data_8S1N # _model_server_result.job_id 7MR1vOdbC_hr4X3OFGbIvA _model_server_result.datetime_utc '2025-09-16 03:37:19' _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 8s1n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 8S1N # _exptl.entry_id 8S1N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method nat _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 8S1N _cell.length_a 41.489 _cell.length_b 90.34 _cell.length_c 107.405 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8S1N _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall 'C 2c 2' _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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 3 _struct_asym.id C _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 OG1 THR 17 A THR 17 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? metalc ? metalc2 B MG MG . A MG 201 1_555 C O1B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc3 B MG MG . A MG 201 1_555 D O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc4 B MG MG . A MG 201 1_555 D O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc5 B MG MG . A MG 201 1_555 D O HOH . A HOH 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc6 B MG MG . A MG 201 1_555 D O HOH . A HOH 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? # _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 8S1N _atom_sites.fract_transf_matrix[1][1] 0.024103 _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] 0.011069 _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] 0.009311 _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 MG A 1 201 1 MG MG . C 3 GDP A 1 202 2 GDP GDP . D 4 HOH A 1 301 57 HOH HOH . D 4 HOH A 2 302 23 HOH HOH . D 4 HOH A 3 303 53 HOH HOH . D 4 HOH A 4 304 58 HOH HOH . D 4 HOH A 5 305 79 HOH HOH . D 4 HOH A 6 306 54 HOH HOH . D 4 HOH A 7 307 96 HOH HOH . D 4 HOH A 8 308 97 HOH HOH . D 4 HOH A 9 309 39 HOH HOH . D 4 HOH A 10 310 2 HOH HOH . D 4 HOH A 11 311 22 HOH HOH . D 4 HOH A 12 312 50 HOH HOH . D 4 HOH A 13 313 83 HOH HOH . D 4 HOH A 14 314 12 HOH HOH . D 4 HOH A 15 315 38 HOH HOH . D 4 HOH A 16 316 98 HOH HOH . D 4 HOH A 17 317 27 HOH HOH . D 4 HOH A 18 318 33 HOH HOH . D 4 HOH A 19 319 65 HOH HOH . D 4 HOH A 20 320 32 HOH HOH . D 4 HOH A 21 321 70 HOH HOH . D 4 HOH A 22 322 24 HOH HOH . D 4 HOH A 23 323 9 HOH HOH . D 4 HOH A 24 324 6 HOH HOH . D 4 HOH A 25 325 89 HOH HOH . D 4 HOH A 26 326 21 HOH HOH . D 4 HOH A 27 327 86 HOH HOH . D 4 HOH A 28 328 7 HOH HOH . D 4 HOH A 29 329 85 HOH HOH . D 4 HOH A 30 330 13 HOH HOH . D 4 HOH A 31 331 44 HOH HOH . D 4 HOH A 32 332 10 HOH HOH . D 4 HOH A 33 333 3 HOH HOH . D 4 HOH A 34 334 28 HOH HOH . D 4 HOH A 35 335 49 HOH HOH . D 4 HOH A 36 336 105 HOH HOH . D 4 HOH A 37 337 51 HOH HOH . D 4 HOH A 38 338 1 HOH HOH . D 4 HOH A 39 339 37 HOH HOH . D 4 HOH A 40 340 30 HOH HOH . D 4 HOH A 41 341 35 HOH HOH . D 4 HOH A 42 342 14 HOH HOH . D 4 HOH A 43 343 11 HOH HOH . D 4 HOH A 44 344 20 HOH HOH . D 4 HOH A 45 345 87 HOH HOH . D 4 HOH A 46 346 43 HOH HOH . D 4 HOH A 47 347 64 HOH HOH . D 4 HOH A 48 348 56 HOH HOH . D 4 HOH A 49 349 15 HOH HOH . D 4 HOH A 50 350 36 HOH HOH . D 4 HOH A 51 351 5 HOH HOH . D 4 HOH A 52 352 17 HOH HOH . D 4 HOH A 53 353 99 HOH HOH . D 4 HOH A 54 354 69 HOH HOH . D 4 HOH A 55 355 84 HOH HOH . D 4 HOH A 56 356 26 HOH HOH . D 4 HOH A 57 357 104 HOH HOH . D 4 HOH A 58 358 68 HOH HOH . D 4 HOH A 59 359 19 HOH HOH . D 4 HOH A 60 360 18 HOH HOH . D 4 HOH A 61 361 60 HOH HOH . D 4 HOH A 62 362 34 HOH HOH . D 4 HOH A 63 363 71 HOH HOH . D 4 HOH A 64 364 74 HOH HOH . D 4 HOH A 65 365 42 HOH HOH . D 4 HOH A 66 366 59 HOH HOH . D 4 HOH A 67 367 92 HOH HOH . D 4 HOH A 68 368 88 HOH HOH . D 4 HOH A 69 369 16 HOH HOH . D 4 HOH A 70 370 103 HOH HOH . D 4 HOH A 71 371 62 HOH HOH . D 4 HOH A 72 372 4 HOH HOH . D 4 HOH A 73 373 93 HOH HOH . D 4 HOH A 74 374 29 HOH HOH . D 4 HOH A 75 375 8 HOH HOH . D 4 HOH A 76 376 94 HOH HOH . D 4 HOH A 77 377 66 HOH HOH . D 4 HOH A 78 378 40 HOH HOH . D 4 HOH A 79 379 102 HOH HOH . D 4 HOH A 80 380 48 HOH HOH . D 4 HOH A 81 381 73 HOH HOH . D 4 HOH A 82 382 95 HOH HOH . D 4 HOH A 83 383 81 HOH HOH . D 4 HOH A 84 384 76 HOH HOH . D 4 HOH A 85 385 45 HOH HOH . D 4 HOH A 86 386 31 HOH HOH . D 4 HOH A 87 387 75 HOH HOH . D 4 HOH A 88 388 52 HOH HOH . D 4 HOH A 89 389 55 HOH HOH . D 4 HOH A 90 390 46 HOH HOH . D 4 HOH A 91 391 63 HOH HOH . D 4 HOH A 92 392 41 HOH HOH . D 4 HOH A 93 393 106 HOH HOH . D 4 HOH A 94 394 80 HOH HOH . D 4 HOH A 95 395 25 HOH HOH . D 4 HOH A 96 396 90 HOH HOH . D 4 HOH A 97 397 91 HOH HOH . D 4 HOH A 98 398 100 HOH HOH . D 4 HOH A 99 399 101 HOH HOH . D 4 HOH A 100 400 47 HOH HOH . D 4 HOH A 101 401 78 HOH HOH . D 4 HOH A 102 402 61 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 . . . C 3 11.855 28.171 18.998 1 21.27 ? PB GDP 202 A 1 HETATM 2 O O1B GDP . . . C 3 11.215 27.302 20.062 1 22.49 ? O1B GDP 202 A 1 HETATM 3 O O2B GDP . . . C 3 11.995 27.496 17.665 1 21.24 ? O2B GDP 202 A 1 HETATM 4 O O3B GDP . . . C 3 13.121 28.858 19.464 1 20.23 ? O3B GDP 202 A 1 HETATM 5 O O3A GDP . . . C 3 10.843 29.369 18.634 1 23.31 ? O3A GDP 202 A 1 HETATM 6 P PA GDP . . . C 3 9.656 29.919 19.562 1 18.86 ? PA GDP 202 A 1 HETATM 7 O O1A GDP . . . C 3 8.503 28.942 19.531 1 19.78 ? O1A GDP 202 A 1 HETATM 8 O O2A GDP . . . C 3 10.218 30.404 20.871 1 23.87 ? O2A GDP 202 A 1 HETATM 9 O O5' GDP . . . C 3 9.242 31.17 18.652 1 25.37 ? O5' GDP 202 A 1 HETATM 10 C C5' GDP . . . C 3 10.222 32.167 18.442 1 23.92 ? C5' GDP 202 A 1 HETATM 11 C C4' GDP . . . C 3 9.576 33.483 18.01 1 21.64 ? C4' GDP 202 A 1 HETATM 12 O O4' GDP . . . C 3 8.742 33.342 16.845 1 21.52 ? O4' GDP 202 A 1 HETATM 13 C C3' GDP . . . C 3 8.645 34.139 19.025 1 25.67 ? C3' GDP 202 A 1 HETATM 14 O O3' GDP . . . C 3 8.768 35.565 18.87 1 27.28 ? O3' GDP 202 A 1 HETATM 15 C C2' GDP . . . C 3 7.233 33.704 18.663 1 24.13 ? C2' GDP 202 A 1 HETATM 16 O O2' GDP . . . C 3 6.253 34.673 19.03 1 32.17 ? O2' GDP 202 A 1 HETATM 17 C C1' GDP . . . C 3 7.343 33.588 17.138 1 22.83 ? C1' GDP 202 A 1 HETATM 18 N N9 GDP . . . C 3 6.443 32.639 16.43 1 22.78 ? N9 GDP 202 A 1 HETATM 19 C C8 GDP . . . C 3 6.36 31.307 16.609 1 24.31 ? C8 GDP 202 A 1 HETATM 20 N N7 GDP . . . C 3 5.438 30.794 15.774 1 23.19 ? N7 GDP 202 A 1 HETATM 21 C C5 GDP . . . C 3 4.907 31.804 15.044 1 26.73 ? C5 GDP 202 A 1 HETATM 22 C C6 GDP . . . C 3 3.881 31.95 13.978 1 25.83 ? C6 GDP 202 A 1 HETATM 23 O O6 GDP . . . C 3 3.265 30.932 13.57 1 25.52 ? O6 GDP 202 A 1 HETATM 24 N N1 GDP . . . C 3 3.64 33.181 13.478 1 23.14 ? N1 GDP 202 A 1 HETATM 25 C C2 GDP . . . C 3 4.295 34.267 13.929 1 25.65 ? C2 GDP 202 A 1 HETATM 26 N N2 GDP . . . C 3 4.032 35.489 13.42 1 29.99 ? N2 GDP 202 A 1 HETATM 27 N N3 GDP . . . C 3 5.24 34.207 14.894 1 25.99 ? N3 GDP 202 A 1 HETATM 28 C C4 GDP . . . C 3 5.574 33.027 15.488 1 24.48 ? C4 GDP 202 A 1 HETATM 29 H H5' GDP . . . C 3 10.788 32.321 19.362 1 28.78 ? H5' GDP 202 A 1 HETATM 30 H "H5''" GDP . . . C 3 10.92 31.834 17.669 1 28.78 ? "H5''" GDP 202 A 1 HETATM 31 H H4' GDP . . . C 3 10.47 34.098 17.845 1 26.05 ? H4' GDP 202 A 1 HETATM 32 H H3' GDP . . . C 3 8.882 33.865 20.061 1 30.89 ? H3' GDP 202 A 1 HETATM 33 H HO3' GDP . . . C 3 8.227 36.009 19.536 1 32.83 ? HO3' GDP 202 A 1 HETATM 34 H H2' GDP . . . C 3 6.906 32.789 19.179 1 29.05 ? H2' GDP 202 A 1 HETATM 35 H HO2' GDP . . . C 3 6.237 34.764 19.993 1 38.69 ? HO2' GDP 202 A 1 HETATM 36 H H1' GDP . . . C 3 6.968 34.543 16.744 1 27.49 ? H1' GDP 202 A 1 HETATM 37 H H8 GDP . . . C 3 6.946 30.737 17.317 1 29.26 ? H8 GDP 202 A 1 HETATM 38 H HN1 GDP . . . C 3 2.93 33.293 12.726 1 27.86 ? HN1 GDP 202 A 1 HETATM 39 H HN21 GDP . . . C 3 4.534 36.301 13.762 1 36.07 ? HN21 GDP 202 A 1 HETATM 40 H HN22 GDP . . . C 3 3.344 35.59 12.7 1 36.07 ? HN22 GDP 202 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #