data_6KX3 # _model_server_result.job_id zNomRUqeMj2sPuYbt7n3HA _model_server_result.datetime_utc '2024-10-11 06:17:05' _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 6kx3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 6KX3 # _exptl.entry_id 6KX3 _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 90 _cell.entry_id 6KX3 _cell.length_a 91.784 _cell.length_b 91.784 _cell.length_c 55.813 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KX3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 107 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 107 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id C8 _struct_conn.ptnr2_label_comp_id 8ZO _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id 8ZO _struct_conn.ptnr2_auth_seq_id 202 _struct_conn.ptnr2_symmetry 1_555 _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 1.677 _struct_conn.pdbx_value_order ? # _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 113 n n PB O2B GDP sing 114 n n PB O3B GDP sing 115 n n PB O3A GDP sing 116 n n O2B HOB2 GDP sing 117 n n O3B HOB3 GDP sing 118 n n O3A PA GDP sing 119 n n PA O1A GDP doub 120 n n PA O2A GDP sing 121 n n PA O5' GDP sing 122 n n O2A HOA2 GDP sing 123 n n O5' C5' GDP sing 124 n n C5' C4' GDP sing 125 n n C5' H5' GDP sing 126 n n C5' "H5''" GDP sing 127 n n C4' O4' GDP sing 128 n n C4' C3' GDP sing 129 n n C4' H4' GDP sing 130 n n O4' C1' GDP sing 131 n n C3' O3' GDP sing 132 n n C3' C2' GDP sing 133 n n C3' H3' GDP sing 134 n n O3' HO3' GDP sing 135 n n C2' O2' GDP sing 136 n n C2' C1' GDP sing 137 n n C2' H2' GDP sing 138 n n O2' HO2' GDP sing 139 n n C1' N9 GDP sing 140 n n C1' H1' GDP sing 141 n n N9 C8 GDP sing 142 n y N9 C4 GDP sing 143 n y C8 N7 GDP doub 144 n y C8 H8 GDP sing 145 n n N7 C5 GDP sing 146 n y C5 C6 GDP sing 147 n n C5 C4 GDP doub 148 n y C6 O6 GDP doub 149 n n C6 N1 GDP sing 150 n n N1 C2 GDP sing 151 n n N1 HN1 GDP sing 152 n n C2 N2 GDP sing 153 n n C2 N3 GDP doub 154 n n N2 HN21 GDP sing 155 n n N2 HN22 GDP sing 156 n n N3 C4 GDP sing 157 n n # _atom_sites.entry_id 6KX3 _atom_sites.fract_transf_matrix[1][1] 0.010895 _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] 0.010895 _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] 0.017917 _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 1 201 200 GDP GDP . C 3 8ZO A 1 202 999 8ZO UNK . D 4 HOH A 1 301 77 HOH HOH . D 4 HOH A 2 302 64 HOH HOH . D 4 HOH A 3 303 60 HOH HOH . D 4 HOH A 4 304 43 HOH HOH . D 4 HOH A 5 305 47 HOH HOH . D 4 HOH A 6 306 70 HOH HOH . D 4 HOH A 7 307 35 HOH HOH . D 4 HOH A 8 308 17 HOH HOH . D 4 HOH A 9 309 4 HOH HOH . D 4 HOH A 10 310 29 HOH HOH . D 4 HOH A 11 311 15 HOH HOH . D 4 HOH A 12 312 30 HOH HOH . D 4 HOH A 13 313 79 HOH HOH . D 4 HOH A 14 314 34 HOH HOH . D 4 HOH A 15 315 22 HOH HOH . D 4 HOH A 16 316 23 HOH HOH . D 4 HOH A 17 317 33 HOH HOH . D 4 HOH A 18 318 25 HOH HOH . D 4 HOH A 19 319 27 HOH HOH . D 4 HOH A 20 320 57 HOH HOH . D 4 HOH A 21 321 28 HOH HOH . D 4 HOH A 22 322 10 HOH HOH . D 4 HOH A 23 323 13 HOH HOH . D 4 HOH A 24 324 21 HOH HOH . D 4 HOH A 25 325 37 HOH HOH . D 4 HOH A 26 326 16 HOH HOH . D 4 HOH A 27 327 65 HOH HOH . D 4 HOH A 28 328 19 HOH HOH . D 4 HOH A 29 329 14 HOH HOH . D 4 HOH A 30 330 1 HOH HOH . D 4 HOH A 31 331 55 HOH HOH . D 4 HOH A 32 332 18 HOH HOH . D 4 HOH A 33 333 46 HOH HOH . D 4 HOH A 34 334 31 HOH HOH . D 4 HOH A 35 335 38 HOH HOH . D 4 HOH A 36 336 2 HOH HOH . D 4 HOH A 37 337 56 HOH HOH . D 4 HOH A 38 338 42 HOH HOH . D 4 HOH A 39 339 32 HOH HOH . D 4 HOH A 40 340 20 HOH HOH . D 4 HOH A 41 341 54 HOH HOH . D 4 HOH A 42 342 7 HOH HOH . D 4 HOH A 43 343 49 HOH HOH . D 4 HOH A 44 344 8 HOH HOH . D 4 HOH A 45 345 5 HOH HOH . D 4 HOH A 46 346 82 HOH HOH . D 4 HOH A 47 347 81 HOH HOH . D 4 HOH A 48 348 69 HOH HOH . D 4 HOH A 49 349 9 HOH HOH . D 4 HOH A 50 350 24 HOH HOH . D 4 HOH A 51 351 44 HOH HOH . D 4 HOH A 52 352 52 HOH HOH . D 4 HOH A 53 353 6 HOH HOH . D 4 HOH A 54 354 3 HOH HOH . D 4 HOH A 55 355 76 HOH HOH . D 4 HOH A 56 356 12 HOH HOH . D 4 HOH A 57 357 58 HOH HOH . D 4 HOH A 58 358 41 HOH HOH . D 4 HOH A 59 359 11 HOH HOH . D 4 HOH A 60 360 85 HOH HOH . D 4 HOH A 61 361 75 HOH HOH . D 4 HOH A 62 362 61 HOH HOH . D 4 HOH A 63 363 51 HOH HOH . D 4 HOH A 64 364 45 HOH HOH . D 4 HOH A 65 365 36 HOH HOH . D 4 HOH A 66 366 53 HOH HOH . D 4 HOH A 67 367 83 HOH HOH . D 4 HOH A 68 368 40 HOH HOH . D 4 HOH A 69 369 63 HOH HOH . D 4 HOH A 70 370 50 HOH HOH . D 4 HOH A 71 371 84 HOH HOH . D 4 HOH A 72 372 78 HOH HOH . D 4 HOH A 73 373 74 HOH HOH . D 4 HOH A 74 374 72 HOH HOH . D 4 HOH A 75 375 48 HOH HOH . D 4 HOH A 76 376 62 HOH HOH . D 4 HOH A 77 377 59 HOH HOH . D 4 HOH A 78 378 71 HOH HOH . D 4 HOH A 79 379 26 HOH HOH . D 4 HOH A 80 380 68 HOH HOH . D 4 HOH A 81 381 39 HOH HOH . D 4 HOH A 82 382 80 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 -5.165 -18.297 -9.601 1 29.53 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 -4.783 -19.71 -9.574 1 27.2 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 -4.155 -17.535 -8.886 1 27.44 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 -6.407 -18.249 -8.844 1 24.32 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 -5.268 -17.849 -11.167 1 30.35 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 -6.367 -16.819 -11.776 1 31.32 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 -7.702 -17.443 -11.88 1 29.26 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 -6.527 -15.675 -10.878 1 29.38 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 -5.798 -16.418 -13.261 1 33.86 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 -4.556 -15.771 -13.305 1 34.81 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 -4.386 -15.165 -14.661 1 36.31 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 -4.34 -16.274 -15.606 1 34.38 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 -5.525 -14.278 -15.059 1 41.42 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 -5.027 -12.942 -15.253 1 49.6 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 -6.323 -15.285 -16.214 1 47.3 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 -7.042 -14.319 -16.675 1 46 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 -5.307 -16.017 -16.695 1 36.75 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 -5.988 -17.241 -16.944 1 38.43 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 -6.663 -17.962 -16.049 1 36.43 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 -7.108 -19.099 -16.663 1 33.19 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 -6.612 -19.046 -18.062 1 37.09 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 -6.663 -19.849 -19.32 1 34.66 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 -7.313 -21.068 -19.398 1 37.85 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 -6.025 -19.404 -20.45 1 42.41 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 -5.34 -18.173 -20.428 1 41.26 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -4.681 -17.735 -21.639 1 41.92 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 -5.262 -17.389 -19.331 1 40.08 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 -5.867 -17.781 -18.132 1 35.69 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #