data_3UMS # _model_server_result.job_id UVeamN5wnO6k2qRmepcGLA _model_server_result.datetime_utc '2024-10-11 00:24:44' _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 3ums # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":355}' # _entry.id 3UMS # _exptl.entry_id 3UMS _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 3UMS _cell.length_a 121.531 _cell.length_b 121.531 _cell.length_c 67.909 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UMS _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _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,E _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 '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 3UMS _atom_sites.fract_transf_matrix[1][1] 0.008228 _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] 0.008228 _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] 0.014726 _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 1 355 355 GDP GDP . C 3 SO4 A 1 356 1 SO4 SO4 . D 4 CL A 1 357 1 CL CL . E 5 HOH A 1 358 2 HOH HOH . E 5 HOH A 2 359 3 HOH HOH . E 5 HOH A 3 360 4 HOH HOH . E 5 HOH A 4 361 5 HOH HOH . E 5 HOH A 5 362 6 HOH HOH . E 5 HOH A 6 363 8 HOH HOH . E 5 HOH A 7 364 9 HOH HOH . E 5 HOH A 8 365 10 HOH HOH . E 5 HOH A 9 366 12 HOH HOH . E 5 HOH A 10 367 13 HOH HOH . E 5 HOH A 11 368 14 HOH HOH . E 5 HOH A 12 369 15 HOH HOH . E 5 HOH A 13 370 16 HOH HOH . E 5 HOH A 14 371 17 HOH HOH . E 5 HOH A 15 372 18 HOH HOH . E 5 HOH A 16 373 20 HOH HOH . E 5 HOH A 17 374 21 HOH HOH . E 5 HOH A 18 375 23 HOH HOH . E 5 HOH A 19 376 24 HOH HOH . E 5 HOH A 20 377 25 HOH HOH . E 5 HOH A 21 378 26 HOH HOH . E 5 HOH A 22 379 27 HOH HOH . E 5 HOH A 23 380 59 HOH HOH . E 5 HOH A 24 381 61 HOH HOH . E 5 HOH A 25 382 62 HOH HOH . E 5 HOH A 26 383 63 HOH HOH . E 5 HOH A 27 384 64 HOH HOH . E 5 HOH A 28 385 65 HOH HOH . E 5 HOH A 29 386 66 HOH HOH . E 5 HOH A 30 387 69 HOH HOH . E 5 HOH A 31 388 71 HOH HOH . E 5 HOH A 32 389 74 HOH HOH . E 5 HOH A 33 390 80 HOH HOH . E 5 HOH A 34 391 81 HOH HOH . E 5 HOH A 35 392 82 HOH HOH . E 5 HOH A 36 393 83 HOH HOH . E 5 HOH A 37 394 84 HOH HOH . E 5 HOH A 38 395 87 HOH HOH . E 5 HOH A 39 396 89 HOH HOH . E 5 HOH A 40 397 90 HOH HOH . E 5 HOH A 41 398 92 HOH HOH . E 5 HOH A 42 399 93 HOH HOH . E 5 HOH A 43 400 95 HOH HOH . E 5 HOH A 44 401 97 HOH HOH . E 5 HOH A 45 402 98 HOH HOH . E 5 HOH A 46 403 99 HOH HOH . E 5 HOH A 47 404 101 HOH HOH . E 5 HOH A 48 405 102 HOH HOH . E 5 HOH A 49 406 103 HOH HOH . E 5 HOH A 50 407 104 HOH HOH . E 5 HOH A 51 408 107 HOH HOH . E 5 HOH A 52 409 108 HOH HOH . E 5 HOH A 53 410 109 HOH HOH . E 5 HOH A 54 411 111 HOH HOH . E 5 HOH A 55 412 112 HOH HOH . E 5 HOH A 56 413 113 HOH HOH . E 5 HOH A 57 414 115 HOH HOH . E 5 HOH A 58 415 117 HOH HOH . E 5 HOH A 59 416 119 HOH HOH . E 5 HOH A 60 417 121 HOH HOH . E 5 HOH A 61 418 122 HOH HOH . E 5 HOH A 62 419 123 HOH HOH . E 5 HOH A 63 420 124 HOH HOH . E 5 HOH A 64 421 125 HOH HOH . E 5 HOH A 65 422 126 HOH HOH . E 5 HOH A 66 423 128 HOH HOH . E 5 HOH A 67 424 129 HOH HOH . E 5 HOH A 68 425 130 HOH HOH . E 5 HOH A 69 426 131 HOH HOH . E 5 HOH A 70 427 132 HOH HOH . E 5 HOH A 71 428 133 HOH HOH . E 5 HOH A 72 429 134 HOH HOH . E 5 HOH A 73 430 135 HOH HOH . E 5 HOH A 74 431 137 HOH HOH . E 5 HOH A 75 432 138 HOH HOH . E 5 HOH A 76 433 139 HOH HOH . E 5 HOH A 77 434 140 HOH HOH . E 5 HOH A 78 435 141 HOH HOH . E 5 HOH A 79 436 142 HOH HOH . E 5 HOH A 80 437 143 HOH HOH . E 5 HOH A 81 438 144 HOH HOH . E 5 HOH A 82 439 146 HOH HOH . E 5 HOH A 83 440 147 HOH HOH . E 5 HOH A 84 441 148 HOH HOH . E 5 HOH A 85 442 156 HOH HOH . E 5 HOH A 86 443 157 HOH HOH . E 5 HOH A 87 444 158 HOH HOH . E 5 HOH A 88 445 159 HOH HOH . E 5 HOH A 89 446 160 HOH HOH . E 5 HOH A 90 447 161 HOH HOH . E 5 HOH A 91 448 162 HOH HOH . E 5 HOH A 92 449 163 HOH HOH . E 5 HOH A 93 450 164 HOH HOH . E 5 HOH A 94 451 166 HOH HOH . E 5 HOH A 95 452 167 HOH HOH . E 5 HOH A 96 453 168 HOH HOH . E 5 HOH A 97 454 169 HOH HOH . E 5 HOH A 98 455 170 HOH HOH . E 5 HOH A 99 456 171 HOH HOH . E 5 HOH A 100 457 172 HOH HOH . E 5 HOH A 101 458 173 HOH HOH . E 5 HOH A 102 459 176 HOH HOH . E 5 HOH A 103 460 177 HOH HOH . E 5 HOH A 104 461 178 HOH HOH . E 5 HOH A 105 462 179 HOH HOH . E 5 HOH A 106 463 180 HOH HOH . E 5 HOH A 107 464 181 HOH HOH . E 5 HOH A 108 465 182 HOH HOH . E 5 HOH A 109 466 183 HOH HOH . E 5 HOH A 110 467 185 HOH HOH . E 5 HOH A 111 468 186 HOH HOH . E 5 HOH A 112 469 189 HOH HOH . E 5 HOH A 113 470 202 HOH HOH . E 5 HOH A 114 471 204 HOH HOH . E 5 HOH A 115 472 205 HOH HOH . E 5 HOH A 116 473 206 HOH HOH . E 5 HOH A 117 474 209 HOH HOH . E 5 HOH A 118 475 210 HOH HOH . E 5 HOH A 119 476 214 HOH HOH . E 5 HOH A 120 477 222 HOH HOH . E 5 HOH A 121 478 224 HOH HOH . E 5 HOH A 122 479 225 HOH HOH . E 5 HOH A 123 480 227 HOH HOH . E 5 HOH A 124 481 228 HOH HOH . E 5 HOH A 125 482 229 HOH HOH . E 5 HOH A 126 483 231 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 -22.406 38.641 -3.443 1 33.86 ? PB GDP 355 A 1 HETATM 2 O O1B GDP . . . B 2 -22.049 38.976 -4.878 1 36.96 ? O1B GDP 355 A 1 HETATM 3 O O2B GDP . . . B 2 -23.506 39.557 -2.969 1 37.46 ? O2B GDP 355 A 1 HETATM 4 O O3B GDP . . . B 2 -22.907 37.214 -3.35 1 31.21 ? O3B GDP 355 A 1 HETATM 5 O O3A GDP . . . B 2 -21.124 38.953 -2.519 1 36.52 ? O3A GDP 355 A 1 HETATM 6 P PA GDP . . . B 2 -20.164 37.78 -2.004 1 30.36 ? PA GDP 355 A 1 HETATM 7 O O1A GDP . . . B 2 -20.837 37.085 -0.846 1 33.39 ? O1A GDP 355 A 1 HETATM 8 O O2A GDP . . . B 2 -19.858 36.813 -3.141 1 30.72 ? O2A GDP 355 A 1 HETATM 9 O O5' GDP . . . B 2 -18.849 38.54 -1.48 1 27.9 ? O5' GDP 355 A 1 HETATM 10 C C5' GDP . . . B 2 -17.937 39.151 -2.376 1 30.9 ? C5' GDP 355 A 1 HETATM 11 C C4' GDP . . . B 2 -16.541 39.06 -1.767 1 34.69 ? C4' GDP 355 A 1 HETATM 12 O O4' GDP . . . B 2 -16.504 39.773 -0.534 1 32.33 ? O4' GDP 355 A 1 HETATM 13 C C3' GDP . . . B 2 -16.183 37.621 -1.432 1 35.47 ? C3' GDP 355 A 1 HETATM 14 O O3' GDP . . . B 2 -14.836 37.345 -1.807 1 30.89 ? O3' GDP 355 A 1 HETATM 15 C C2' GDP . . . B 2 -16.345 37.529 0.075 1 33.39 ? C2' GDP 355 A 1 HETATM 16 O O2' GDP . . . B 2 -15.447 36.591 0.657 1 30.15 ? O2' GDP 355 A 1 HETATM 17 C C1' GDP . . . B 2 -16.054 38.932 0.541 1 32.11 ? C1' GDP 355 A 1 HETATM 18 N N9 GDP . . . B 2 -16.796 39.36 1.744 1 31.72 ? N9 GDP 355 A 1 HETATM 19 C C8 GDP . . . B 2 -18.13 39.34 1.911 1 29.76 ? C8 GDP 355 A 1 HETATM 20 N N7 GDP . . . B 2 -18.464 39.888 3.102 1 33.7 ? N7 GDP 355 A 1 HETATM 21 C C5 GDP . . . B 2 -17.332 40.306 3.693 1 37.35 ? C5 GDP 355 A 1 HETATM 22 C C6 GDP . . . B 2 -16.956 40.966 4.963 1 34.29 ? C6 GDP 355 A 1 HETATM 23 O O6 GDP . . . B 2 -17.837 41.272 5.778 1 31.84 ? O6 GDP 355 A 1 HETATM 24 N N1 GDP . . . B 2 -15.666 41.215 5.204 1 35.87 ? N1 GDP 355 A 1 HETATM 25 C C2 GDP . . . B 2 -14.706 40.885 4.313 1 35.88 ? C2 GDP 355 A 1 HETATM 26 N N2 GDP . . . B 2 -13.403 41.154 4.571 1 37.64 ? N2 GDP 355 A 1 HETATM 27 N N3 GDP . . . B 2 -14.976 40.28 3.14 1 35.52 ? N3 GDP 355 A 1 HETATM 28 C C4 GDP . . . B 2 -16.238 39.962 2.785 1 36.84 ? C4 GDP 355 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 28 #