data_5M5N # _model_server_result.job_id xSwrE46cEF_YasAv6DIfHg _model_server_result.datetime_utc '2024-11-23 23:16:58' _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 5m5n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 5M5N # _exptl.entry_id 5M5N _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _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 6 _struct_asym.id F _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 metalc ? metalc1 D MG MG . A MG 501 1_555 E O3G GTP . A GTP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc2 H MG MG . C MG 501 1_555 I O2B ANP . C ANP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc3 H MG MG . C MG 501 1_555 I O3G ANP . C ANP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? # _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 5M5N _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 MG A 1 501 1208 MG MG . E 5 GTP A 1 502 1209 GTP GTP . F 6 GDP B 1 501 1222 GDP GDP . G 7 TA1 B 1 502 1223 TA1 TA1 . H 4 MG C 1 501 1218 MG MG . I 8 ANP C 1 502 1219 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 . . . F 6 193.524 260.925 269.872 1 22.28 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . F 6 192.513 261.374 268.897 1 23.59 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . F 6 194.767 261.561 269.806 1 23.44 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . F 6 192.847 260.943 271.359 1 25.3 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . F 6 193.831 259.422 269.517 1 19.52 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . F 6 195.279 258.682 269.126 1 20.51 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . F 6 195.759 259.217 267.821 1 23.36 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . F 6 196.207 258.912 270.308 1 18 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . F 6 194.816 257.213 268.917 1 16.66 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . F 6 195.745 256.098 269.066 1 7.65 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . F 6 195.879 255.253 267.891 1 2.51 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . F 6 196.462 256.061 266.793 1 2 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . F 6 196.935 254.095 268.013 1 3.46 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . F 6 196.357 252.946 267.296 1 2.32 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . F 6 198.237 254.514 267.288 1 2.23 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . F 6 199.037 253.507 266.646 1 2 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . F 6 197.739 255.515 266.248 1 2 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . F 6 198.641 256.642 266.007 1 5.88 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . F 6 198.803 257.688 267.071 1 9.42 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . F 6 199.705 258.449 266.307 1 10.36 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . F 6 200.066 258.052 265.09 1 10.45 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . F 6 200.854 258.334 263.955 1 13.51 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . F 6 201.573 259.467 264.002 1 11.34 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . F 6 200.9 257.57 262.84 1 10.31 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . F 6 200.082 256.328 262.806 1 5.81 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . F 6 200.295 255.738 261.649 1 6.23 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . F 6 199.367 256.007 263.802 1 4.23 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . F 6 199.326 256.817 264.875 1 7.64 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #