data_6ZL3 # _model_server_result.job_id kJ999pVd8JQwNnqbnT1laQ _model_server_result.datetime_utc '2024-11-22 22:13:00' _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 6zl3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 6ZL3 # _exptl.entry_id 6ZL3 _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 120 _cell.entry_id 6ZL3 _cell.length_a 93.067 _cell.length_b 93.067 _cell.length_c 55.441 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ZL3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # _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 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 18 A SER 17 1_555 B NA NA . A NA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc2 B NA NA . A NA 201 1_555 C O2B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc3 B NA NA . A NA 201 1_555 E O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc4 B NA NA . A NA 201 1_555 E O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc5 B NA NA . A NA 201 1_555 E O HOH . A HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc6 B NA NA . A NA 201 1_555 E O HOH . A HOH 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? # _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 129 n n PB O2B GDP sing 130 n n PB O3B GDP sing 131 n n PB O3A GDP sing 132 n n O2B HOB2 GDP sing 133 n n O3B HOB3 GDP sing 134 n n O3A PA GDP sing 135 n n PA O1A GDP doub 136 n n PA O2A GDP sing 137 n n PA O5' GDP sing 138 n n O2A HOA2 GDP sing 139 n n O5' C5' GDP sing 140 n n C5' C4' GDP sing 141 n n C5' H5' GDP sing 142 n n C5' "H5''" GDP sing 143 n n C4' O4' GDP sing 144 n n C4' C3' GDP sing 145 n n C4' H4' GDP sing 146 n n O4' C1' GDP sing 147 n n C3' O3' GDP sing 148 n n C3' C2' GDP sing 149 n n C3' H3' GDP sing 150 n n O3' HO3' GDP sing 151 n n C2' O2' GDP sing 152 n n C2' C1' GDP sing 153 n n C2' H2' GDP sing 154 n n O2' HO2' GDP sing 155 n n C1' N9 GDP sing 156 n n C1' H1' GDP sing 157 n n N9 C8 GDP sing 158 n y N9 C4 GDP sing 159 n y C8 N7 GDP doub 160 n y C8 H8 GDP sing 161 n n N7 C5 GDP sing 162 n y C5 C6 GDP sing 163 n n C5 C4 GDP doub 164 n y C6 O6 GDP doub 165 n n C6 N1 GDP sing 166 n n N1 C2 GDP sing 167 n n N1 HN1 GDP sing 168 n n C2 N2 GDP sing 169 n n C2 N3 GDP doub 170 n n N2 HN21 GDP sing 171 n n N2 HN22 GDP sing 172 n n N3 C4 GDP sing 173 n n # _atom_sites.entry_id 6ZL3 _atom_sites.fract_transf_matrix[1][1] 0.010745 _atom_sites.fract_transf_matrix[1][2] 0.006204 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012407 _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] 0.018037 _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 NA A 1 201 1 NA NA . C 3 GDP A 1 202 1 GDP GDP . D 4 EZZ A 1 203 1 EZZ LIG . E 5 HOH A 1 301 75 HOH HOH . E 5 HOH A 2 302 7 HOH HOH . E 5 HOH A 3 303 118 HOH HOH . E 5 HOH A 4 304 134 HOH HOH . E 5 HOH A 5 305 106 HOH HOH . E 5 HOH A 6 306 68 HOH HOH . E 5 HOH A 7 307 76 HOH HOH . E 5 HOH A 8 308 3 HOH HOH . E 5 HOH A 9 309 6 HOH HOH . E 5 HOH A 10 310 129 HOH HOH . E 5 HOH A 11 311 16 HOH HOH . E 5 HOH A 12 312 138 HOH HOH . E 5 HOH A 13 313 110 HOH HOH . E 5 HOH A 14 314 139 HOH HOH . E 5 HOH A 15 315 2 HOH HOH . E 5 HOH A 16 316 70 HOH HOH . E 5 HOH A 17 317 83 HOH HOH . E 5 HOH A 18 318 22 HOH HOH . E 5 HOH A 19 319 74 HOH HOH . E 5 HOH A 20 320 29 HOH HOH . E 5 HOH A 21 321 123 HOH HOH . E 5 HOH A 22 322 13 HOH HOH . E 5 HOH A 23 323 86 HOH HOH . E 5 HOH A 24 324 98 HOH HOH . E 5 HOH A 25 325 97 HOH HOH . E 5 HOH A 26 326 100 HOH HOH . E 5 HOH A 27 327 87 HOH HOH . E 5 HOH A 28 328 143 HOH HOH . E 5 HOH A 29 329 17 HOH HOH . E 5 HOH A 30 330 78 HOH HOH . E 5 HOH A 31 331 19 HOH HOH . E 5 HOH A 32 332 113 HOH HOH . E 5 HOH A 33 333 95 HOH HOH . E 5 HOH A 34 334 11 HOH HOH . E 5 HOH A 35 335 79 HOH HOH . E 5 HOH A 36 336 40 HOH HOH . E 5 HOH A 37 337 65 HOH HOH . E 5 HOH A 38 338 23 HOH HOH . E 5 HOH A 39 339 80 HOH HOH . E 5 HOH A 40 340 102 HOH HOH . E 5 HOH A 41 341 27 HOH HOH . E 5 HOH A 42 342 90 HOH HOH . E 5 HOH A 43 343 91 HOH HOH . E 5 HOH A 44 344 14 HOH HOH . E 5 HOH A 45 345 20 HOH HOH . E 5 HOH A 46 346 94 HOH HOH . E 5 HOH A 47 347 15 HOH HOH . E 5 HOH A 48 348 121 HOH HOH . E 5 HOH A 49 349 1 HOH HOH . E 5 HOH A 50 350 125 HOH HOH . E 5 HOH A 51 351 89 HOH HOH . E 5 HOH A 52 352 107 HOH HOH . E 5 HOH A 53 353 41 HOH HOH . E 5 HOH A 54 354 128 HOH HOH . E 5 HOH A 55 355 114 HOH HOH . E 5 HOH A 56 356 39 HOH HOH . E 5 HOH A 57 357 4 HOH HOH . E 5 HOH A 58 358 105 HOH HOH . E 5 HOH A 59 359 84 HOH HOH . E 5 HOH A 60 360 9 HOH HOH . E 5 HOH A 61 361 127 HOH HOH . E 5 HOH A 62 362 130 HOH HOH . E 5 HOH A 63 363 45 HOH HOH . E 5 HOH A 64 364 24 HOH HOH . E 5 HOH A 65 365 141 HOH HOH . E 5 HOH A 66 366 124 HOH HOH . E 5 HOH A 67 367 81 HOH HOH . E 5 HOH A 68 368 10 HOH HOH . E 5 HOH A 69 369 26 HOH HOH . E 5 HOH A 70 370 18 HOH HOH . E 5 HOH A 71 371 122 HOH HOH . E 5 HOH A 72 372 5 HOH HOH . E 5 HOH A 73 373 33 HOH HOH . E 5 HOH A 74 374 12 HOH HOH . E 5 HOH A 75 375 137 HOH HOH . E 5 HOH A 76 376 104 HOH HOH . E 5 HOH A 77 377 37 HOH HOH . E 5 HOH A 78 378 131 HOH HOH . E 5 HOH A 79 379 120 HOH HOH . E 5 HOH A 80 380 42 HOH HOH . E 5 HOH A 81 381 43 HOH HOH . E 5 HOH A 82 382 61 HOH HOH . E 5 HOH A 83 383 140 HOH HOH . E 5 HOH A 84 384 32 HOH HOH . E 5 HOH A 85 385 101 HOH HOH . E 5 HOH A 86 386 63 HOH HOH . E 5 HOH A 87 387 88 HOH HOH . E 5 HOH A 88 388 93 HOH HOH . E 5 HOH A 89 389 109 HOH HOH . E 5 HOH A 90 390 92 HOH HOH . E 5 HOH A 91 391 133 HOH HOH . E 5 HOH A 92 392 46 HOH HOH . E 5 HOH A 93 393 96 HOH HOH . E 5 HOH A 94 394 66 HOH HOH . E 5 HOH A 95 395 119 HOH HOH . E 5 HOH A 96 396 116 HOH HOH . E 5 HOH A 97 397 142 HOH HOH . E 5 HOH A 98 398 77 HOH HOH . E 5 HOH A 99 399 38 HOH HOH . E 5 HOH A 100 400 126 HOH HOH . E 5 HOH A 101 401 82 HOH HOH . E 5 HOH A 102 402 111 HOH HOH . E 5 HOH A 103 403 73 HOH HOH . E 5 HOH A 104 404 34 HOH HOH . E 5 HOH A 105 405 25 HOH HOH . E 5 HOH A 106 406 59 HOH HOH . E 5 HOH A 107 407 8 HOH HOH . E 5 HOH A 108 408 132 HOH HOH . E 5 HOH A 109 409 103 HOH HOH . E 5 HOH A 110 410 135 HOH HOH . E 5 HOH A 111 411 35 HOH HOH . E 5 HOH A 112 412 44 HOH HOH . E 5 HOH A 113 413 64 HOH HOH . E 5 HOH A 114 414 112 HOH HOH . E 5 HOH A 115 415 117 HOH HOH . E 5 HOH A 116 416 62 HOH HOH . E 5 HOH A 117 417 67 HOH HOH . E 5 HOH A 118 418 57 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 30.452 -26.311 18.321 1 38.98 ? PB GDP 202 A 1 HETATM 2 O O1B GDP . . . C 3 30.984 -27.371 17.353 1 38.01 ? O1B GDP 202 A 1 HETATM 3 O O2B GDP . . . C 3 29.15 -26.614 18.992 1 37.5 ? O2B GDP 202 A 1 HETATM 4 O O3B GDP . . . C 3 31.57 -26.07 19.399 1 39.95 ? O3B GDP 202 A 1 HETATM 5 O O3A GDP . . . C 3 30.242 -25.004 17.44 1 40.04 ? O3A GDP 202 A 1 HETATM 6 P PA GDP . . . C 3 29.181 -23.817 17.523 1 41.69 ? PA GDP 202 A 1 HETATM 7 O O1A GDP . . . C 3 27.831 -24.241 17.092 1 42.62 ? O1A GDP 202 A 1 HETATM 8 O O2A GDP . . . C 3 29.137 -23.344 18.998 1 42.31 ? O2A GDP 202 A 1 HETATM 9 O O5' GDP . . . C 3 29.782 -22.707 16.588 1 41.34 ? O5' GDP 202 A 1 HETATM 10 C C5' GDP . . . C 3 31.111 -22.197 16.834 1 41.92 ? C5' GDP 202 A 1 HETATM 11 C C4' GDP . . . C 3 31.265 -20.869 16.134 1 42.58 ? C4' GDP 202 A 1 HETATM 12 O O4' GDP . . . C 3 31.132 -21.054 14.709 1 42.38 ? O4' GDP 202 A 1 HETATM 13 C C3' GDP . . . C 3 30.262 -19.775 16.506 1 43.37 ? C3' GDP 202 A 1 HETATM 14 O O3' GDP . . . C 3 30.921 -18.511 16.426 1 44.35 ? O3' GDP 202 A 1 HETATM 15 C C2' GDP . . . C 3 29.204 -19.908 15.409 1 42.95 ? C2' GDP 202 A 1 HETATM 16 O O2' GDP . . . C 3 28.52 -18.691 15.137 1 44.11 ? O2' GDP 202 A 1 HETATM 17 C C1' GDP . . . C 3 30.078 -20.25 14.212 1 42.05 ? C1' GDP 202 A 1 HETATM 18 N N9 GDP . . . C 3 29.372 -20.994 13.15 1 40.74 ? N9 GDP 202 A 1 HETATM 19 C C8 GDP . . . C 3 28.72 -22.191 13.275 1 40.09 ? C8 GDP 202 A 1 HETATM 20 N N7 GDP . . . C 3 28.243 -22.648 12.142 1 39.99 ? N7 GDP 202 A 1 HETATM 21 C C5 GDP . . . C 3 28.603 -21.691 11.209 1 39.81 ? C5 GDP 202 A 1 HETATM 22 C C6 GDP . . . C 3 28.403 -21.628 9.79 1 40.28 ? C6 GDP 202 A 1 HETATM 23 O O6 GDP . . . C 3 27.921 -22.491 9.058 1 40.74 ? O6 GDP 202 A 1 HETATM 24 N N1 GDP . . . C 3 28.925 -20.472 9.244 1 40.31 ? N1 GDP 202 A 1 HETATM 25 C C2 GDP . . . C 3 29.583 -19.496 9.941 1 39.83 ? C2 GDP 202 A 1 HETATM 26 N N2 GDP . . . C 3 30.024 -18.451 9.239 1 39.9 ? N2 GDP 202 A 1 HETATM 27 N N3 GDP . . . C 3 29.799 -19.548 11.254 1 39.38 ? N3 GDP 202 A 1 HETATM 28 C C4 GDP . . . C 3 29.291 -20.657 11.821 1 39.9 ? C4 GDP 202 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 40 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #