data_4L8G # _model_server_result.job_id XnVpEwN7y3s4QAbmtO2NQQ _model_server_result.datetime_utc '2024-10-15 16:17:00' _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 4l8g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4L8G # _exptl.entry_id 4L8G _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 4L8G _cell.length_a 82.146 _cell.length_b 82.146 _cell.length_c 39.513 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L8G _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc2 B O1B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc3 C MG MG . A MG 202 1_555 E O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc7 D NA NA . A NA 203 1_555 E O HOH . A HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc8 D NA NA . A NA 203 1_555 E O HOH . A HOH 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc9 D NA NA . A NA 203 1_555 E O HOH . A HOH 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? # _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 4L8G _atom_sites.fract_transf_matrix[1][1] 0.012173 _atom_sites.fract_transf_matrix[1][2] 0.007028 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014057 _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] 0.025308 _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 1 201 220 GDP GDP . C 3 MG A 1 202 200 MG MG . D 4 NA A 1 203 205 NA NA . E 5 HOH A 1 301 1 HOH HOH . E 5 HOH A 2 302 2 HOH HOH . E 5 HOH A 3 303 3 HOH HOH . E 5 HOH A 4 304 4 HOH HOH . E 5 HOH A 5 305 5 HOH HOH . E 5 HOH A 6 306 6 HOH HOH . E 5 HOH A 7 307 7 HOH HOH . E 5 HOH A 8 308 8 HOH HOH . E 5 HOH A 9 309 9 HOH HOH . E 5 HOH A 10 310 10 HOH HOH . E 5 HOH A 11 311 11 HOH HOH . E 5 HOH A 12 312 12 HOH HOH . E 5 HOH A 13 313 13 HOH HOH . E 5 HOH A 14 314 14 HOH HOH . E 5 HOH A 15 315 15 HOH HOH . E 5 HOH A 16 316 16 HOH HOH . E 5 HOH A 17 317 17 HOH HOH . E 5 HOH A 18 318 18 HOH HOH . E 5 HOH A 19 319 19 HOH HOH . E 5 HOH A 20 320 20 HOH HOH . E 5 HOH A 21 321 21 HOH HOH . E 5 HOH A 22 322 22 HOH HOH . E 5 HOH A 23 323 23 HOH HOH . E 5 HOH A 24 324 24 HOH HOH . E 5 HOH A 25 325 25 HOH HOH . E 5 HOH A 26 326 26 HOH HOH . E 5 HOH A 27 327 27 HOH HOH . E 5 HOH A 28 328 28 HOH HOH . E 5 HOH A 29 329 29 HOH HOH . E 5 HOH A 30 330 30 HOH HOH . E 5 HOH A 31 331 31 HOH HOH . E 5 HOH A 32 332 32 HOH HOH . E 5 HOH A 33 333 33 HOH HOH . E 5 HOH A 34 334 34 HOH HOH . E 5 HOH A 35 335 35 HOH HOH . E 5 HOH A 36 336 36 HOH HOH . E 5 HOH A 37 337 37 HOH HOH . E 5 HOH A 38 338 38 HOH HOH . E 5 HOH A 39 339 39 HOH HOH . E 5 HOH A 40 340 40 HOH HOH . E 5 HOH A 41 341 41 HOH HOH . E 5 HOH A 42 342 42 HOH HOH . E 5 HOH A 43 343 43 HOH HOH . E 5 HOH A 44 344 44 HOH HOH . E 5 HOH A 45 345 45 HOH HOH . E 5 HOH A 46 346 46 HOH HOH . E 5 HOH A 47 347 47 HOH HOH . E 5 HOH A 48 348 48 HOH HOH . E 5 HOH A 49 349 49 HOH HOH . E 5 HOH A 50 350 50 HOH HOH . E 5 HOH A 51 351 51 HOH HOH . E 5 HOH A 52 352 52 HOH HOH . E 5 HOH A 53 353 53 HOH HOH . E 5 HOH A 54 354 54 HOH HOH . E 5 HOH A 55 355 55 HOH HOH . E 5 HOH A 56 356 56 HOH HOH . E 5 HOH A 57 357 57 HOH HOH . E 5 HOH A 58 358 58 HOH HOH . E 5 HOH A 59 359 59 HOH HOH . E 5 HOH A 60 360 60 HOH HOH . E 5 HOH A 61 361 61 HOH HOH . E 5 HOH A 62 362 62 HOH HOH . E 5 HOH A 63 363 63 HOH HOH . E 5 HOH A 64 364 64 HOH HOH . E 5 HOH A 65 365 65 HOH HOH . E 5 HOH A 66 366 66 HOH HOH . E 5 HOH A 67 367 67 HOH HOH . E 5 HOH A 68 368 68 HOH HOH . E 5 HOH A 69 369 69 HOH HOH . E 5 HOH A 70 370 70 HOH HOH . E 5 HOH A 71 371 71 HOH HOH . E 5 HOH A 72 372 72 HOH HOH . E 5 HOH A 73 373 73 HOH HOH . E 5 HOH A 74 374 74 HOH HOH . E 5 HOH A 75 375 75 HOH HOH . E 5 HOH A 76 376 76 HOH HOH . E 5 HOH A 77 377 77 HOH HOH . E 5 HOH A 78 378 78 HOH HOH . E 5 HOH A 79 379 79 HOH HOH . E 5 HOH A 80 380 80 HOH HOH . E 5 HOH A 81 381 81 HOH HOH . E 5 HOH A 82 382 82 HOH HOH . E 5 HOH A 83 383 83 HOH HOH . E 5 HOH A 84 384 84 HOH HOH . E 5 HOH A 85 385 85 HOH HOH . E 5 HOH A 86 386 86 HOH HOH . E 5 HOH A 87 387 87 HOH HOH . E 5 HOH A 88 388 88 HOH HOH . E 5 HOH A 89 389 89 HOH HOH . E 5 HOH A 90 390 90 HOH HOH . E 5 HOH A 91 391 91 HOH HOH . E 5 HOH A 92 392 92 HOH HOH . E 5 HOH A 93 393 93 HOH HOH . E 5 HOH A 94 394 94 HOH HOH . E 5 HOH A 95 395 95 HOH HOH . E 5 HOH A 96 396 96 HOH HOH . E 5 HOH A 97 397 97 HOH HOH . E 5 HOH A 98 398 98 HOH HOH . E 5 HOH A 99 399 99 HOH HOH . E 5 HOH A 100 400 100 HOH HOH . E 5 HOH A 101 401 101 HOH HOH . E 5 HOH A 102 402 102 HOH HOH . E 5 HOH A 103 403 103 HOH HOH . E 5 HOH A 104 404 104 HOH HOH . E 5 HOH A 105 405 105 HOH HOH . E 5 HOH A 106 406 106 HOH HOH . E 5 HOH A 107 407 107 HOH HOH . E 5 HOH A 108 408 108 HOH HOH . E 5 HOH A 109 409 109 HOH HOH . E 5 HOH A 110 410 110 HOH HOH . E 5 HOH A 111 411 111 HOH HOH . E 5 HOH A 112 412 112 HOH HOH . E 5 HOH A 113 413 113 HOH HOH . E 5 HOH A 114 414 114 HOH HOH . E 5 HOH A 115 415 115 HOH HOH . E 5 HOH A 116 416 116 HOH HOH . E 5 HOH A 117 417 117 HOH HOH . E 5 HOH A 118 418 118 HOH HOH . E 5 HOH A 119 419 119 HOH HOH . E 5 HOH A 120 420 120 HOH HOH . E 5 HOH A 121 421 121 HOH HOH . E 5 HOH A 122 422 122 HOH HOH . E 5 HOH A 123 423 123 HOH HOH . E 5 HOH A 124 424 124 HOH HOH . E 5 HOH A 125 425 125 HOH HOH . E 5 HOH A 126 426 126 HOH HOH . E 5 HOH A 127 427 127 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 36.019 -8.789 289.007 1 14.3 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 35.369 -7.545 289.604 1 14.66 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 36.265 -9.865 290.041 1 15.55 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 35.264 -9.337 287.815 1 14.33 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 37.425 -8.407 288.356 1 13.51 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 38.34 -7.06 288.7 1 14.79 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 38.658 -7.08 290.187 1 16.7 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 37.761 -5.89 288.102 1 15.14 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 39.603 -7.361 287.852 1 12.72 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 40.473 -8.476 288.15 1 13.73 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 41.935 -8.188 287.805 1 14.48 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 42.015 -8.072 286.366 1 14.11 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 42.481 -6.907 288.38 1 14.42 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 43.843 -7.181 288.673 1 16.86 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 42.281 -5.946 287.237 1 14.13 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 43.283 -4.916 287.234 1 17.8 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 42.518 -6.788 286.028 1 14.63 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 41.88 -6.357 284.786 1 14.13 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 40.583 -6.056 284.702 1 13.16 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 40.223 -5.688 283.491 1 13.15 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 41.371 -5.792 282.768 1 14.11 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 41.729 -5.478 281.405 1 13.66 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 40.911 -5.142 280.556 1 14.98 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 43.01 -5.732 281.114 1 14.31 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 43.961 -6.122 281.962 1 15.36 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 45.231 -6.291 281.516 1 17.79 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 43.72 -6.393 283.235 1 15.43 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 42.458 -6.205 283.6 1 14.41 ? C4 GDP 201 A 1 HETATM 29 H H5' GDP . . . B 2 40.138 -9.352 287.59 1 16.47 ? H5' GDP 201 A 1 HETATM 30 H "H5''" GDP . . . B 2 40.396 -8.716 289.213 1 16.47 ? "H5''" GDP 201 A 1 HETATM 31 H H4' GDP . . . B 2 42.556 -9.027 288.15 1 17.37 ? H4' GDP 201 A 1 HETATM 32 H H3' GDP . . . B 2 41.91 -6.599 289.267 1 17.31 ? H3' GDP 201 A 1 HETATM 33 H HO3' GDP . . . B 2 44.273 -6.375 288.99 1 20.23 ? HO3' GDP 201 A 1 HETATM 34 H H2' GDP . . . B 2 41.261 -5.536 287.237 1 16.96 ? H2' GDP 201 A 1 HETATM 35 H HO2' GDP . . . B 2 43.2 -4.384 288.037 1 21.36 ? HO2' GDP 201 A 1 HETATM 36 H H1' GDP . . . B 2 41.444 -6.604 286.178 1 17.55 ? H1' GDP 201 A 1 HETATM 37 H H8 GDP . . . B 2 39.899 -6.114 285.539 1 15.8 ? H8 GDP 201 A 1 HETATM 38 H HN1 GDP . . . B 2 43.308 -5.55 280.134 1 17.18 ? HN1 GDP 201 A 1 HETATM 39 H HN21 GDP . . . B 2 45.952 -6.602 282.151 1 21.34 ? HN21 GDP 201 A 1 HETATM 40 H HN22 GDP . . . B 2 45.454 -6.11 280.548 1 21.34 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 40 #