data_8TY2 # _model_server_result.job_id XMrx0KtEZKNaZOVkngMoZw _model_server_result.datetime_utc '2025-04-05 09:50:36' _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 8ty2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8TY2 # _exptl.entry_id 8TY2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 8TY2 _cell.length_a 39.41 _cell.length_b 42.115 _cell.length_c 92.006 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TY2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # 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 OG SER 17 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc2 B O3B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc3 C MG MG . A MG 202 1_555 D O HOH . A HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc4 C MG MG . A MG 202 1_555 D O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc5 C MG MG . A MG 202 1_555 D O HOH . A HOH 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc6 C MG MG . A MG 202 1_555 D O HOH . A HOH 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 8TY2 _atom_sites.fract_transf_matrix[1][1] 0.025374 _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] 0.023745 _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] 0.010869 _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 GDP A 1 201 170 GDP GDP . C 3 MG A 1 202 171 MG MG . D 4 HOH A 1 301 89 HOH HOH . D 4 HOH A 2 302 119 HOH HOH . D 4 HOH A 3 303 110 HOH HOH . D 4 HOH A 4 304 41 HOH HOH . D 4 HOH A 5 305 33 HOH HOH . D 4 HOH A 6 306 56 HOH HOH . D 4 HOH A 7 307 55 HOH HOH . D 4 HOH A 8 308 108 HOH HOH . D 4 HOH A 9 309 69 HOH HOH . D 4 HOH A 10 310 66 HOH HOH . D 4 HOH A 11 311 42 HOH HOH . D 4 HOH A 12 312 67 HOH HOH . D 4 HOH A 13 313 9 HOH HOH . D 4 HOH A 14 314 109 HOH HOH . D 4 HOH A 15 315 73 HOH HOH . D 4 HOH A 16 316 75 HOH HOH . D 4 HOH A 17 317 7 HOH HOH . D 4 HOH A 18 318 46 HOH HOH . D 4 HOH A 19 319 15 HOH HOH . D 4 HOH A 20 320 6 HOH HOH . D 4 HOH A 21 321 2 HOH HOH . D 4 HOH A 22 322 29 HOH HOH . D 4 HOH A 23 323 22 HOH HOH . D 4 HOH A 24 324 50 HOH HOH . D 4 HOH A 25 325 20 HOH HOH . D 4 HOH A 26 326 8 HOH HOH . D 4 HOH A 27 327 44 HOH HOH . D 4 HOH A 28 328 36 HOH HOH . D 4 HOH A 29 329 1 HOH HOH . D 4 HOH A 30 330 70 HOH HOH . D 4 HOH A 31 331 11 HOH HOH . D 4 HOH A 32 332 65 HOH HOH . D 4 HOH A 33 333 48 HOH HOH . D 4 HOH A 34 334 14 HOH HOH . D 4 HOH A 35 335 34 HOH HOH . D 4 HOH A 36 336 28 HOH HOH . D 4 HOH A 37 337 13 HOH HOH . D 4 HOH A 38 338 64 HOH HOH . D 4 HOH A 39 339 37 HOH HOH . D 4 HOH A 40 340 23 HOH HOH . D 4 HOH A 41 341 5 HOH HOH . D 4 HOH A 42 342 62 HOH HOH . D 4 HOH A 43 343 92 HOH HOH . D 4 HOH A 44 344 60 HOH HOH . D 4 HOH A 45 345 10 HOH HOH . D 4 HOH A 46 346 84 HOH HOH . D 4 HOH A 47 347 17 HOH HOH . D 4 HOH A 48 348 102 HOH HOH . D 4 HOH A 49 349 95 HOH HOH . D 4 HOH A 50 350 4 HOH HOH . D 4 HOH A 51 351 49 HOH HOH . D 4 HOH A 52 352 25 HOH HOH . D 4 HOH A 53 353 18 HOH HOH . D 4 HOH A 54 354 27 HOH HOH . D 4 HOH A 55 355 71 HOH HOH . D 4 HOH A 56 356 63 HOH HOH . D 4 HOH A 57 357 88 HOH HOH . D 4 HOH A 58 358 115 HOH HOH . D 4 HOH A 59 359 54 HOH HOH . D 4 HOH A 60 360 16 HOH HOH . D 4 HOH A 61 361 118 HOH HOH . D 4 HOH A 62 362 59 HOH HOH . D 4 HOH A 63 363 19 HOH HOH . D 4 HOH A 64 364 32 HOH HOH . D 4 HOH A 65 365 52 HOH HOH . D 4 HOH A 66 366 100 HOH HOH . D 4 HOH A 67 367 82 HOH HOH . D 4 HOH A 68 368 72 HOH HOH . D 4 HOH A 69 369 58 HOH HOH . D 4 HOH A 70 370 114 HOH HOH . D 4 HOH A 71 371 81 HOH HOH . D 4 HOH A 72 372 21 HOH HOH . D 4 HOH A 73 373 51 HOH HOH . D 4 HOH A 74 374 12 HOH HOH . D 4 HOH A 75 375 112 HOH HOH . D 4 HOH A 76 376 80 HOH HOH . D 4 HOH A 77 377 39 HOH HOH . D 4 HOH A 78 378 38 HOH HOH . D 4 HOH A 79 379 47 HOH HOH . D 4 HOH A 80 380 35 HOH HOH . D 4 HOH A 81 381 101 HOH HOH . D 4 HOH A 82 382 106 HOH HOH . D 4 HOH A 83 383 93 HOH HOH . D 4 HOH A 84 384 24 HOH HOH . D 4 HOH A 85 385 57 HOH HOH . D 4 HOH A 86 386 31 HOH HOH . D 4 HOH A 87 387 78 HOH HOH . D 4 HOH A 88 388 45 HOH HOH . D 4 HOH A 89 389 79 HOH HOH . D 4 HOH A 90 390 104 HOH HOH . D 4 HOH A 91 391 97 HOH HOH . D 4 HOH A 92 392 53 HOH HOH . D 4 HOH A 93 393 120 HOH HOH . D 4 HOH A 94 394 103 HOH HOH . D 4 HOH A 95 395 74 HOH HOH . D 4 HOH A 96 396 116 HOH HOH . D 4 HOH A 97 397 99 HOH HOH . D 4 HOH A 98 398 30 HOH HOH . D 4 HOH A 99 399 68 HOH HOH . D 4 HOH A 100 400 61 HOH HOH . D 4 HOH A 101 401 117 HOH HOH . D 4 HOH A 102 402 111 HOH HOH . D 4 HOH A 103 403 43 HOH HOH . D 4 HOH A 104 404 105 HOH HOH . D 4 HOH A 105 405 26 HOH HOH . D 4 HOH A 106 406 113 HOH HOH . D 4 HOH A 107 407 40 HOH HOH . D 4 HOH A 108 408 77 HOH HOH . D 4 HOH A 109 409 87 HOH HOH . D 4 HOH A 110 410 98 HOH HOH . D 4 HOH A 111 411 91 HOH HOH . D 4 HOH A 112 412 76 HOH HOH . D 4 HOH A 113 413 86 HOH HOH . D 4 HOH A 114 414 83 HOH HOH . D 4 HOH A 115 415 96 HOH HOH . D 4 HOH A 116 416 94 HOH HOH . D 4 HOH A 117 417 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 P PB GDP . . . B 2 -10.308 -7.358 -16.19 1 16.59 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -10.665 -7.844 -17.579 1 19.43 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -9.954 -5.904 -16.239 1 16.88 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -11.386 -7.683 -15.173 1 17.31 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -8.945 -8.105 -15.772 1 19.22 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -8.755 -9.377 -14.812 1 19.08 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -9.568 -10.55 -15.303 1 21.49 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -8.955 -9 -13.379 1 19.78 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -7.194 -9.681 -15.033 1 19.73 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -6.765 -10.068 -16.33 1 20.76 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -5.527 -10.931 -16.151 1 19.99 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -4.469 -10.153 -15.559 1 21.76 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -5.746 -12.111 -15.206 1 23.81 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -5.013 -13.241 -15.676 1 27.77 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -5.182 -11.709 -13.851 1 24.16 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -4.581 -12.776 -13.127 1 29.27 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -4.084 -10.738 -14.297 1 21.52 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -3.808 -9.637 -13.383 1 19.64 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -4.687 -8.736 -12.935 1 18.54 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -4.058 -7.875 -12.103 1 17.51 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -2.763 -8.224 -12.053 1 18.71 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -1.586 -7.716 -11.36 1 18.19 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -1.677 -6.704 -10.644 1 18.73 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -0.418 -8.334 -11.575 1 18.34 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -0.335 -9.424 -12.378 1 20.95 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 0.852 -10.033 -12.556 1 23.8 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -1.382 -9.961 -13.052 1 20.47 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -2.6 -9.383 -12.918 1 18.61 ? C4 GDP 201 A 1 HETATM 29 H H4' GDP . . . B 2 -5.276 -11.298 -17.156 1 24.09 ? H4' GDP 201 A 1 HETATM 30 H H3' GDP . . . B 2 -6.813 -12.369 -15.149 1 28.68 ? H3' GDP 201 A 1 HETATM 31 H H2' GDP . . . B 2 -5.956 -11.33 -13.169 1 29.09 ? H2' GDP 201 A 1 HETATM 32 H HO2' GDP . . . B 2 -5.257 -13.423 -12.885 1 35.22 ? HO2' GDP 201 A 1 HETATM 33 H H1' GDP . . . B 2 -3.178 -11.357 -14.343 1 25.93 ? H1' GDP 201 A 1 HETATM 34 H H8 GDP . . . B 2 -5.737 -8.7 -13.198 1 22.34 ? H8 GDP 201 A 1 HETATM 35 H HN1 GDP . . . B 2 0.442 -7.972 -11.117 1 22.12 ? HN1 GDP 201 A 1 HETATM 36 H HN21 GDP . . . B 2 0.926 -10.841 -13.16 1 28.67 ? HN21 GDP 201 A 1 HETATM 37 H HN22 GDP . . . B 2 1.664 -9.686 -12.094 1 28.67 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 37 #