data_1WQ1 # _model_server_result.job_id gtKRHbTJFF5V5o3N7-X9ZA _model_server_result.datetime_utc '2024-11-05 05:44:39' _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 1wq1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":167}' # _entry.id 1WQ1 # _exptl.entry_id 1WQ1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 108.4 _cell.angle_gamma 90 _cell.entry_id 1WQ1 _cell.length_a 71.9 _cell.length_b 41.1 _cell.length_c 89 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1WQ1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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,G _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 4 _struct_asym.id D _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 disulf ? disulf1 B SG CYS 58 G CYS 771 1_555 B SG CYS 163 G CYS 876 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc1 A OG SER 17 R SER 17 1_555 C MG MG . R MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc2 A OG1 THR 35 R THR 35 1_555 C MG MG . R MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc3 D O2B GDP . R GDP 167 1_555 C MG MG . R MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.845 ? metalc ? metalc4 D O3B GDP . R GDP 167 1_555 E AL AF3 . R AF3 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc5 D O2B GDP . R GDP 167 1_555 E AL AF3 . R AF3 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.665 ? metalc ? metalc6 C MG MG . R MG 168 1_555 E F2 AF3 . R AF3 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc7 C MG MG . R MG 168 1_555 F O HOH . R HOH 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc8 E AL AF3 . R AF3 169 1_555 F O HOH . R HOH 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc9 E AL AF3 . R AF3 169 1_555 B NH1 ARG 76 G ARG 789 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.4 ? # _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 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 1WQ1 _atom_sites.fract_transf_matrix[1][1] 0.013908 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004627 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024331 _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] 0.011841 _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 MG R 1 168 168 MG MG . D 4 GDP R 1 167 167 GDP GDP . E 5 AF3 R 1 169 169 AF3 AF3 . F 6 HOH R 1 201 201 HOH HOH . F 6 HOH R 2 202 202 HOH HOH . F 6 HOH R 3 203 203 HOH HOH . F 6 HOH R 4 204 204 HOH HOH . F 6 HOH R 5 206 206 HOH HOH . F 6 HOH R 6 210 210 HOH HOH . F 6 HOH R 7 215 215 HOH HOH . F 6 HOH R 8 217 217 HOH HOH . F 6 HOH R 9 219 219 HOH HOH . F 6 HOH R 10 221 221 HOH HOH . F 6 HOH R 11 230 230 HOH HOH . G 6 HOH G 1 205 205 HOH HOH . G 6 HOH G 2 207 207 HOH HOH . G 6 HOH G 3 208 208 HOH HOH . G 6 HOH G 4 209 209 HOH HOH . G 6 HOH G 5 211 211 HOH HOH . G 6 HOH G 6 212 212 HOH HOH . G 6 HOH G 7 213 213 HOH HOH . G 6 HOH G 8 214 214 HOH HOH . G 6 HOH G 9 216 216 HOH HOH . G 6 HOH G 10 218 218 HOH HOH . G 6 HOH G 11 220 220 HOH HOH . G 6 HOH G 12 222 222 HOH HOH . G 6 HOH G 13 223 223 HOH HOH . G 6 HOH G 14 224 224 HOH HOH . G 6 HOH G 15 225 225 HOH HOH . G 6 HOH G 16 226 226 HOH HOH . G 6 HOH G 17 227 227 HOH HOH . G 6 HOH G 18 228 228 HOH HOH . G 6 HOH G 19 229 229 HOH HOH . G 6 HOH G 20 231 231 HOH HOH . G 6 HOH G 21 232 232 HOH HOH . G 6 HOH G 22 233 233 HOH HOH . G 6 HOH G 23 234 234 HOH HOH . G 6 HOH G 24 235 235 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 . . . D 4 -16.868 21.143 19.255 1 20.33 ? PB GDP 167 R 1 HETATM 2 O O1B GDP . . . D 4 -16.04 20.92 20.429 1 24.57 ? O1B GDP 167 R 1 HETATM 3 O O2B GDP . . . D 4 -16.213 21.136 17.968 1 11.02 ? O2B GDP 167 R 1 HETATM 4 O O3B GDP . . . D 4 -18.037 20.055 19.253 1 19.72 ? O3B GDP 167 R 1 HETATM 5 O O3A GDP . . . D 4 -17.677 22.513 19.422 1 16.99 ? O3A GDP 167 R 1 HETATM 6 P PA GDP . . . D 4 -17.388 23.88 18.632 1 17.48 ? PA GDP 167 R 1 HETATM 7 O O1A GDP . . . D 4 -15.985 24.234 18.823 1 16.03 ? O1A GDP 167 R 1 HETATM 8 O O2A GDP . . . D 4 -17.855 23.713 17.267 1 23.96 ? O2A GDP 167 R 1 HETATM 9 O O5' GDP . . . D 4 -18.328 24.941 19.396 1 13.56 ? O5' GDP 167 R 1 HETATM 10 C C5' GDP . . . D 4 -19.671 24.622 19.682 1 17.16 ? C5' GDP 167 R 1 HETATM 11 C C4' GDP . . . D 4 -20.496 25.854 20.087 1 22.29 ? C4' GDP 167 R 1 HETATM 12 O O4' GDP . . . D 4 -20.01 26.544 21.261 1 22.57 ? O4' GDP 167 R 1 HETATM 13 C C3' GDP . . . D 4 -20.481 26.932 18.996 1 26.32 ? C3' GDP 167 R 1 HETATM 14 O O3' GDP . . . D 4 -21.737 27.663 18.94 1 24.07 ? O3' GDP 167 R 1 HETATM 15 C C2' GDP . . . D 4 -19.324 27.804 19.458 1 26.15 ? C2' GDP 167 R 1 HETATM 16 O O2' GDP . . . D 4 -19.326 29.106 18.859 1 26.98 ? O2' GDP 167 R 1 HETATM 17 C C1' GDP . . . D 4 -19.57 27.873 20.937 1 25.16 ? C1' GDP 167 R 1 HETATM 18 N N9 GDP . . . D 4 -18.342 28.176 21.675 1 30.24 ? N9 GDP 167 R 1 HETATM 19 C C8 GDP . . . D 4 -17.151 27.592 21.6 1 30.9 ? C8 GDP 167 R 1 HETATM 20 N N7 GDP . . . D 4 -16.241 28.057 22.388 1 33.16 ? N7 GDP 167 R 1 HETATM 21 C C5 GDP . . . D 4 -16.884 29.015 23.109 1 32.89 ? C5 GDP 167 R 1 HETATM 22 C C6 GDP . . . D 4 -16.414 29.866 24.159 1 31.93 ? C6 GDP 167 R 1 HETATM 23 O O6 GDP . . . D 4 -15.324 29.909 24.766 1 32.52 ? O6 GDP 167 R 1 HETATM 24 N N1 GDP . . . D 4 -17.407 30.711 24.563 1 26.98 ? N1 GDP 167 R 1 HETATM 25 C C2 GDP . . . D 4 -18.679 30.744 24.09 1 27.31 ? C2 GDP 167 R 1 HETATM 26 N N2 GDP . . . D 4 -19.486 31.664 24.597 1 24.71 ? N2 GDP 167 R 1 HETATM 27 N N3 GDP . . . D 4 -19.129 29.928 23.139 1 32.58 ? N3 GDP 167 R 1 HETATM 28 C C4 GDP . . . D 4 -18.181 29.102 22.679 1 31.99 ? C4 GDP 167 R 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #