data_5VBE # _model_server_result.job_id WpsK1eB745bahsTHoEbpog _model_server_result.datetime_utc '2024-11-05 03:50:33' _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 5vbe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 5VBE # _exptl.entry_id 5VBE _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 5VBE _cell.length_a 92.648 _cell.length_b 92.648 _cell.length_c 120.532 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VBE _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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 # 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 22 A SER 17 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc2 B O2B GDP . A GDP 201 1_555 D MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc3 D MG MG . A MG 203 1_555 E O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc4 D MG MG . A MG 203 1_555 E O HOH . A HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc5 D MG MG . A MG 203 1_555 E O HOH . A HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc6 D MG MG . A MG 203 1_555 E O HOH . A HOH 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? # _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 124 n n PB O2B GDP sing 125 n n PB O3B GDP sing 126 n n PB O3A GDP sing 127 n n O2B HOB2 GDP sing 128 n n O3B HOB3 GDP sing 129 n n O3A PA GDP sing 130 n n PA O1A GDP doub 131 n n PA O2A GDP sing 132 n n PA O5' GDP sing 133 n n O2A HOA2 GDP sing 134 n n O5' C5' GDP sing 135 n n C5' C4' GDP sing 136 n n C5' H5' GDP sing 137 n n C5' "H5''" GDP sing 138 n n C4' O4' GDP sing 139 n n C4' C3' GDP sing 140 n n C4' H4' GDP sing 141 n n O4' C1' GDP sing 142 n n C3' O3' GDP sing 143 n n C3' C2' GDP sing 144 n n C3' H3' GDP sing 145 n n O3' HO3' GDP sing 146 n n C2' O2' GDP sing 147 n n C2' C1' GDP sing 148 n n C2' H2' GDP sing 149 n n O2' HO2' GDP sing 150 n n C1' N9 GDP sing 151 n n C1' H1' GDP sing 152 n n N9 C8 GDP sing 153 n y N9 C4 GDP sing 154 n y C8 N7 GDP doub 155 n y C8 H8 GDP sing 156 n n N7 C5 GDP sing 157 n y C5 C6 GDP sing 158 n n C5 C4 GDP doub 159 n y C6 O6 GDP doub 160 n n C6 N1 GDP sing 161 n n N1 C2 GDP sing 162 n n N1 HN1 GDP sing 163 n n C2 N2 GDP sing 164 n n C2 N3 GDP doub 165 n n N2 HN21 GDP sing 166 n n N2 HN22 GDP sing 167 n n N3 C4 GDP sing 168 n n # _atom_sites.entry_id 5VBE _atom_sites.fract_transf_matrix[1][1] 0.010794 _atom_sites.fract_transf_matrix[1][2] 0.006232 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012463 _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] 0.008297 _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 1 201 203 GDP GDP . C 3 92V A 1 202 251 92V LIG . D 4 MG A 1 203 1 MG MG . E 5 HOH A 1 301 75 HOH HOH . E 5 HOH A 2 302 38 HOH HOH . E 5 HOH A 3 303 124 HOH HOH . E 5 HOH A 4 304 85 HOH HOH . E 5 HOH A 5 305 111 HOH HOH . E 5 HOH A 6 306 72 HOH HOH . E 5 HOH A 7 307 80 HOH HOH . E 5 HOH A 8 308 51 HOH HOH . E 5 HOH A 9 309 53 HOH HOH . E 5 HOH A 10 310 12 HOH HOH . E 5 HOH A 11 311 79 HOH HOH . E 5 HOH A 12 312 44 HOH HOH . E 5 HOH A 13 313 14 HOH HOH . E 5 HOH A 14 314 57 HOH HOH . E 5 HOH A 15 315 54 HOH HOH . E 5 HOH A 16 316 62 HOH HOH . E 5 HOH A 17 317 15 HOH HOH . E 5 HOH A 18 318 73 HOH HOH . E 5 HOH A 19 319 7 HOH HOH . E 5 HOH A 20 320 1 HOH HOH . E 5 HOH A 21 321 20 HOH HOH . E 5 HOH A 22 322 97 HOH HOH . E 5 HOH A 23 323 26 HOH HOH . E 5 HOH A 24 324 34 HOH HOH . E 5 HOH A 25 325 61 HOH HOH . E 5 HOH A 26 326 8 HOH HOH . E 5 HOH A 27 327 10 HOH HOH . E 5 HOH A 28 328 84 HOH HOH . E 5 HOH A 29 329 59 HOH HOH . E 5 HOH A 30 330 40 HOH HOH . E 5 HOH A 31 331 55 HOH HOH . E 5 HOH A 32 332 50 HOH HOH . E 5 HOH A 33 333 56 HOH HOH . E 5 HOH A 34 334 67 HOH HOH . E 5 HOH A 35 335 83 HOH HOH . E 5 HOH A 36 336 103 HOH HOH . E 5 HOH A 37 337 9 HOH HOH . E 5 HOH A 38 338 63 HOH HOH . E 5 HOH A 39 339 74 HOH HOH . E 5 HOH A 40 340 121 HOH HOH . E 5 HOH A 41 341 2 HOH HOH . E 5 HOH A 42 342 70 HOH HOH . E 5 HOH A 43 343 31 HOH HOH . E 5 HOH A 44 344 120 HOH HOH . E 5 HOH A 45 345 16 HOH HOH . E 5 HOH A 46 346 22 HOH HOH . E 5 HOH A 47 347 33 HOH HOH . E 5 HOH A 48 348 45 HOH HOH . E 5 HOH A 49 349 37 HOH HOH . E 5 HOH A 50 350 60 HOH HOH . E 5 HOH A 51 351 90 HOH HOH . E 5 HOH A 52 352 153 HOH HOH . E 5 HOH A 53 353 76 HOH HOH . E 5 HOH A 54 354 3 HOH HOH . E 5 HOH A 55 355 87 HOH HOH . E 5 HOH A 56 356 18 HOH HOH . E 5 HOH A 57 357 42 HOH HOH . E 5 HOH A 58 358 46 HOH HOH . E 5 HOH A 59 359 32 HOH HOH . E 5 HOH A 60 360 4 HOH HOH . E 5 HOH A 61 361 5 HOH HOH . E 5 HOH A 62 362 95 HOH HOH . E 5 HOH A 63 363 36 HOH HOH . E 5 HOH A 64 364 88 HOH HOH . E 5 HOH A 65 365 49 HOH HOH . E 5 HOH A 66 366 64 HOH HOH . E 5 HOH A 67 367 150 HOH HOH . E 5 HOH A 68 368 98 HOH HOH . E 5 HOH A 69 369 164 HOH HOH . E 5 HOH A 70 370 6 HOH HOH . E 5 HOH A 71 371 69 HOH HOH . E 5 HOH A 72 372 92 HOH HOH . E 5 HOH A 73 373 158 HOH HOH . E 5 HOH A 74 374 99 HOH HOH . E 5 HOH A 75 375 27 HOH HOH . E 5 HOH A 76 376 11 HOH HOH . E 5 HOH A 77 377 102 HOH HOH . E 5 HOH A 78 378 108 HOH HOH . E 5 HOH A 79 379 152 HOH HOH . E 5 HOH A 80 380 23 HOH HOH . E 5 HOH A 81 381 58 HOH HOH . E 5 HOH A 82 382 29 HOH HOH . E 5 HOH A 83 383 86 HOH HOH . E 5 HOH A 84 384 82 HOH HOH . E 5 HOH A 85 385 30 HOH HOH . E 5 HOH A 86 386 52 HOH HOH . E 5 HOH A 87 387 35 HOH HOH . E 5 HOH A 88 388 81 HOH HOH . E 5 HOH A 89 389 13 HOH HOH . E 5 HOH A 90 390 96 HOH HOH . E 5 HOH A 91 391 94 HOH HOH . E 5 HOH A 92 392 77 HOH HOH . E 5 HOH A 93 393 71 HOH HOH . E 5 HOH A 94 394 163 HOH HOH . E 5 HOH A 95 395 105 HOH HOH . E 5 HOH A 96 396 66 HOH HOH . E 5 HOH A 97 397 114 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 -8.661 13.648 -21.219 1 22.33 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -9.341 12.769 -22.287 1 17.32 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -9.732 14.658 -20.644 1 19.01 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -7.98 12.783 -20.142 1 19.51 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -7.556 14.503 -22.007 1 17.5 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -7.189 16.048 -21.847 1 18.18 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -8.246 16.898 -22.42 1 19 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -6.821 16.269 -20.393 1 20.35 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -5.894 16.158 -22.751 1 18.77 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -4.78 15.305 -22.53 1 16.68 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -3.551 15.891 -23.174 1 18.51 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -3.588 15.877 -24.494 1 17.38 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -3.38 17.472 -22.785 1 20.07 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -1.901 17.651 -22.6 1 22.11 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -3.864 18.124 -23.752 1 16.99 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -3.175 19.429 -24.011 1 21.94 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -3.567 17.248 -25.051 1 18.51 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -4.479 17.335 -25.994 1 17.53 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -5.821 17.155 -26.016 1 15.42 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -6.275 17.319 -27.267 1 16.02 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -5.212 17.568 -28.055 1 14.43 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -5.115 17.802 -29.536 1 15.93 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -6.109 17.815 -30.253 1 15.46 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -3.843 18.037 -30.076 1 15.92 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -2.687 18.046 -29.252 1 15.21 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -1.475 18.273 -29.86 1 19.42 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -2.766 17.799 -27.839 1 16.09 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -4.074 17.547 -27.26 1 13.15 ? C4 GDP 201 A 1 HETATM 29 H H5' GDP . . . B 2 -4.956 14.458 -22.894 1 20.17 ? H5' GDP 201 A 1 HETATM 30 H "H5''" GDP . . . B 2 -4.626 15.219 -21.557 1 20.17 ? "H5''" GDP 201 A 1 HETATM 31 H H4' GDP . . . B 2 -2.764 15.398 -22.87 1 22.37 ? H4' GDP 201 A 1 HETATM 32 H H3' GDP . . . B 2 -3.868 17.681 -21.94 1 24.24 ? H3' GDP 201 A 1 HETATM 33 H HO3' GDP . . . B 2 -1.598 17.025 -22.095 1 26.68 ? HO3' GDP 201 A 1 HETATM 34 H H2' GDP . . . B 2 -4.896 18.264 -23.627 1 20.55 ? H2' GDP 201 A 1 HETATM 35 H HO2' GDP . . . B 2 -3.714 19.96 -24.526 1 26.48 ? HO2' GDP 201 A 1 HETATM 36 H H1' GDP . . . B 2 -2.657 17.463 -25.419 1 22.36 ? H1' GDP 201 A 1 HETATM 37 H H8 GDP . . . B 2 -6.366 16.978 -25.251 1 18.66 ? H8 GDP 201 A 1 HETATM 38 H HN1 GDP . . . B 2 -3.757 18.195 -30.971 1 19.26 ? HN1 GDP 201 A 1 HETATM 39 H HN21 GDP . . . B 2 -1.438 18.418 -30.738 1 23.46 ? HN21 GDP 201 A 1 HETATM 40 H HN22 GDP . . . B 2 -0.688 18.278 -29.351 1 23.46 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 40 #