data_6M9W # _model_server_result.job_id G2jcFC2uSLVvMAQu4YLIsA _model_server_result.datetime_utc '2024-11-02 08:34:56' _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 6m9w # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6M9W # _exptl.entry_id 6M9W _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 120 _cell.entry_id 6M9W _cell.length_a 77.858 _cell.length_b 77.858 _cell.length_c 55.726 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6M9W _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1 A,B,C 2 1,2 # 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' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 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 '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 6M9W _atom_sites.fract_transf_matrix[1][1] 0.012844 _atom_sites.fract_transf_matrix[1][2] 0.007415 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014831 _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] 0.017945 _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 1 GDP GDP . C 3 HOH A 1 301 162 HOH HOH . C 3 HOH A 2 302 108 HOH HOH . C 3 HOH A 3 303 178 HOH HOH . C 3 HOH A 4 304 165 HOH HOH . C 3 HOH A 5 305 15 HOH HOH . C 3 HOH A 6 306 163 HOH HOH . C 3 HOH A 7 307 208 HOH HOH . C 3 HOH A 8 308 164 HOH HOH . C 3 HOH A 9 309 168 HOH HOH . C 3 HOH A 10 310 95 HOH HOH . C 3 HOH A 11 311 44 HOH HOH . C 3 HOH A 12 312 181 HOH HOH . C 3 HOH A 13 313 5 HOH HOH . C 3 HOH A 14 314 25 HOH HOH . C 3 HOH A 15 315 70 HOH HOH . C 3 HOH A 16 316 63 HOH HOH . C 3 HOH A 17 317 148 HOH HOH . C 3 HOH A 18 318 216 HOH HOH . C 3 HOH A 19 319 66 HOH HOH . C 3 HOH A 20 320 93 HOH HOH . C 3 HOH A 21 321 48 HOH HOH . C 3 HOH A 22 322 71 HOH HOH . C 3 HOH A 23 323 55 HOH HOH . C 3 HOH A 24 324 167 HOH HOH . C 3 HOH A 25 325 141 HOH HOH . C 3 HOH A 26 326 116 HOH HOH . C 3 HOH A 27 327 100 HOH HOH . C 3 HOH A 28 328 169 HOH HOH . C 3 HOH A 29 329 112 HOH HOH . C 3 HOH A 30 330 16 HOH HOH . C 3 HOH A 31 331 217 HOH HOH . C 3 HOH A 32 332 49 HOH HOH . C 3 HOH A 33 333 180 HOH HOH . C 3 HOH A 34 334 151 HOH HOH . C 3 HOH A 35 335 125 HOH HOH . C 3 HOH A 36 336 82 HOH HOH . C 3 HOH A 37 337 24 HOH HOH . C 3 HOH A 38 338 1 HOH HOH . C 3 HOH A 39 339 155 HOH HOH . C 3 HOH A 40 340 215 HOH HOH . C 3 HOH A 41 341 45 HOH HOH . C 3 HOH A 42 342 58 HOH HOH . C 3 HOH A 43 343 18 HOH HOH . C 3 HOH A 44 344 84 HOH HOH . C 3 HOH A 45 345 12 HOH HOH . C 3 HOH A 46 346 32 HOH HOH . C 3 HOH A 47 347 101 HOH HOH . C 3 HOH A 48 348 80 HOH HOH . C 3 HOH A 49 349 50 HOH HOH . C 3 HOH A 50 350 13 HOH HOH . C 3 HOH A 51 351 142 HOH HOH . C 3 HOH A 52 352 68 HOH HOH . C 3 HOH A 53 353 30 HOH HOH . C 3 HOH A 54 354 124 HOH HOH . C 3 HOH A 55 355 39 HOH HOH . C 3 HOH A 56 356 4 HOH HOH . C 3 HOH A 57 357 17 HOH HOH . C 3 HOH A 58 358 10 HOH HOH . C 3 HOH A 59 359 102 HOH HOH . C 3 HOH A 60 360 136 HOH HOH . C 3 HOH A 61 361 47 HOH HOH . C 3 HOH A 62 362 199 HOH HOH . C 3 HOH A 63 363 156 HOH HOH . C 3 HOH A 64 364 14 HOH HOH . C 3 HOH A 65 365 46 HOH HOH . C 3 HOH A 66 366 21 HOH HOH . C 3 HOH A 67 367 20 HOH HOH . C 3 HOH A 68 368 188 HOH HOH . C 3 HOH A 69 369 137 HOH HOH . C 3 HOH A 70 370 135 HOH HOH . C 3 HOH A 71 371 81 HOH HOH . C 3 HOH A 72 372 41 HOH HOH . C 3 HOH A 73 373 27 HOH HOH . C 3 HOH A 74 374 51 HOH HOH . C 3 HOH A 75 375 85 HOH HOH . C 3 HOH A 76 376 2 HOH HOH . C 3 HOH A 77 377 38 HOH HOH . C 3 HOH A 78 378 185 HOH HOH . C 3 HOH A 79 379 127 HOH HOH . C 3 HOH A 80 380 61 HOH HOH . C 3 HOH A 81 381 42 HOH HOH . C 3 HOH A 82 382 11 HOH HOH . C 3 HOH A 83 383 26 HOH HOH . C 3 HOH A 84 384 67 HOH HOH . C 3 HOH A 85 385 29 HOH HOH . C 3 HOH A 86 386 144 HOH HOH . C 3 HOH A 87 387 3 HOH HOH . C 3 HOH A 88 388 65 HOH HOH . C 3 HOH A 89 389 103 HOH HOH . C 3 HOH A 90 390 94 HOH HOH . C 3 HOH A 91 391 33 HOH HOH . C 3 HOH A 92 392 34 HOH HOH . C 3 HOH A 93 393 115 HOH HOH . C 3 HOH A 94 394 134 HOH HOH . C 3 HOH A 95 395 28 HOH HOH . C 3 HOH A 96 396 213 HOH HOH . C 3 HOH A 97 397 140 HOH HOH . C 3 HOH A 98 398 37 HOH HOH . C 3 HOH A 99 399 138 HOH HOH . C 3 HOH A 100 400 59 HOH HOH . C 3 HOH A 101 401 8 HOH HOH . C 3 HOH A 102 402 7 HOH HOH . C 3 HOH A 103 403 83 HOH HOH . C 3 HOH A 104 404 176 HOH HOH . C 3 HOH A 105 405 121 HOH HOH . C 3 HOH A 106 406 122 HOH HOH . C 3 HOH A 107 407 91 HOH HOH . C 3 HOH A 108 408 149 HOH HOH . C 3 HOH A 109 409 90 HOH HOH . C 3 HOH A 110 410 6 HOH HOH . C 3 HOH A 111 411 150 HOH HOH . C 3 HOH A 112 412 159 HOH HOH . C 3 HOH A 113 413 36 HOH HOH . C 3 HOH A 114 414 212 HOH HOH . C 3 HOH A 115 415 166 HOH HOH . C 3 HOH A 116 416 193 HOH HOH . C 3 HOH A 117 417 88 HOH HOH . C 3 HOH A 118 418 89 HOH HOH . C 3 HOH A 119 419 99 HOH HOH . C 3 HOH A 120 420 145 HOH HOH . C 3 HOH A 121 421 182 HOH HOH . C 3 HOH A 122 422 60 HOH HOH . C 3 HOH A 123 423 192 HOH HOH . C 3 HOH A 124 424 75 HOH HOH . C 3 HOH A 125 425 22 HOH HOH . C 3 HOH A 126 426 183 HOH HOH . C 3 HOH A 127 427 77 HOH HOH . C 3 HOH A 128 428 19 HOH HOH . C 3 HOH A 129 429 175 HOH HOH . C 3 HOH A 130 430 126 HOH HOH . C 3 HOH A 131 431 56 HOH HOH . C 3 HOH A 132 432 40 HOH HOH . C 3 HOH A 133 433 43 HOH HOH . C 3 HOH A 134 434 53 HOH HOH . C 3 HOH A 135 435 35 HOH HOH . C 3 HOH A 136 436 9 HOH HOH . C 3 HOH A 137 437 78 HOH HOH . C 3 HOH A 138 438 123 HOH HOH . C 3 HOH A 139 439 153 HOH HOH . C 3 HOH A 140 440 133 HOH HOH . C 3 HOH A 141 441 107 HOH HOH . C 3 HOH A 142 442 204 HOH HOH . C 3 HOH A 143 443 96 HOH HOH . C 3 HOH A 144 444 104 HOH HOH . C 3 HOH A 145 445 31 HOH HOH . C 3 HOH A 146 446 23 HOH HOH . C 3 HOH A 147 447 118 HOH HOH . C 3 HOH A 148 448 205 HOH HOH . C 3 HOH A 149 449 161 HOH HOH . C 3 HOH A 150 450 105 HOH HOH . C 3 HOH A 151 451 69 HOH HOH . C 3 HOH A 152 452 87 HOH HOH . C 3 HOH A 153 453 98 HOH HOH . C 3 HOH A 154 454 52 HOH HOH . C 3 HOH A 155 455 54 HOH HOH . C 3 HOH A 156 456 79 HOH HOH . C 3 HOH A 157 457 158 HOH HOH . C 3 HOH A 158 458 113 HOH HOH . C 3 HOH A 159 459 214 HOH HOH . C 3 HOH A 160 460 170 HOH HOH . C 3 HOH A 161 461 76 HOH HOH . C 3 HOH A 162 462 209 HOH HOH . C 3 HOH A 163 463 201 HOH HOH . C 3 HOH A 164 464 190 HOH HOH . C 3 HOH A 165 465 171 HOH HOH . C 3 HOH A 166 466 147 HOH HOH . C 3 HOH A 167 467 72 HOH HOH . C 3 HOH A 168 468 194 HOH HOH . C 3 HOH A 169 469 86 HOH HOH . C 3 HOH A 170 470 97 HOH HOH . C 3 HOH A 171 471 210 HOH HOH . C 3 HOH A 172 472 191 HOH HOH . C 3 HOH A 173 473 143 HOH HOH . C 3 HOH A 174 474 172 HOH HOH . C 3 HOH A 175 475 195 HOH HOH . C 3 HOH A 176 476 157 HOH HOH . C 3 HOH A 177 477 57 HOH HOH . C 3 HOH A 178 478 173 HOH HOH . C 3 HOH A 179 479 114 HOH HOH . C 3 HOH A 180 480 64 HOH HOH . C 3 HOH A 181 481 200 HOH HOH . C 3 HOH A 182 482 211 HOH HOH . C 3 HOH A 183 483 196 HOH HOH . C 3 HOH A 184 484 152 HOH HOH . C 3 HOH A 185 485 92 HOH HOH . C 3 HOH A 186 486 139 HOH HOH . C 3 HOH A 187 487 198 HOH HOH . C 3 HOH A 188 488 74 HOH HOH . C 3 HOH A 189 489 203 HOH HOH . C 3 HOH A 190 490 111 HOH HOH . C 3 HOH A 191 491 128 HOH HOH . C 3 HOH A 192 492 186 HOH HOH . C 3 HOH A 193 493 202 HOH HOH . C 3 HOH A 194 494 132 HOH HOH . C 3 HOH A 195 495 106 HOH HOH . C 3 HOH A 196 496 207 HOH HOH . C 3 HOH A 197 497 187 HOH HOH . C 3 HOH A 198 498 189 HOH HOH . C 3 HOH A 199 499 174 HOH HOH . C 3 HOH A 200 500 120 HOH HOH . C 3 HOH A 201 501 73 HOH HOH . C 3 HOH A 202 502 129 HOH HOH . C 3 HOH A 203 503 206 HOH HOH . C 3 HOH A 204 504 154 HOH HOH . C 3 HOH A 205 505 179 HOH HOH . C 3 HOH A 206 506 62 HOH HOH . C 3 HOH A 207 507 146 HOH HOH . C 3 HOH A 208 508 110 HOH HOH . C 3 HOH A 209 509 109 HOH HOH . C 3 HOH A 210 510 130 HOH HOH . C 3 HOH A 211 511 117 HOH HOH . C 3 HOH A 212 512 160 HOH HOH . C 3 HOH A 213 513 197 HOH HOH . C 3 HOH A 214 514 184 HOH HOH . C 3 HOH A 215 515 131 HOH HOH . C 3 HOH A 216 516 119 HOH HOH . C 3 HOH A 217 517 177 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 24.339 31.802 7.604 1 15.59 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 25.049 31.266 6.382 1 17.15 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 25.352 32.356 8.578 1 15.29 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 23.356 32.877 7.213 1 15.84 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 23.609 30.59 8.372 1 14.99 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 22.09 30.118 8.151 1 16.59 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 21.777 29.868 6.693 1 18 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 21.112 31.076 8.785 1 16.45 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 22.104 28.734 8.969 1 16.74 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 22.773 27.599 8.425 1 19.01 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 22.144 26.356 9.02 1 18.34 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 22.257 26.404 10.445 1 18.63 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 20.659 26.266 8.695 1 19.64 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 20.308 24.915 8.411 1 23.57 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 19.956 26.731 9.959 1 19.44 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 18.688 26.116 10.149 1 24.45 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 20.956 26.318 11.031 1 17.49 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 20.9 27.173 12.225 1 15.21 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 20.986 28.515 12.282 1 14.75 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 20.907 28.932 13.571 1 16.22 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 20.787 27.839 14.345 1 16.4 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 20.661 27.545 15.786 1 15.85 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 20.653 28.461 16.636 1 17.51 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 20.565 26.261 16.154 1 16.07 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 20.573 25.242 15.274 1 16.56 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 20.467 23.972 15.731 1 18.47 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 20.684 25.434 13.944 1 16.78 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 20.79 26.684 13.447 1 16.31 ? C4 GDP 201 A 1 HETATM 29 H H4' GDP . . . B 2 22.669 25.487 8.599 1 22 ? H4' GDP 201 A 1 HETATM 30 H H3' GDP . . . B 2 20.38 26.866 7.817 1 23.55 ? H3' GDP 201 A 1 HETATM 31 H HO3' GDP . . . B 2 19.374 24.869 8.164 1 28.28 ? HO3' GDP 201 A 1 HETATM 32 H H2' GDP . . . B 2 19.71 27.802 9.954 1 23.32 ? H2' GDP 201 A 1 HETATM 33 H HO2' GDP . . . B 2 18.108 26.338 9.409 1 29.33 ? HO2' GDP 201 A 1 HETATM 34 H H1' GDP . . . B 2 20.706 25.299 11.358 1 20.98 ? H1' GDP 201 A 1 HETATM 35 H H8 GDP . . . B 2 21.101 29.166 11.425 1 17.69 ? H8 GDP 201 A 1 HETATM 36 H HN1 GDP . . . B 2 20.482 26.041 17.167 1 19.27 ? HN1 GDP 201 A 1 HETATM 37 H HN21 GDP . . . B 2 20.384 23.797 16.723 1 22.15 ? HN21 GDP 201 A 1 HETATM 38 H HN22 GDP . . . B 2 20.471 23.199 15.081 1 22.15 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 38 #