data_8JJS # _model_server_result.job_id JJS_TjOhJ5dRcEa6kVZRZw _model_server_result.datetime_utc '2025-07-05 09:52:10' _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 8jjs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 8JJS # _exptl.entry_id 8JJS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 120 _cell.entry_id 8JJS _cell.length_a 66.596 _cell.length_b 66.596 _cell.length_c 86.613 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JJS _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _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,I _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 3 _struct_asym.id C _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 covale ? covale1 B C MAA 1 I MAA 1 1_555 B N ILE 2 I ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale2 B N MAA 1 I MAA 1 1_555 B CG 7TK 11 I 7TK 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? covale ? covale3 B C ILE 2 I ILE 2 1_555 B N SAR 3 I SAR 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.358 ? covale ? covale4 B C SAR 3 I SAR 3 1_555 B N SAR 4 I SAR 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale5 B C SAR 4 I SAR 4 1_555 B N 7T2 5 I 7T2 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale6 B C 7T2 5 I 7T2 5 1_555 B N SAR 6 I SAR 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? covale ? covale7 B C SAR 6 I SAR 6 1_555 B N IAE 7 I IAE 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale8 B C IAE 7 I IAE 7 1_555 B N LEU 8 I LEU 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale9 B C LEU 8 I LEU 8 1_555 B N MEA 9 I MEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.367 ? covale ? covale10 B C MEA 9 I MEA 9 1_555 B N MLE 10 I MLE 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? covale ? covale11 B C MLE 10 I MLE 10 1_555 B N 7TK 11 I 7TK 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? metalc ? metalc1 A OG SER 22 A SER 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc2 C O3B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc3 D MG MG . A MG 202 1_555 H O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc4 D MG MG . A MG 202 1_555 H O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc5 D MG MG . A MG 202 1_555 H O HOH . A HOH 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc6 D MG MG . A MG 202 1_555 H O HOH . A HOH 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? # _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 136 n n PB O2B GDP sing 137 n n PB O3B GDP sing 138 n n PB O3A GDP sing 139 n n O2B HOB2 GDP sing 140 n n O3B HOB3 GDP sing 141 n n O3A PA GDP sing 142 n n PA O1A GDP doub 143 n n PA O2A GDP sing 144 n n PA O5' GDP sing 145 n n O2A HOA2 GDP sing 146 n n O5' C5' GDP sing 147 n n C5' C4' GDP sing 148 n n C5' H5' GDP sing 149 n n C5' "H5''" GDP sing 150 n n C4' O4' GDP sing 151 n n C4' C3' GDP sing 152 n n C4' H4' GDP sing 153 n n O4' C1' GDP sing 154 n n C3' O3' GDP sing 155 n n C3' C2' GDP sing 156 n n C3' H3' GDP sing 157 n n O3' HO3' GDP sing 158 n n C2' O2' GDP sing 159 n n C2' C1' GDP sing 160 n n C2' H2' GDP sing 161 n n O2' HO2' GDP sing 162 n n C1' N9 GDP sing 163 n n C1' H1' GDP sing 164 n n N9 C8 GDP sing 165 n y N9 C4 GDP sing 166 n y C8 N7 GDP doub 167 n y C8 H8 GDP sing 168 n n N7 C5 GDP sing 169 n y C5 C6 GDP sing 170 n n C5 C4 GDP doub 171 n y C6 O6 GDP doub 172 n n C6 N1 GDP sing 173 n n N1 C2 GDP sing 174 n n N1 HN1 GDP sing 175 n n C2 N2 GDP sing 176 n n C2 N3 GDP doub 177 n n N2 HN21 GDP sing 178 n n N2 HN22 GDP sing 179 n n N3 C4 GDP sing 180 n n # _atom_sites.entry_id 8JJS _atom_sites.fract_transf_matrix[1][1] 0.015016 _atom_sites.fract_transf_matrix[1][2] 0.008669 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017339 _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] 0.011546 _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 3 GDP A 1 201 201 GDP GDP . D 4 MG A 1 202 202 MG MG . E 5 SO4 A 1 203 203 SO4 SO4 . F 5 SO4 A 1 204 204 SO4 SO4 . G 5 SO4 A 1 205 205 SO4 SO4 . H 6 HOH A 1 301 301 HOH HOH . H 6 HOH A 2 302 302 HOH HOH . H 6 HOH A 3 303 303 HOH HOH . H 6 HOH A 4 304 304 HOH HOH . H 6 HOH A 5 305 305 HOH HOH . H 6 HOH A 6 306 306 HOH HOH . H 6 HOH A 7 307 307 HOH HOH . H 6 HOH A 8 308 308 HOH HOH . H 6 HOH A 9 309 309 HOH HOH . H 6 HOH A 10 310 310 HOH HOH . H 6 HOH A 11 311 311 HOH HOH . H 6 HOH A 12 312 312 HOH HOH . H 6 HOH A 13 313 313 HOH HOH . H 6 HOH A 14 314 314 HOH HOH . H 6 HOH A 15 315 315 HOH HOH . H 6 HOH A 16 316 316 HOH HOH . H 6 HOH A 17 317 317 HOH HOH . H 6 HOH A 18 318 318 HOH HOH . H 6 HOH A 19 319 319 HOH HOH . H 6 HOH A 20 320 320 HOH HOH . H 6 HOH A 21 321 321 HOH HOH . H 6 HOH A 22 322 322 HOH HOH . H 6 HOH A 23 323 323 HOH HOH . H 6 HOH A 24 324 324 HOH HOH . H 6 HOH A 25 325 325 HOH HOH . H 6 HOH A 26 326 326 HOH HOH . H 6 HOH A 27 327 327 HOH HOH . H 6 HOH A 28 328 328 HOH HOH . H 6 HOH A 29 329 329 HOH HOH . H 6 HOH A 30 330 330 HOH HOH . H 6 HOH A 31 331 331 HOH HOH . H 6 HOH A 32 332 332 HOH HOH . H 6 HOH A 33 333 333 HOH HOH . H 6 HOH A 34 334 334 HOH HOH . H 6 HOH A 35 335 335 HOH HOH . H 6 HOH A 36 336 336 HOH HOH . H 6 HOH A 37 337 337 HOH HOH . H 6 HOH A 38 338 338 HOH HOH . H 6 HOH A 39 339 339 HOH HOH . H 6 HOH A 40 340 340 HOH HOH . H 6 HOH A 41 341 341 HOH HOH . H 6 HOH A 42 342 342 HOH HOH . H 6 HOH A 43 343 343 HOH HOH . H 6 HOH A 44 344 344 HOH HOH . H 6 HOH A 45 345 345 HOH HOH . H 6 HOH A 46 346 346 HOH HOH . H 6 HOH A 47 347 347 HOH HOH . H 6 HOH A 48 348 348 HOH HOH . H 6 HOH A 49 349 349 HOH HOH . H 6 HOH A 50 350 350 HOH HOH . H 6 HOH A 51 351 351 HOH HOH . H 6 HOH A 52 352 352 HOH HOH . H 6 HOH A 53 353 353 HOH HOH . H 6 HOH A 54 354 354 HOH HOH . H 6 HOH A 55 355 355 HOH HOH . H 6 HOH A 56 356 356 HOH HOH . H 6 HOH A 57 357 357 HOH HOH . H 6 HOH A 58 358 358 HOH HOH . H 6 HOH A 59 359 359 HOH HOH . H 6 HOH A 60 360 360 HOH HOH . H 6 HOH A 61 361 361 HOH HOH . H 6 HOH A 62 362 362 HOH HOH . H 6 HOH A 63 363 363 HOH HOH . H 6 HOH A 64 364 364 HOH HOH . H 6 HOH A 65 365 365 HOH HOH . H 6 HOH A 66 366 366 HOH HOH . H 6 HOH A 67 367 367 HOH HOH . H 6 HOH A 68 368 368 HOH HOH . H 6 HOH A 69 369 369 HOH HOH . H 6 HOH A 70 370 370 HOH HOH . H 6 HOH A 71 371 371 HOH HOH . H 6 HOH A 72 372 372 HOH HOH . H 6 HOH A 73 373 373 HOH HOH . H 6 HOH A 74 374 374 HOH HOH . H 6 HOH A 75 375 375 HOH HOH . H 6 HOH A 76 376 376 HOH HOH . H 6 HOH A 77 377 377 HOH HOH . H 6 HOH A 78 378 378 HOH HOH . H 6 HOH A 79 379 379 HOH HOH . H 6 HOH A 80 380 380 HOH HOH . H 6 HOH A 81 381 381 HOH HOH . H 6 HOH A 82 382 382 HOH HOH . H 6 HOH A 83 383 383 HOH HOH . H 6 HOH A 84 384 384 HOH HOH . H 6 HOH A 85 385 385 HOH HOH . H 6 HOH A 86 386 386 HOH HOH . H 6 HOH A 87 387 387 HOH HOH . H 6 HOH A 88 388 388 HOH HOH . H 6 HOH A 89 389 389 HOH HOH . H 6 HOH A 90 390 390 HOH HOH . H 6 HOH A 91 391 391 HOH HOH . H 6 HOH A 92 392 392 HOH HOH . H 6 HOH A 93 393 393 HOH HOH . H 6 HOH A 94 394 394 HOH HOH . H 6 HOH A 95 395 395 HOH HOH . H 6 HOH A 96 396 396 HOH HOH . H 6 HOH A 97 397 397 HOH HOH . H 6 HOH A 98 398 398 HOH HOH . H 6 HOH A 99 399 399 HOH HOH . H 6 HOH A 100 400 400 HOH HOH . H 6 HOH A 101 401 401 HOH HOH . H 6 HOH A 102 402 402 HOH HOH . H 6 HOH A 103 403 403 HOH HOH . H 6 HOH A 104 404 404 HOH HOH . H 6 HOH A 105 405 405 HOH HOH . H 6 HOH A 106 406 406 HOH HOH . H 6 HOH A 107 407 407 HOH HOH . H 6 HOH A 108 408 408 HOH HOH . H 6 HOH A 109 409 409 HOH HOH . H 6 HOH A 110 410 410 HOH HOH . H 6 HOH A 111 411 411 HOH HOH . H 6 HOH A 112 412 412 HOH HOH . H 6 HOH A 113 413 413 HOH HOH . H 6 HOH A 114 414 414 HOH HOH . H 6 HOH A 115 415 415 HOH HOH . H 6 HOH A 116 416 416 HOH HOH . H 6 HOH A 117 417 417 HOH HOH . H 6 HOH A 118 418 418 HOH HOH . H 6 HOH A 119 419 419 HOH HOH . I 6 HOH I 1 101 101 HOH HOH . I 6 HOH I 2 102 102 HOH HOH . I 6 HOH I 3 103 103 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 . . . C 3 38.225 -15.53 -16.679 1 14.14 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 3 37.714 -14.494 -17.659 1 14.16 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 3 38.973 -16.657 -17.355 1 14.17 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 3 37.172 -16.034 -15.713 1 12.23 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 3 39.304 -14.795 -15.776 1 15.74 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 3 39.689 -14.867 -14.228 1 16.36 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 3 40.027 -16.289 -13.988 1 16.91 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 3 38.639 -14.189 -13.442 1 16.34 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 3 41.001 -13.955 -14.158 1 17.11 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 3 42.174 -14.333 -14.92 1 18.32 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 3 43.402 -13.764 -14.251 1 19.11 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 3 43.341 -12.317 -14.258 1 19.17 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 3 43.573 -14.166 -12.783 1 20.55 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 3 44.958 -14.307 -12.475 1 22.53 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 3 42.956 -12.979 -12.036 1 20.24 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 3 43.464 -12.809 -10.715 1 20.87 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 3 43.384 -11.823 -12.934 1 19.41 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 3 42.498 -10.652 -12.839 1 19.02 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 3 41.141 -10.625 -13.028 1 18.18 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 3 40.631 -9.421 -12.925 1 18.01 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 3 41.718 -8.607 -12.652 1 18.52 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 3 41.814 -7.187 -12.481 1 19.37 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 3 40.916 -6.354 -12.589 1 19.79 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 3 43.113 -6.777 -12.251 1 19.8 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 3 44.204 -7.603 -12.192 1 20.6 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 3 45.383 -7.027 -11.919 1 21.06 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 3 44.135 -8.925 -12.365 1 19.73 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 3 42.876 -9.354 -12.594 1 19.02 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #