data_7YUZ # _model_server_result.job_id RIFxoygQ8cUJcM1FbnISZw _model_server_result.datetime_utc '2024-11-09 02:21:56' _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 7yuz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 7YUZ # _exptl.entry_id 7YUZ _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 7YUZ _cell.length_a 66.012 _cell.length_b 66.012 _cell.length_c 86.33 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YUZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 covale ? covale1 B C MAA 1 I MAA 1 1_555 B N ILE 2 I ILE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale2 B N MAA 1 I MAA 1 1_555 B CG 7TK 11 I 7TK 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.361 ? covale ? covale3 B C ILE 2 I ILE 2 1_555 B N SAR 3 I SAR 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale4 B C SAR 3 I SAR 3 1_555 B N SAR 4 I SAR 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? covale ? covale5 B C SAR 4 I SAR 4 1_555 B N 7T2 5 I 7T2 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale6 B C 7T2 5 I 7T2 5 1_555 B N SAR 6 I SAR 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? covale ? covale7 B C SAR 6 I SAR 6 1_555 B N FCL 7 I FCL 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale8 B C FCL 7 I FCL 7 1_555 B N TRP 8 I TRP 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale9 B C TRP 8 I TRP 8 1_555 B N MEA 9 I MEA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? covale ? covale10 B C MEA 9 I MEA 9 1_555 B N MVA 10 I MVA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.363 ? covale ? covale11 B C MVA 10 I MVA 10 1_555 B N 7TK 11 I 7TK 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? metalc ? metalc1 A OG SER 22 A SER 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc2 C O3B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? # _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 159 n n PB O2B GDP sing 160 n n PB O3B GDP sing 161 n n PB O3A GDP sing 162 n n O2B HOB2 GDP sing 163 n n O3B HOB3 GDP sing 164 n n O3A PA GDP sing 165 n n PA O1A GDP doub 166 n n PA O2A GDP sing 167 n n PA O5' GDP sing 168 n n O2A HOA2 GDP sing 169 n n O5' C5' GDP sing 170 n n C5' C4' GDP sing 171 n n C5' H5' GDP sing 172 n n C5' "H5''" GDP sing 173 n n C4' O4' GDP sing 174 n n C4' C3' GDP sing 175 n n C4' H4' GDP sing 176 n n O4' C1' GDP sing 177 n n C3' O3' GDP sing 178 n n C3' C2' GDP sing 179 n n C3' H3' GDP sing 180 n n O3' HO3' GDP sing 181 n n C2' O2' GDP sing 182 n n C2' C1' GDP sing 183 n n C2' H2' GDP sing 184 n n O2' HO2' GDP sing 185 n n C1' N9 GDP sing 186 n n C1' H1' GDP sing 187 n n N9 C8 GDP sing 188 n y N9 C4 GDP sing 189 n y C8 N7 GDP doub 190 n y C8 H8 GDP sing 191 n n N7 C5 GDP sing 192 n y C5 C6 GDP sing 193 n n C5 C4 GDP doub 194 n y C6 O6 GDP doub 195 n n C6 N1 GDP sing 196 n n N1 C2 GDP sing 197 n n N1 HN1 GDP sing 198 n n C2 N2 GDP sing 199 n n C2 N3 GDP doub 200 n n N2 HN21 GDP sing 201 n n N2 HN22 GDP sing 202 n n N3 C4 GDP sing 203 n n # _atom_sites.entry_id 7YUZ _atom_sites.fract_transf_matrix[1][1] 0.015149 _atom_sites.fract_transf_matrix[1][2] 0.008746 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017492 _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] 0.011583 _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 IOD A 1 203 301 IOD IOD . F 6 HOH A 1 301 28 HOH HOH . F 6 HOH A 2 302 7 HOH HOH . F 6 HOH A 3 303 4 HOH HOH . F 6 HOH A 4 304 10 HOH HOH . F 6 HOH A 5 305 30 HOH HOH . F 6 HOH A 6 306 20 HOH HOH . F 6 HOH A 7 307 16 HOH HOH . F 6 HOH A 8 308 18 HOH HOH . F 6 HOH A 9 309 1 HOH HOH . F 6 HOH A 10 310 6 HOH HOH . F 6 HOH A 11 311 23 HOH HOH . F 6 HOH A 12 312 5 HOH HOH . F 6 HOH A 13 313 2 HOH HOH . F 6 HOH A 14 314 15 HOH HOH . F 6 HOH A 15 315 3 HOH HOH . F 6 HOH A 16 316 25 HOH HOH . F 6 HOH A 17 317 19 HOH HOH . F 6 HOH A 18 318 14 HOH HOH . F 6 HOH A 19 319 29 HOH HOH . F 6 HOH A 20 320 21 HOH HOH . F 6 HOH A 21 321 8 HOH HOH . F 6 HOH A 22 322 22 HOH HOH . F 6 HOH A 23 323 11 HOH HOH . F 6 HOH A 24 324 12 HOH HOH . F 6 HOH A 25 325 13 HOH HOH . F 6 HOH A 26 326 9 HOH HOH . F 6 HOH A 27 327 17 HOH HOH . F 6 HOH A 28 328 24 HOH HOH . F 6 HOH A 29 329 26 HOH HOH . F 6 HOH A 30 330 27 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 39.803 -14.909 16.351 1 41.13 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 3 39.578 -14.131 15.15 1 41.09 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 3 40.435 -16.242 15.928 1 40.16 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 3 38.64 -15.057 17.273 1 40.03 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 3 40.918 -14.098 17.153 1 42.46 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 3 41.207 -13.798 18.698 1 42.28 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 3 40.181 -12.893 19.233 1 42.72 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 3 41.131 -15.048 19.521 1 41.03 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 3 42.652 -13.154 18.58 1 43.25 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 3 43.787 -13.792 17.968 1 45.65 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 3 45.011 -13.299 18.695 1 48.29 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 3 45.241 -11.904 18.374 1 49.12 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 3 44.912 -13.368 20.219 1 49.74 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 3 46.177 -13.695 20.785 1 50.65 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 3 44.448 -11.955 20.589 1 50.02 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 3 44.759 -11.575 21.919 1 50.28 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 3 45.186 -11.117 19.55 1 49.74 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 3 44.512 -9.851 19.228 1 50.44 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 3 43.171 -9.649 19.032 1 50.27 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 3 42.861 -8.405 18.766 1 50.73 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 3 44.078 -7.74 18.779 1 51.32 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 3 44.423 -6.345 18.549 1 51.2 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 3 43.693 -5.46 18.126 1 51.09 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 3 45.771 -6.107 18.718 1 51.46 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 3 46.711 -7.055 19.028 1 51.85 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 3 47.974 -6.636 19.147 1 51.75 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 3 46.424 -8.346 19.209 1 51.91 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 3 45.104 -8.619 19.073 1 51.43 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #