 10.711 0.86 58.2 ? C6A HQG 300 A 1 HETATM 15 C C8A HQG . . . B 2 -32.176 -8.799 12.611 0.68 53.37 ? C8A HQG 300 A 1 HETATM 16 N N1A HQG . . . B 2 -32.617 -12.814 10.724 0.86 58.33 ? N1A HQG 300 A 1 HETATM 17 N N3A HQG . . . B 2 -31.06 -12.109 12.344 1 54.39 ? N3A HQG 300 A 1 HETATM 18 N N6A HQG . . . B 2 -34.265 -11.569 9.763 1 60.68 ? N6A HQG 300 A 1 HETATM 19 N N7A HQG . . . B 2 -33 -9.344 11.71 0.94 55.32 ? N7A HQG 300 A 1 HETATM 20 N N9A HQG . . . B 2 -31.318 -9.743 12.991 0.69 52.83 ? N9A HQG 300 A 1 HETATM 21 O O1A HQG . . . B 2 -29.713 -7.864 20.711 0.92 45.68 -1 O1A HQG 300 A 1 HETATM 22 O O1N HQG . . . B 2 -29.922 -4.367 17.564 0.91 47.48 -1 O1N HQG 300 A 1 HETATM 23 O O1Z HQG . . . B 2 -25.656 -2.259 25.127 0.99 48.03 ? O1Z HQG 300 A 1 HETATM 24 O O2A HQG . . . B 2 -32.087 -8.246 19.916 0.97 47.93 ? O2A HQG 300 A 1 HETATM 25 O O2B HQG . . . B 2 -29.116 -7.633 13.446 1 51.05 ? O2B HQG 300 A 1 HETATM 26 O O2D HQG . . . B 2 -27.615 -0.31 21.667 0.89 47.28 ? O2D HQG 300 A 1 HETATM 27 O O2N HQG . . . B 2 -28.21 -6.133 18.17 1 47.47 ? O2N HQG 300 A 1 HETATM 28 O O2Z HQG . . . B 2 -27.634 -1.154 26.057 0.83 45.05 -1 O2Z HQG 300 A 1 HETATM 29 O O3 HQG . . . B 2 -30.727 -6.472 18.743 0.95 46.91 ? O3 HQG 300 A 1 HETATM 30 O O3B HQG . . . B 2 -28.028 -8.848 15.49 1 49.24 ? O3B HQG 300 A 1 HETATM 31 O O3D HQG . . . B 2 -28.765 -1.058 19.654 0.49 47.02 ? O3D HQG 300 A 1 HETATM 32 O O3Z HQG . . . B 2 -27.774 -3.524 25.39 1 44.38 -1 O3Z HQG 300 A 1 HETATM 33 O O4B HQG . . . B 2 -30.805 -10.356 15.296 0.96 50.76 ? O4B HQG 300 A 1 HETATM 34 O O4D HQG . . . B 2 -28.809 -3.4 22.366 0.84 45.07 ? O4D HQG 300 A 1 HETATM 35 O O4Z HQG . . . B 2 -27.639 -1.783 23.544 0.49 45.92 ? O4Z HQG 300 A 1 HETATM 36 O O5B HQG . . . B 2 -30.047 -9.038 18.472 1 47.43 ? O5B HQG 300 A 1 HETATM 37 O O5D HQG . . . B 2 -29.233 -4.686 20.052 0.83 46 ? O5D HQG 300 A 1 HETATM 38 P PA HQG . . . B 2 -30.659 -7.917 19.544 1 46.8 ? PA HQG 300 A 1 HETATM 39 P PN HQG . . . B 2 -29.469 -5.414 18.569 0.92 46.84 ? PN HQG 300 A 1 HETATM 40 P PZ HQG . . . B 2 -27.159 -2.191 25.071 0.97 45.67 ? PZ HQG 300 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #