data_6YR8 # _model_server_result.job_id '_NpTdrVjF3KDlHeSqYzo4w' _model_server_result.datetime_utc '2025-02-26 15:04:51' _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 6yr8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 6YR8 # _exptl.entry_id 6YR8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 6YR8 _cell.length_a 71.574 _cell.length_b 71.574 _cell.length_c 144.39 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YR8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F _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 OG SER 20 A SER 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc2 C O3B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc3 D MG MG . A MG 202 1_555 E O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc4 D MG MG . A MG 202 1_555 E O HOH . A HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc5 D MG MG . A MG 202 1_555 E O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc6 D MG MG . A MG 202 1_555 E O HOH . A HOH 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? # _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 6YR8 _atom_sites.fract_transf_matrix[1][1] 0.013972 _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] 0.013972 _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] 0.006926 _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 C 3 GDP A 1 201 201 GDP GDP . D 4 MG A 1 202 202 MG MG . E 5 HOH A 1 301 4 HOH HOH . E 5 HOH A 2 302 85 HOH HOH . E 5 HOH A 3 303 29 HOH HOH . E 5 HOH A 4 304 18 HOH HOH . E 5 HOH A 5 305 73 HOH HOH . E 5 HOH A 6 306 86 HOH HOH . E 5 HOH A 7 307 8 HOH HOH . E 5 HOH A 8 308 7 HOH HOH . E 5 HOH A 9 309 60 HOH HOH . E 5 HOH A 10 310 15 HOH HOH . E 5 HOH A 11 311 117 HOH HOH . E 5 HOH A 12 312 68 HOH HOH . E 5 HOH A 13 313 97 HOH HOH . E 5 HOH A 14 314 19 HOH HOH . E 5 HOH A 15 315 34 HOH HOH . E 5 HOH A 16 316 3 HOH HOH . E 5 HOH A 17 317 78 HOH HOH . E 5 HOH A 18 318 36 HOH HOH . E 5 HOH A 19 319 17 HOH HOH . E 5 HOH A 20 320 1 HOH HOH . E 5 HOH A 21 321 72 HOH HOH . E 5 HOH A 22 322 74 HOH HOH . E 5 HOH A 23 323 110 HOH HOH . E 5 HOH A 24 324 5 HOH HOH . E 5 HOH A 25 325 49 HOH HOH . E 5 HOH A 26 326 38 HOH HOH . E 5 HOH A 27 327 32 HOH HOH . E 5 HOH A 28 328 30 HOH HOH . E 5 HOH A 29 329 111 HOH HOH . E 5 HOH A 30 330 20 HOH HOH . E 5 HOH A 31 331 76 HOH HOH . E 5 HOH A 32 332 108 HOH HOH . E 5 HOH A 33 333 2 HOH HOH . E 5 HOH A 34 334 54 HOH HOH . E 5 HOH A 35 335 57 HOH HOH . E 5 HOH A 36 336 56 HOH HOH . E 5 HOH A 37 337 39 HOH HOH . E 5 HOH A 38 338 109 HOH HOH . E 5 HOH A 39 339 45 HOH HOH . E 5 HOH A 40 340 43 HOH HOH . E 5 HOH A 41 341 82 HOH HOH . E 5 HOH A 42 342 27 HOH HOH . E 5 HOH A 43 343 52 HOH HOH . E 5 HOH A 44 344 61 HOH HOH . E 5 HOH A 45 345 42 HOH HOH . E 5 HOH A 46 346 96 HOH HOH . E 5 HOH A 47 347 100 HOH HOH . E 5 HOH A 48 348 104 HOH HOH . E 5 HOH A 49 349 55 HOH HOH . E 5 HOH A 50 350 28 HOH HOH . E 5 HOH A 51 351 89 HOH HOH . E 5 HOH A 52 352 31 HOH HOH . E 5 HOH A 53 353 105 HOH HOH . E 5 HOH A 54 354 79 HOH HOH . E 5 HOH A 55 355 16 HOH HOH . E 5 HOH A 56 356 26 HOH HOH . E 5 HOH A 57 357 101 HOH HOH . E 5 HOH A 58 358 95 HOH HOH . E 5 HOH A 59 359 77 HOH HOH . E 5 HOH A 60 360 40 HOH HOH . E 5 HOH A 61 361 91 HOH HOH . E 5 HOH A 62 362 58 HOH HOH . E 5 HOH A 63 363 121 HOH HOH . E 5 HOH A 64 364 35 HOH HOH . E 5 HOH A 65 365 98 HOH HOH . E 5 HOH A 66 366 83 HOH HOH . E 5 HOH A 67 367 118 HOH HOH . E 5 HOH A 68 368 88 HOH HOH . F 5 HOH B 1 201 21 HOH HOH . F 5 HOH B 2 202 122 HOH HOH . F 5 HOH B 3 203 64 HOH HOH . F 5 HOH B 4 204 25 HOH HOH . F 5 HOH B 5 205 14 HOH HOH . F 5 HOH B 6 206 71 HOH HOH . F 5 HOH B 7 207 67 HOH HOH . F 5 HOH B 8 208 99 HOH HOH . F 5 HOH B 9 209 66 HOH HOH . F 5 HOH B 10 210 9 HOH HOH . F 5 HOH B 11 211 23 HOH HOH . F 5 HOH B 12 212 106 HOH HOH . F 5 HOH B 13 213 6 HOH HOH . F 5 HOH B 14 214 22 HOH HOH . F 5 HOH B 15 215 92 HOH HOH . F 5 HOH B 16 216 24 HOH HOH . F 5 HOH B 17 217 84 HOH HOH . F 5 HOH B 18 218 70 HOH HOH . F 5 HOH B 19 219 11 HOH HOH . F 5 HOH B 20 220 13 HOH HOH . F 5 HOH B 21 221 94 HOH HOH . F 5 HOH B 22 222 37 HOH HOH . F 5 HOH B 23 223 65 HOH HOH . F 5 HOH B 24 224 87 HOH HOH . F 5 HOH B 25 225 10 HOH HOH . F 5 HOH B 26 226 107 HOH HOH . F 5 HOH B 27 227 12 HOH HOH . F 5 HOH B 28 228 80 HOH HOH . F 5 HOH B 29 229 62 HOH HOH . F 5 HOH B 30 230 46 HOH HOH . F 5 HOH B 31 231 41 HOH HOH . F 5 HOH B 32 232 51 HOH HOH . F 5 HOH B 33 233 93 HOH HOH . F 5 HOH B 34 234 103 HOH HOH . F 5 HOH B 35 235 47 HOH HOH . F 5 HOH B 36 236 48 HOH HOH . F 5 HOH B 37 237 53 HOH HOH . F 5 HOH B 38 238 81 HOH HOH . F 5 HOH B 39 239 44 HOH HOH . F 5 HOH B 40 240 63 HOH HOH . F 5 HOH B 41 241 102 HOH HOH . F 5 HOH B 42 242 69 HOH HOH . F 5 HOH B 43 243 50 HOH HOH . F 5 HOH B 44 244 59 HOH HOH . F 5 HOH B 45 245 123 HOH HOH . F 5 HOH B 46 246 114 HOH HOH . F 5 HOH B 47 247 90 HOH HOH . F 5 HOH B 48 248 113 HOH HOH . F 5 HOH B 49 249 120 HOH HOH . F 5 HOH B 50 250 75 HOH HOH . F 5 HOH B 51 251 124 HOH HOH . F 5 HOH B 52 252 115 HOH HOH . F 5 HOH B 53 253 33 HOH HOH . F 5 HOH B 54 254 116 HOH HOH . F 5 HOH B 55 255 119 HOH HOH . F 5 HOH B 56 256 112 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 18.966 -11.517 39.228 1 64.56 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 3 20.098 -11.102 38.314 1 64.74 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 3 19.498 -11.899 40.607 1 64.5 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 3 17.825 -10.544 39.35 1 61.67 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 3 18.454 -12.871 38.531 1 63.89 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 3 17.086 -13.098 37.729 1 64.48 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 3 17.062 -12.157 36.552 1 65.48 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 3 15.963 -13.077 38.729 1 66.72 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 3 17.224 -14.613 37.198 1 68.12 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 3 18.47 -15.076 36.622 1 71.87 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 3 18.237 -16.223 35.636 1 74.59 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 3 18.085 -17.434 36.384 1 73.03 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 3 16.948 -16.033 34.843 1 75.89 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 3 17.029 -16.544 33.506 1 79.73 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 3 15.948 -16.817 35.667 1 75.03 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 3 14.876 -17.333 34.901 1 79.76 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 3 16.763 -17.938 36.287 1 73.42 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 3 16.277 -18.271 37.64 1 72.18 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 3 16.096 -17.423 38.691 1 69.63 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 3 15.638 -18.066 39.779 1 68.99 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 3 15.518 -19.354 39.417 1 73.81 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 3 15.092 -20.615 40.054 1 74.5 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 3 14.732 -20.626 41.235 1 73.43 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 3 15.11 -21.746 39.335 1 77.11 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 3 15.513 -21.783 38.051 1 78.19 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 3 15.507 -22.957 37.373 1 81.87 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 3 15.914 -20.672 37.395 1 77.43 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 3 15.939 -19.475 38.011 1 74.27 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #