data_8AFB # _model_server_result.job_id pKTY3yRwilai5qK4BrcLrA _model_server_result.datetime_utc '2024-11-16 22:01:35' _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 8afb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 8AFB # _exptl.entry_id 8AFB _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 95.67 _cell.angle_gamma 90 _cell.entry_id 8AFB _cell.length_a 68.675 _cell.length_b 40.513 _cell.length_c 56.472 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8AFB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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 covale ? covale1 A SG CYS 13 A CYS 12 1_555 D C42 LXD . A LXD 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.763 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc2 B O1B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc3 C MG MG . A MG 202 1_555 E O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc4 C MG MG . A MG 202 1_555 E O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc5 C MG MG . A MG 202 1_555 E O HOH . A HOH 324 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc6 C MG MG . A MG 202 1_555 E O HOH . A HOH 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? # _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 8AFB _atom_sites.fract_transf_matrix[1][1] 0.014561 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001446 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024683 _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] 0.017795 _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 1 201 201 GDP GDP . C 3 MG A 1 202 202 MG MG . D 4 LXD A 1 203 1 LXD LIG . E 5 HOH A 1 301 37 HOH HOH . E 5 HOH A 2 302 56 HOH HOH . E 5 HOH A 3 303 15 HOH HOH . E 5 HOH A 4 304 17 HOH HOH . E 5 HOH A 5 305 138 HOH HOH . E 5 HOH A 6 306 76 HOH HOH . E 5 HOH A 7 307 67 HOH HOH . E 5 HOH A 8 308 14 HOH HOH . E 5 HOH A 9 309 87 HOH HOH . E 5 HOH A 10 310 132 HOH HOH . E 5 HOH A 11 311 24 HOH HOH . E 5 HOH A 12 312 64 HOH HOH . E 5 HOH A 13 313 11 HOH HOH . E 5 HOH A 14 314 33 HOH HOH . E 5 HOH A 15 315 8 HOH HOH . E 5 HOH A 16 316 111 HOH HOH . E 5 HOH A 17 317 10 HOH HOH . E 5 HOH A 18 318 90 HOH HOH . E 5 HOH A 19 319 49 HOH HOH . E 5 HOH A 20 320 128 HOH HOH . E 5 HOH A 21 321 121 HOH HOH . E 5 HOH A 22 322 7 HOH HOH . E 5 HOH A 23 323 52 HOH HOH . E 5 HOH A 24 324 19 HOH HOH . E 5 HOH A 25 325 32 HOH HOH . E 5 HOH A 26 326 41 HOH HOH . E 5 HOH A 27 327 16 HOH HOH . E 5 HOH A 28 328 34 HOH HOH . E 5 HOH A 29 329 75 HOH HOH . E 5 HOH A 30 330 29 HOH HOH . E 5 HOH A 31 331 91 HOH HOH . E 5 HOH A 32 332 1 HOH HOH . E 5 HOH A 33 333 59 HOH HOH . E 5 HOH A 34 334 60 HOH HOH . E 5 HOH A 35 335 84 HOH HOH . E 5 HOH A 36 336 106 HOH HOH . E 5 HOH A 37 337 93 HOH HOH . E 5 HOH A 38 338 9 HOH HOH . E 5 HOH A 39 339 109 HOH HOH . E 5 HOH A 40 340 100 HOH HOH . E 5 HOH A 41 341 115 HOH HOH . E 5 HOH A 42 342 117 HOH HOH . E 5 HOH A 43 343 40 HOH HOH . E 5 HOH A 44 344 80 HOH HOH . E 5 HOH A 45 345 114 HOH HOH . E 5 HOH A 46 346 113 HOH HOH . E 5 HOH A 47 347 54 HOH HOH . E 5 HOH A 48 348 25 HOH HOH . E 5 HOH A 49 349 3 HOH HOH . E 5 HOH A 50 350 20 HOH HOH . E 5 HOH A 51 351 30 HOH HOH . E 5 HOH A 52 352 46 HOH HOH . E 5 HOH A 53 353 31 HOH HOH . E 5 HOH A 54 354 135 HOH HOH . E 5 HOH A 55 355 27 HOH HOH . E 5 HOH A 56 356 28 HOH HOH . E 5 HOH A 57 357 86 HOH HOH . E 5 HOH A 58 358 65 HOH HOH . E 5 HOH A 59 359 63 HOH HOH . E 5 HOH A 60 360 103 HOH HOH . E 5 HOH A 61 361 58 HOH HOH . E 5 HOH A 62 362 47 HOH HOH . E 5 HOH A 63 363 68 HOH HOH . E 5 HOH A 64 364 96 HOH HOH . E 5 HOH A 65 365 123 HOH HOH . E 5 HOH A 66 366 133 HOH HOH . E 5 HOH A 67 367 71 HOH HOH . E 5 HOH A 68 368 36 HOH HOH . E 5 HOH A 69 369 70 HOH HOH . E 5 HOH A 70 370 99 HOH HOH . E 5 HOH A 71 371 5 HOH HOH . E 5 HOH A 72 372 69 HOH HOH . E 5 HOH A 73 373 53 HOH HOH . E 5 HOH A 74 374 26 HOH HOH . E 5 HOH A 75 375 12 HOH HOH . E 5 HOH A 76 376 57 HOH HOH . E 5 HOH A 77 377 18 HOH HOH . E 5 HOH A 78 378 39 HOH HOH . E 5 HOH A 79 379 88 HOH HOH . E 5 HOH A 80 380 112 HOH HOH . E 5 HOH A 81 381 23 HOH HOH . E 5 HOH A 82 382 38 HOH HOH . E 5 HOH A 83 383 104 HOH HOH . E 5 HOH A 84 384 130 HOH HOH . E 5 HOH A 85 385 21 HOH HOH . E 5 HOH A 86 386 92 HOH HOH . E 5 HOH A 87 387 66 HOH HOH . E 5 HOH A 88 388 48 HOH HOH . E 5 HOH A 89 389 43 HOH HOH . E 5 HOH A 90 390 22 HOH HOH . E 5 HOH A 91 391 50 HOH HOH . E 5 HOH A 92 392 72 HOH HOH . E 5 HOH A 93 393 102 HOH HOH . E 5 HOH A 94 394 13 HOH HOH . E 5 HOH A 95 395 129 HOH HOH . E 5 HOH A 96 396 62 HOH HOH . E 5 HOH A 97 397 108 HOH HOH . E 5 HOH A 98 398 81 HOH HOH . E 5 HOH A 99 399 35 HOH HOH . E 5 HOH A 100 400 73 HOH HOH . E 5 HOH A 101 401 6 HOH HOH . E 5 HOH A 102 402 42 HOH HOH . E 5 HOH A 103 403 45 HOH HOH . E 5 HOH A 104 404 78 HOH HOH . E 5 HOH A 105 405 82 HOH HOH . E 5 HOH A 106 406 55 HOH HOH . E 5 HOH A 107 407 101 HOH HOH . E 5 HOH A 108 408 79 HOH HOH . E 5 HOH A 109 409 51 HOH HOH . E 5 HOH A 110 410 131 HOH HOH . E 5 HOH A 111 411 97 HOH HOH . E 5 HOH A 112 412 118 HOH HOH . E 5 HOH A 113 413 105 HOH HOH . E 5 HOH A 114 414 74 HOH HOH . E 5 HOH A 115 415 77 HOH HOH . E 5 HOH A 116 416 107 HOH HOH . E 5 HOH A 117 417 134 HOH HOH . E 5 HOH A 118 418 119 HOH HOH . E 5 HOH A 119 419 127 HOH HOH . E 5 HOH A 120 420 44 HOH HOH . E 5 HOH A 121 421 61 HOH HOH . E 5 HOH A 122 422 137 HOH HOH . E 5 HOH A 123 423 136 HOH HOH . E 5 HOH A 124 424 85 HOH HOH . E 5 HOH A 125 425 116 HOH HOH . E 5 HOH A 126 426 120 HOH HOH . E 5 HOH A 127 427 83 HOH HOH . E 5 HOH A 128 428 122 HOH HOH . E 5 HOH A 129 429 95 HOH HOH . E 5 HOH A 130 430 124 HOH HOH . E 5 HOH A 131 431 94 HOH HOH . E 5 HOH A 132 432 125 HOH HOH . E 5 HOH A 133 433 89 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 14.044 -8.24 9.437 1 6.91 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 15.458 -8.714 9.074 1 6.55 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 13.156 -9.387 9.933 1 7.66 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 14.03 -7.032 10.353 1 6.41 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 13.425 -7.643 8.083 1 7.37 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 13.568 -8.067 6.549 1 7.21 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 14.76 -7.462 5.92 1 8.04 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 13.434 -9.571 6.473 1 8.34 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 12.314 -7.395 5.87 1 7.35 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 10.987 -7.696 6.345 1 9.3 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 9.97 -7.331 5.292 1 7.85 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 9.974 -5.9 5.097 1 7.64 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 10.157 -7.945 3.908 1 8.42 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 8.886 -8.222 3.325 1 10.64 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 10.908 -6.852 3.149 1 8.25 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 10.675 -6.898 1.75 1 9.63 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 10.279 -5.601 3.751 1 8.13 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 11.143 -4.421 3.739 1 6.48 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 12.363 -4.275 4.359 1 6.03 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 12.822 -3.052 4.302 1 6.3 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 11.862 -2.355 3.584 1 7.05 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 11.786 -0.981 3.195 1 6.47 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 12.557 -0.07 3.501 1 7.91 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 10.648 -0.696 2.464 1 7.18 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 9.667 -1.597 2.157 1 8.03 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 8.629 -1.14 1.451 1 10.94 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 9.704 -2.878 2.528 1 7.89 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 10.829 -3.19 3.223 1 7.4 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #