data_8VGQ # _model_server_result.job_id Xtu5Ed4MzhKy4SUv0ElYzA _model_server_result.datetime_utc '2024-12-10 04:52:09' _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 8vgq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":202}' # _entry.id 8VGQ # _exptl.entry_id 8VGQ _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 8VGQ _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VGQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 ? _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 5 _struct_asym.id E _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 11 H CYS 11 1_555 B SG CYS 156 H CYS 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf3 B SG CYS 117 H CYS 108 1_555 B SG CYS 158 H CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 B SG CYS 149 H CYS 144 1_555 B SG CYS 206 H CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 C SG CYS 21 L CYS 23 1_555 C SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 C SG CYS 40 L CYS 40 1_555 C SG CYS 169 L CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf7 C SG CYS 80 L CYS 80 1_555 C SG CYS 173 L CYS 171 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 C SG CYS 137 L CYS 134 1_555 C SG CYS 197 L CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A SG CYS 13 A CYS 12 1_555 D C A1AAW . A A1AAW 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.764 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 F MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc2 E O1B GDP . A GDP 202 1_555 F MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.915 ? # _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 144 n n PB O2B GDP sing 145 n n PB O3B GDP sing 146 n n PB O3A GDP sing 147 n n O2B HOB2 GDP sing 148 n n O3B HOB3 GDP sing 149 n n O3A PA GDP sing 150 n n PA O1A GDP doub 151 n n PA O2A GDP sing 152 n n PA O5' GDP sing 153 n n O2A HOA2 GDP sing 154 n n O5' C5' GDP sing 155 n n C5' C4' GDP sing 156 n n C5' H5' GDP sing 157 n n C5' "H5''" GDP sing 158 n n C4' O4' GDP sing 159 n n C4' C3' GDP sing 160 n n C4' H4' GDP sing 161 n n O4' C1' GDP sing 162 n n C3' O3' GDP sing 163 n n C3' C2' GDP sing 164 n n C3' H3' GDP sing 165 n n O3' HO3' GDP sing 166 n n C2' O2' GDP sing 167 n n C2' C1' GDP sing 168 n n C2' H2' GDP sing 169 n n O2' HO2' GDP sing 170 n n C1' N9 GDP sing 171 n n C1' H1' GDP sing 172 n n N9 C8 GDP sing 173 n y N9 C4 GDP sing 174 n y C8 N7 GDP doub 175 n y C8 H8 GDP sing 176 n n N7 C5 GDP sing 177 n y C5 C6 GDP sing 178 n n C5 C4 GDP doub 179 n y C6 O6 GDP doub 180 n n C6 N1 GDP sing 181 n n N1 C2 GDP sing 182 n n N1 HN1 GDP sing 183 n n C2 N2 GDP sing 184 n n C2 N3 GDP doub 185 n n N2 HN21 GDP sing 186 n n N2 HN22 GDP sing 187 n n N3 C4 GDP sing 188 n n # _atom_sites.entry_id 8VGQ _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 D 4 A1AAW A 1 201 203 A1AAW MKZ . E 5 GDP A 1 202 204 GDP GDP . F 6 MG A 1 203 203 MG MG . G 7 HOH A 1 301 9 HOH HOH . G 7 HOH A 2 302 5 HOH HOH . G 7 HOH A 3 303 18 HOH HOH . G 7 HOH A 4 304 31 HOH HOH . G 7 HOH A 5 305 33 HOH HOH . G 7 HOH A 6 306 21 HOH HOH . G 7 HOH A 7 307 20 HOH HOH . G 7 HOH A 8 308 32 HOH HOH . H 7 HOH H 1 301 16 HOH HOH . H 7 HOH H 2 302 8 HOH HOH . H 7 HOH H 3 303 2 HOH HOH . H 7 HOH H 4 304 40 HOH HOH . H 7 HOH H 5 305 3 HOH HOH . H 7 HOH H 6 306 7 HOH HOH . H 7 HOH H 7 307 35 HOH HOH . H 7 HOH H 8 308 19 HOH HOH . H 7 HOH H 9 309 37 HOH HOH . H 7 HOH H 10 310 6 HOH HOH . H 7 HOH H 11 311 4 HOH HOH . H 7 HOH H 12 312 13 HOH HOH . H 7 HOH H 13 313 17 HOH HOH . H 7 HOH H 14 314 38 HOH HOH . H 7 HOH H 15 315 34 HOH HOH . H 7 HOH H 16 316 39 HOH HOH . H 7 HOH H 17 317 1 HOH HOH . H 7 HOH H 18 318 15 HOH HOH . I 7 HOH L 1 301 14 HOH HOH . I 7 HOH L 2 302 27 HOH HOH . I 7 HOH L 3 303 12 HOH HOH . I 7 HOH L 4 304 26 HOH HOH . I 7 HOH L 5 305 23 HOH HOH . I 7 HOH L 6 306 10 HOH HOH . I 7 HOH L 7 307 25 HOH HOH . I 7 HOH L 8 308 11 HOH HOH . I 7 HOH L 9 309 36 HOH HOH . I 7 HOH L 10 310 22 HOH HOH . I 7 HOH L 11 311 29 HOH HOH . I 7 HOH L 12 312 28 HOH HOH . I 7 HOH L 13 313 30 HOH HOH . I 7 HOH L 14 314 24 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 . . . E 5 96.574 103.225 107.752 1 123.2 ? PB GDP 202 A 1 HETATM 2 O O1B GDP . . . E 5 97.277 104.547 107.826 1 119.41 ? O1B GDP 202 A 1 HETATM 3 O O2B GDP . . . E 5 95.557 103.062 108.834 1 116.51 ? O2B GDP 202 A 1 HETATM 4 O O3B GDP . . . E 5 97.597 102.158 107.941 1 125.36 ? O3B GDP 202 A 1 HETATM 5 O O3A GDP . . . E 5 95.831 102.954 106.362 1 120.79 ? O3A GDP 202 A 1 HETATM 6 P PA GDP . . . E 5 96.071 103.759 105.009 1 123.23 ? PA GDP 202 A 1 HETATM 7 O O1A GDP . . . E 5 97.522 103.819 104.678 1 123.42 ? O1A GDP 202 A 1 HETATM 8 O O2A GDP . . . E 5 95.469 105.117 105.074 1 117.01 ? O2A GDP 202 A 1 HETATM 9 O O5' GDP . . . E 5 95.282 102.914 103.915 1 123.43 ? O5' GDP 202 A 1 HETATM 10 C C5' GDP . . . E 5 95.884 101.708 103.484 1 123.93 ? C5' GDP 202 A 1 HETATM 11 C C4' GDP . . . E 5 95.524 101.417 102.042 1 127.52 ? C4' GDP 202 A 1 HETATM 12 O O4' GDP . . . E 5 94.122 101.329 101.849 1 128.12 ? O4' GDP 202 A 1 HETATM 13 C C3' GDP . . . E 5 95.992 102.534 101.147 1 130.76 ? C3' GDP 202 A 1 HETATM 14 O O3' GDP . . . E 5 96.635 101.985 100.009 1 137.92 ? O3' GDP 202 A 1 HETATM 15 C C2' GDP . . . E 5 94.762 103.237 100.668 1 128.29 ? C2' GDP 202 A 1 HETATM 16 O O2' GDP . . . E 5 94.943 103.499 99.289 1 133.9 ? O2' GDP 202 A 1 HETATM 17 C C1' GDP . . . E 5 93.694 102.196 100.81 1 125.83 ? C1' GDP 202 A 1 HETATM 18 N N9 GDP . . . E 5 92.384 102.772 101.148 1 123.1 ? N9 GDP 202 A 1 HETATM 19 C C8 GDP . . . E 5 92.104 103.561 102.18 1 120.36 ? C8 GDP 202 A 1 HETATM 20 N N7 GDP . . . E 5 90.801 103.891 102.177 1 120.11 ? N7 GDP 202 A 1 HETATM 21 C C5 GDP . . . E 5 90.236 103.317 101.119 1 119.18 ? C5 GDP 202 A 1 HETATM 22 C C6 GDP . . . E 5 88.898 103.262 100.532 1 121.33 ? C6 GDP 202 A 1 HETATM 23 O O6 GDP . . . E 5 87.953 103.867 101.053 1 126.63 ? O6 GDP 202 A 1 HETATM 24 N N1 GDP . . . E 5 88.712 102.557 99.433 1 119.27 ? N1 GDP 202 A 1 HETATM 25 C C2 GDP . . . E 5 89.709 101.9 98.858 1 121.47 ? C2 GDP 202 A 1 HETATM 26 N N2 GDP . . . E 5 89.44 101.203 97.743 1 126.44 ? N2 GDP 202 A 1 HETATM 27 N N3 GDP . . . E 5 90.963 101.901 99.336 1 123.51 ? N3 GDP 202 A 1 HETATM 28 C C4 GDP . . . E 5 91.279 102.58 100.447 1 122.19 ? C4 GDP 202 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 578 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 28 #