data_7LI3 # _model_server_result.job_id PAR5eUbP5O9NCNDZQkF9mw _model_server_result.datetime_utc '2024-12-22 02:10:15' _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 7li3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2601}' # _entry.id 7LI3 # _exptl.entry_id 7LI3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 7LI3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LI3 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 132 n n PB O2B GDP sing 133 n n PB O3B GDP sing 134 n n PB O3A GDP sing 135 n n O2B HOB2 GDP sing 136 n n O3B HOB3 GDP sing 137 n n O3A PA GDP sing 138 n n PA O1A GDP doub 139 n n PA O2A GDP sing 140 n n PA O5' GDP sing 141 n n O2A HOA2 GDP sing 142 n n O5' C5' GDP sing 143 n n C5' C4' GDP sing 144 n n C5' H5' GDP sing 145 n n C5' "H5''" GDP sing 146 n n C4' O4' GDP sing 147 n n C4' C3' GDP sing 148 n n C4' H4' GDP sing 149 n n O4' C1' GDP sing 150 n n C3' O3' GDP sing 151 n n C3' C2' GDP sing 152 n n C3' H3' GDP sing 153 n n O3' HO3' GDP sing 154 n n C2' O2' GDP sing 155 n n C2' C1' GDP sing 156 n n C2' H2' GDP sing 157 n n O2' HO2' GDP sing 158 n n C1' N9 GDP sing 159 n n C1' H1' GDP sing 160 n n N9 C8 GDP sing 161 n y N9 C4 GDP sing 162 n y C8 N7 GDP doub 163 n y C8 H8 GDP sing 164 n n N7 C5 GDP sing 165 n y C5 C6 GDP sing 166 n n C5 C4 GDP doub 167 n y C6 O6 GDP doub 168 n n C6 N1 GDP sing 169 n n N1 C2 GDP sing 170 n n N1 HN1 GDP sing 171 n n C2 N2 GDP sing 172 n n C2 N3 GDP doub 173 n n N2 HN21 GDP sing 174 n n N2 HN22 GDP sing 175 n n N3 C4 GDP sing 176 n n # _atom_sites.entry_id 7LI3 _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 B 2 GDP A 1 2601 2601 GDP GDP . C 3 ATP A 1 2602 2701 ATP ATP . # 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 . . . B 2 192.316 172.646 265.657 1 77.18 ? PB GDP 2601 A 1 HETATM 2 O O1B GDP . . . B 2 192.485 171.749 264.461 1 77.18 ? O1B GDP 2601 A 1 HETATM 3 O O2B GDP . . . B 2 191.775 173.976 265.215 1 77.18 ? O2B GDP 2601 A 1 HETATM 4 O O3B GDP . . . B 2 193.647 172.839 266.327 1 77.18 ? O3B GDP 2601 A 1 HETATM 5 O O3A GDP . . . B 2 191.309 171.972 266.704 1 77.18 ? O3A GDP 2601 A 1 HETATM 6 P PA GDP . . . B 2 191.984 171.254 267.964 1 77.18 ? PA GDP 2601 A 1 HETATM 7 O O1A GDP . . . B 2 193.047 170.304 267.478 1 77.18 ? O1A GDP 2601 A 1 HETATM 8 O O2A GDP . . . B 2 192.585 172.292 268.875 1 77.18 ? O2A GDP 2601 A 1 HETATM 9 O O5' GDP . . . B 2 190.806 170.457 268.713 1 77.18 ? O5' GDP 2601 A 1 HETATM 10 C C5' GDP . . . B 2 190.923 170.229 270.114 1 77.18 ? C5' GDP 2601 A 1 HETATM 11 C C4' GDP . . . B 2 190.597 168.783 270.454 1 77.18 ? C4' GDP 2601 A 1 HETATM 12 O O4' GDP . . . B 2 191.746 168.169 271.04 1 77.18 ? O4' GDP 2601 A 1 HETATM 13 C C3' GDP . . . B 2 189.475 168.686 271.473 1 77.18 ? C3' GDP 2601 A 1 HETATM 14 O O3' GDP . . . B 2 188.315 168.105 270.874 1 77.18 ? O3' GDP 2601 A 1 HETATM 15 C C2' GDP . . . B 2 189.98 167.776 272.572 1 77.18 ? C2' GDP 2601 A 1 HETATM 16 O O2' GDP . . . B 2 189.113 166.648 272.705 1 77.18 ? O2' GDP 2601 A 1 HETATM 17 C C1' GDP . . . B 2 191.354 167.318 272.12 1 77.18 ? C1' GDP 2601 A 1 HETATM 18 N N9 GDP . . . B 2 192.321 167.385 273.246 1 77.18 ? N9 GDP 2601 A 1 HETATM 19 C C8 GDP . . . B 2 193.286 168.307 273.412 1 77.18 ? C8 GDP 2601 A 1 HETATM 20 N N7 GDP . . . B 2 193.994 168.076 274.548 1 77.18 ? N7 GDP 2601 A 1 HETATM 21 C C5 GDP . . . B 2 193.472 166.985 275.132 1 77.18 ? C5 GDP 2601 A 1 HETATM 22 C C6 GDP . . . B 2 193.744 166.193 276.35 1 77.18 ? C6 GDP 2601 A 1 HETATM 23 O O6 GDP . . . B 2 194.66 166.513 277.132 1 77.18 ? O6 GDP 2601 A 1 HETATM 24 N N1 GDP . . . B 2 192.977 165.129 276.6 1 77.18 ? N1 GDP 2601 A 1 HETATM 25 C C2 GDP . . . B 2 191.981 164.76 275.778 1 77.18 ? C2 GDP 2601 A 1 HETATM 26 N N2 GDP . . . B 2 191.253 163.666 276.103 1 77.18 ? N2 GDP 2601 A 1 HETATM 27 N N3 GDP . . . B 2 191.675 165.435 274.641 1 77.18 ? N3 GDP 2601 A 1 HETATM 28 C C4 GDP . . . B 2 192.373 166.534 274.272 1 77.18 ? C4 GDP 2601 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #