data_1D5C # _model_server_result.job_id I02ZOeD3Q62onsOK_BtfMg _model_server_result.datetime_utc '2024-10-11 06:26:10' _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 1d5c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 1D5C # _exptl.entry_id 1D5C _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 1D5C _cell.length_a 81.2 _cell.length_b 81.2 _cell.length_c 90.84 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D5C _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 ? _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 covale ? covale1 A C PHE 21 A PHE 31 1_555 A N MSE 22 A MSE 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C MSE 22 A MSE 32 1_555 A N TYR 23 A TYR 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C GLY 129 A GLY 139 1_555 A N MSE 130 A MSE 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 A C MSE 130 A MSE 140 1_555 A N GLN 131 A GLN 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale5 A C THR 138 A THR 148 1_555 A N MSE 139 A MSE 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 A C MSE 139 A MSE 149 1_555 A N PHE 140 A PHE 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 B MG MG . A MG 300 1_555 D O HOH . A HOH 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc2 B MG MG . A MG 300 1_555 D O HOH . A HOH 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc3 B MG MG . A MG 300 1_555 D O HOH . A HOH 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc4 B MG MG . A MG 300 1_555 A OG1 THR 15 A THR 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc5 B MG MG . A MG 300 1_555 C O3B GDP . A GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc6 B MG MG . A MG 300 1_555 D O HOH . A HOH 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? # _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 ? # _atom_sites.entry_id 1D5C _atom_sites.fract_transf_matrix[1][1] 0.012315 _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] 0.012315 _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] 0.011008 _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 1 300 300 MG MG . C 3 GDP A 1 201 201 GDP GDP . D 4 HOH A 1 301 1 HOH HOH . D 4 HOH A 2 302 2 HOH HOH . D 4 HOH A 3 303 3 HOH HOH . D 4 HOH A 4 304 4 HOH HOH . D 4 HOH A 5 305 5 HOH HOH . D 4 HOH A 6 306 6 HOH HOH . D 4 HOH A 7 307 7 HOH HOH . D 4 HOH A 8 308 8 HOH HOH . D 4 HOH A 9 309 9 HOH HOH . D 4 HOH A 10 310 10 HOH HOH . D 4 HOH A 11 311 11 HOH HOH . D 4 HOH A 12 312 12 HOH HOH . D 4 HOH A 13 313 13 HOH HOH . D 4 HOH A 14 314 14 HOH HOH . D 4 HOH A 15 315 15 HOH HOH . D 4 HOH A 16 316 16 HOH HOH . D 4 HOH A 17 317 17 HOH HOH . D 4 HOH A 18 318 18 HOH HOH . D 4 HOH A 19 319 19 HOH HOH . D 4 HOH A 20 320 20 HOH HOH . D 4 HOH A 21 321 21 HOH HOH . D 4 HOH A 22 322 22 HOH HOH . D 4 HOH A 23 323 23 HOH HOH . D 4 HOH A 24 324 24 HOH HOH . D 4 HOH A 25 325 25 HOH HOH . D 4 HOH A 26 326 26 HOH HOH . D 4 HOH A 27 327 27 HOH HOH . D 4 HOH A 28 328 28 HOH HOH . D 4 HOH A 29 329 29 HOH HOH . D 4 HOH A 30 330 30 HOH HOH . D 4 HOH A 31 331 31 HOH HOH . D 4 HOH A 32 332 32 HOH HOH . D 4 HOH A 33 333 33 HOH HOH . D 4 HOH A 34 334 34 HOH HOH . D 4 HOH A 35 335 35 HOH HOH . D 4 HOH A 36 336 36 HOH HOH . D 4 HOH A 37 337 37 HOH HOH . D 4 HOH A 38 338 38 HOH HOH . D 4 HOH A 39 339 39 HOH HOH . D 4 HOH A 40 340 40 HOH HOH . D 4 HOH A 41 341 41 HOH HOH . D 4 HOH A 42 342 42 HOH HOH . D 4 HOH A 43 343 43 HOH HOH . D 4 HOH A 44 344 44 HOH HOH . D 4 HOH A 45 345 45 HOH HOH . D 4 HOH A 46 346 46 HOH HOH . D 4 HOH A 47 347 47 HOH HOH . D 4 HOH A 48 348 48 HOH HOH . D 4 HOH A 49 349 49 HOH HOH . D 4 HOH A 50 350 50 HOH HOH . D 4 HOH A 51 351 51 HOH HOH . D 4 HOH A 52 352 52 HOH HOH . D 4 HOH A 53 353 53 HOH HOH . D 4 HOH A 54 354 54 HOH HOH . D 4 HOH A 55 355 55 HOH HOH . D 4 HOH A 56 356 56 HOH HOH . D 4 HOH A 57 357 57 HOH HOH . D 4 HOH A 58 358 58 HOH HOH . D 4 HOH A 59 359 59 HOH HOH . D 4 HOH A 60 360 60 HOH HOH . D 4 HOH A 61 361 61 HOH HOH . D 4 HOH A 62 362 62 HOH HOH . D 4 HOH A 63 363 63 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 24.449 14.309 11.596 1 26.97 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 3 23.128 13.756 11.297 1 25.44 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 3 25.551 13.541 11.026 1 25.38 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 3 24.594 15.738 11.16 1 23.27 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 3 24.632 14.211 13.187 1 25.64 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 3 24.607 15.326 14.358 1 26.72 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 3 23.306 16 14.315 1 28.65 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 3 25.788 16.197 14.173 1 26.3 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 3 24.849 14.375 15.622 1 28.4 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 3 23.865 13.418 16.073 1 31.02 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 3 23.762 13.374 17.607 1 31.87 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 3 25.036 12.874 18.139 1 33.03 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 3 23.557 14.749 18.26 1 32.71 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 3 22.627 14.528 19.34 1 33.05 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 3 24.978 15.155 18.705 1 32.53 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 3 24.958 16.089 19.825 1 35.36 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 3 25.662 13.825 19.038 1 31.88 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 3 27.153 13.848 18.753 1 32.64 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 3 27.854 14.349 17.651 1 31.42 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 3 29.156 14.216 17.701 1 30.9 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 3 29.348 13.582 18.916 1 31.45 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 3 30.539 13.142 19.591 1 31.67 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 3 31.697 13.239 19.207 1 31.74 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 3 30.311 12.53 20.83 1 32.19 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 3 29.03 12.342 21.412 1 32.59 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 3 28.949 11.752 22.592 1 32.88 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 3 27.904 12.747 20.8 1 31.85 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 3 28.114 13.351 19.574 1 32.02 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #