data_3GEE # _model_server_result.job_id 6OYS5N90NQ_mlNK1TRKa2A _model_server_result.datetime_utc '2024-12-22 06:24:17' _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 3gee # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":474}' # _entry.id 3GEE # _exptl.entry_id 3GEE _exptl.method 'X-RAY DIFFRACTION' # _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 3GEE _cell.length_a 130.804 _cell.length_b 130.804 _cell.length_c 200.611 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GEE _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 10_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 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 142 n n PB O2B GDP sing 143 n n PB O3B GDP sing 144 n n PB O3A GDP sing 145 n n O2B HOB2 GDP sing 146 n n O3B HOB3 GDP sing 147 n n O3A PA GDP sing 148 n n PA O1A GDP doub 149 n n PA O2A GDP sing 150 n n PA O5' GDP sing 151 n n O2A HOA2 GDP sing 152 n n O5' C5' GDP sing 153 n n C5' C4' GDP sing 154 n n C5' H5' GDP sing 155 n n C5' "H5''" GDP sing 156 n n C4' O4' GDP sing 157 n n C4' C3' GDP sing 158 n n C4' H4' GDP sing 159 n n O4' C1' GDP sing 160 n n C3' O3' GDP sing 161 n n C3' C2' GDP sing 162 n n C3' H3' GDP sing 163 n n O3' HO3' GDP sing 164 n n C2' O2' GDP sing 165 n n C2' C1' GDP sing 166 n n C2' H2' GDP sing 167 n n O2' HO2' GDP sing 168 n n C1' N9 GDP sing 169 n n C1' H1' GDP sing 170 n n N9 C8 GDP sing 171 n y N9 C4 GDP sing 172 n y C8 N7 GDP doub 173 n y C8 H8 GDP sing 174 n n N7 C5 GDP sing 175 n y C5 C6 GDP sing 176 n n C5 C4 GDP doub 177 n y C6 O6 GDP doub 178 n n C6 N1 GDP sing 179 n n N1 C2 GDP sing 180 n n N1 HN1 GDP sing 181 n n C2 N2 GDP sing 182 n n C2 N3 GDP doub 183 n n N2 HN21 GDP sing 184 n n N2 HN22 GDP sing 185 n n N3 C4 GDP sing 186 n n # _atom_sites.entry_id 3GEE _atom_sites.fract_transf_matrix[1][1] 0.007645 _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] 0.007645 _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] 0.004985 _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 1 474 474 GDP GDP . C 3 FON A 1 475 475 FON FON . # 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 17.289 2.245 -7.883 1 130.76 ? PB GDP 474 A 1 HETATM 2 O O1B GDP . . . B 2 16.942 2.317 -6.416 1 130.96 ? O1B GDP 474 A 1 HETATM 3 O O2B GDP . . . B 2 18.654 2.84 -8.126 1 130.69 ? O2B GDP 474 A 1 HETATM 4 O O3B GDP . . . B 2 16.252 2.995 -8.683 1 130.9 ? O3B GDP 474 A 1 HETATM 5 O O3A GDP . . . B 2 17.304 0.711 -8.349 1 131.04 ? O3A GDP 474 A 1 HETATM 6 P PA GDP . . . B 2 15.984 -0.196 -8.216 1 131.24 ? PA GDP 474 A 1 HETATM 7 O O1A GDP . . . B 2 16.059 -1.043 -6.975 1 131.19 ? O1A GDP 474 A 1 HETATM 8 O O2A GDP . . . B 2 14.738 0.659 -8.211 1 131.3 ? O2A GDP 474 A 1 HETATM 9 O O5' GDP . . . B 2 16.042 -1.134 -9.521 1 131.13 ? O5' GDP 474 A 1 HETATM 10 C C5' GDP . . . B 2 15.758 -0.589 -10.808 1 130.89 ? C5' GDP 474 A 1 HETATM 11 C C4' GDP . . . B 2 15.272 -1.702 -11.724 1 130.64 ? C4' GDP 474 A 1 HETATM 12 O O4' GDP . . . B 2 16.256 -2.739 -11.794 1 130.47 ? O4' GDP 474 A 1 HETATM 13 C C3' GDP . . . B 2 13.987 -2.324 -11.202 1 130.67 ? C3' GDP 474 A 1 HETATM 14 O O3' GDP . . . B 2 12.9 -1.991 -12.073 1 130.79 ? O3' GDP 474 A 1 HETATM 15 C C2' GDP . . . B 2 14.246 -3.823 -11.132 1 130.69 ? C2' GDP 474 A 1 HETATM 16 O O2' GDP . . . B 2 13.311 -4.567 -11.922 1 130.85 ? O2' GDP 474 A 1 HETATM 17 C C1' GDP . . . B 2 15.657 -4.031 -11.664 1 130.32 ? C1' GDP 474 A 1 HETATM 18 N N9 GDP . . . B 2 16.452 -4.876 -10.737 1 130.14 ? N9 GDP 474 A 1 HETATM 19 C C8 GDP . . . B 2 16.912 -4.5 -9.529 1 130.14 ? C8 GDP 474 A 1 HETATM 20 N N7 GDP . . . B 2 17.605 -5.503 -8.933 1 130.11 ? N7 GDP 474 A 1 HETATM 21 C C5 GDP . . . B 2 17.6 -6.553 -9.771 1 130.02 ? C5 GDP 474 A 1 HETATM 22 C C6 GDP . . . B 2 18.153 -7.932 -9.761 1 130.17 ? C6 GDP 474 A 1 HETATM 23 O O6 GDP . . . B 2 18.808 -8.364 -8.788 1 130.15 ? O6 GDP 474 A 1 HETATM 24 N N1 GDP . . . B 2 17.921 -8.709 -10.83 1 130.27 ? N1 GDP 474 A 1 HETATM 25 C C2 GDP . . . B 2 17.216 -8.28 -11.898 1 130.2 ? C2 GDP 474 A 1 HETATM 26 N N2 GDP . . . B 2 17.034 -9.135 -12.933 1 130.1 ? N2 GDP 474 A 1 HETATM 27 N N3 GDP . . . B 2 16.684 -7.027 -11.974 1 130.14 ? N3 GDP 474 A 1 HETATM 28 C C4 GDP . . . B 2 16.839 -6.136 -10.961 1 130.04 ? C4 GDP 474 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 519 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #