data_8UTY # _model_server_result.job_id UgABl5fmVIZxsAFNi7Zjyw _model_server_result.datetime_utc '2024-10-11 02:19:18' _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 8uty # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":501}' # _entry.id 8UTY # _exptl.entry_id 8UTY _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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,J,K,L,M,N,O,P,Q,R,S,T _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 J N N ? 6 N N 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 metalc ? metalc1 A OE2 GLU 71 A GLU 71 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc2 H O1G GTP . A GTP 501 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? metalc ? metalc3 H O3B GTP . A GTP 501 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? metalc ? metalc4 H O1B GTP . A GTP 501 1_555 I MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc5 C OE1 GLU 71 E GLU 71 1_555 M MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc6 C OE2 GLU 71 E GLU 71 1_555 M MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? metalc ? metalc7 L O1G GTP . E GTP 501 1_555 M MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc8 L O3B GTP . E GTP 501 1_555 M MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc9 L O1B GTP . E GTP 501 1_555 M MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc10 E OG SER 104 K SER 104 1_555 P MG MG . K MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc11 E OG SER 215 K SER 215 1_555 P MG MG . K MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc12 P MG MG . K MG 501 1_555 Q O2B ANP . K ANP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc13 P MG MG . K MG 501 1_555 Q O1G ANP . K ANP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? metalc ? metalc14 F OE1 GLU 71 S GLU 71 1_555 S MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.835 ? metalc ? metalc15 F OE2 GLU 71 S GLU 71 1_555 S MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc16 R O3B GTP . S GTP 501 1_555 S MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc17 R O1B GTP . S GTP 501 1_555 S MG MG . S MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? # _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 133 n n PB O2B GDP sing 134 n n PB O3B GDP sing 135 n n PB O3A GDP sing 136 n n O2B HOB2 GDP sing 137 n n O3B HOB3 GDP sing 138 n n O3A PA GDP sing 139 n n PA O1A GDP doub 140 n n PA O2A GDP sing 141 n n PA O5' GDP sing 142 n n O2A HOA2 GDP sing 143 n n O5' C5' GDP sing 144 n n C5' C4' GDP sing 145 n n C5' H5' GDP sing 146 n n C5' "H5''" GDP sing 147 n n C4' O4' GDP sing 148 n n C4' C3' GDP sing 149 n n C4' H4' GDP sing 150 n n O4' C1' GDP sing 151 n n C3' O3' GDP sing 152 n n C3' C2' GDP sing 153 n n C3' H3' GDP sing 154 n n O3' HO3' GDP sing 155 n n C2' O2' GDP sing 156 n n C2' C1' GDP sing 157 n n C2' H2' GDP sing 158 n n O2' HO2' GDP sing 159 n n C1' N9 GDP sing 160 n n C1' H1' GDP sing 161 n n N9 C8 GDP sing 162 n y N9 C4 GDP sing 163 n y C8 N7 GDP doub 164 n y C8 H8 GDP sing 165 n n N7 C5 GDP sing 166 n y C5 C6 GDP sing 167 n n C5 C4 GDP doub 168 n y C6 O6 GDP doub 169 n n C6 N1 GDP sing 170 n n N1 C2 GDP sing 171 n n N1 HN1 GDP sing 172 n n C2 N2 GDP sing 173 n n C2 N3 GDP doub 174 n n N2 HN21 GDP sing 175 n n N2 HN22 GDP sing 176 n n N3 C4 GDP sing 177 n n # _atom_sites.entry_id 8UTY _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 H 4 GTP A 1 501 501 GTP GTP . I 5 MG A 1 502 502 MG MG . J 6 GDP B 1 501 501 GDP GDP . K 7 TA1 B 1 502 502 TA1 TA1 . L 4 GTP E 1 501 501 GTP GTP . M 5 MG E 1 502 502 MG MG . N 6 GDP I 1 501 501 GDP GDP . O 7 TA1 I 1 502 502 TA1 TA1 . P 5 MG K 1 501 501 MG MG . Q 8 ANP K 1 502 502 ANP ANP . R 4 GTP S 1 501 501 GTP GTP . S 5 MG S 1 502 502 MG MG . T 8 ANP N 1 501 501 ANP ANP . # 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 . . . N 6 182.007 199.251 262.174 1 78.32 ? PB GDP 501 I 1 HETATM 2 O O1B GDP . . . N 6 180.835 199.87 261.454 1 82.61 ? O1B GDP 501 I 1 HETATM 3 O O2B GDP . . . N 6 181.978 197.754 262.001 1 88.05 ? O2B GDP 501 I 1 HETATM 4 O O3B GDP . . . N 6 181.937 199.593 263.641 1 72.64 ? O3B GDP 501 I 1 HETATM 5 O O3A GDP . . . N 6 183.373 199.827 261.556 1 75.02 ? O3A GDP 501 I 1 HETATM 6 P PA GDP . . . N 6 183.787 201.356 261.817 1 82.51 ? PA GDP 501 I 1 HETATM 7 O O1A GDP . . . N 6 182.929 202.273 260.983 1 88.39 ? O1A GDP 501 I 1 HETATM 8 O O2A GDP . . . N 6 183.675 201.697 263.282 1 92.97 ? O2A GDP 501 I 1 HETATM 9 O O5' GDP . . . N 6 185.315 201.428 261.327 1 71.23 ? O5' GDP 501 I 1 HETATM 10 C C5' GDP . . . N 6 186.203 202.391 261.886 1 73.68 ? C5' GDP 501 I 1 HETATM 11 C C4' GDP . . . N 6 187.069 202.947 260.768 1 73.7 ? C4' GDP 501 I 1 HETATM 12 O O4' GDP . . . N 6 186.218 203.604 259.831 1 78.13 ? O4' GDP 501 I 1 HETATM 13 C C3' GDP . . . N 6 188.083 203.964 261.263 1 82.97 ? C3' GDP 501 I 1 HETATM 14 O O3' GDP . . . N 6 189.411 203.459 261.086 1 89.46 ? O3' GDP 501 I 1 HETATM 15 C C2' GDP . . . N 6 187.861 205.219 260.442 1 82.4 ? C2' GDP 501 I 1 HETATM 16 O O2' GDP . . . N 6 189.04 205.578 259.717 1 92.54 ? O2' GDP 501 I 1 HETATM 17 C C1' GDP . . . N 6 186.728 204.89 259.48 1 83.49 ? C1' GDP 501 I 1 HETATM 18 N N9 GDP . . . N 6 185.634 205.888 259.568 1 81.3 ? N9 GDP 501 I 1 HETATM 19 C C8 GDP . . . N 6 184.786 206.033 260.605 1 83.97 ? C8 GDP 501 I 1 HETATM 20 N N7 GDP . . . N 6 183.9 207.031 260.361 1 83.34 ? N7 GDP 501 I 1 HETATM 21 C C5 GDP . . . N 6 184.172 207.531 259.144 1 74.12 ? C5 GDP 501 I 1 HETATM 22 C C6 GDP . . . N 6 183.617 208.596 258.281 1 82.97 ? C6 GDP 501 I 1 HETATM 23 O O6 GDP . . . N 6 182.646 209.283 258.66 1 95.14 ? O6 GDP 501 I 1 HETATM 24 N N1 GDP . . . N 6 184.182 208.803 257.087 1 79.82 ? N1 GDP 501 I 1 HETATM 25 C C2 GDP . . . N 6 185.231 208.073 256.66 1 77.23 ? C2 GDP 501 I 1 HETATM 26 N N2 GDP . . . N 6 185.76 208.332 255.439 1 84.93 ? N2 GDP 501 I 1 HETATM 27 N N3 GDP . . . N 6 185.79 207.082 257.399 1 73.37 ? N3 GDP 501 I 1 HETATM 28 C C4 GDP . . . N 6 185.312 206.771 258.624 1 73.41 ? C4 GDP 501 I 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #