data_3DU7 # _model_server_result.job_id exv6qSsNClGiff7Caz8V-A _model_server_result.datetime_utc '2024-11-27 13:21:23' _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 3du7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":603}' # _entry.id 3DU7 # _exptl.entry_id 3DU7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 8 _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 ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 3DU7 _cell.length_a 327.126 _cell.length_b 327.126 _cell.length_c 53.672 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DU7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_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 _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 x,y,z _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 ? 8 L N N ? 8 M N 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 140 n n PB O2B GDP sing 141 n n PB O3B GDP sing 142 n n PB O3A GDP sing 143 n n O2B HOB2 GDP sing 144 n n O3B HOB3 GDP sing 145 n n O3A PA GDP sing 146 n n PA O1A GDP doub 147 n n PA O2A GDP sing 148 n n PA O5' GDP sing 149 n n O2A HOA2 GDP sing 150 n n O5' C5' GDP sing 151 n n C5' C4' GDP sing 152 n n C5' H5' GDP sing 153 n n C5' "H5''" GDP sing 154 n n C4' O4' GDP sing 155 n n C4' C3' GDP sing 156 n n C4' H4' GDP sing 157 n n O4' C1' GDP sing 158 n n C3' O3' GDP sing 159 n n C3' C2' GDP sing 160 n n C3' H3' GDP sing 161 n n O3' HO3' GDP sing 162 n n C2' O2' GDP sing 163 n n C2' C1' GDP sing 164 n n C2' H2' GDP sing 165 n n O2' HO2' GDP sing 166 n n C1' N9 GDP sing 167 n n C1' H1' GDP sing 168 n n N9 C8 GDP sing 169 n y N9 C4 GDP sing 170 n y C8 N7 GDP doub 171 n y C8 H8 GDP sing 172 n n N7 C5 GDP sing 173 n y C5 C6 GDP sing 174 n n C5 C4 GDP doub 175 n y C6 O6 GDP doub 176 n n C6 N1 GDP sing 177 n n N1 C2 GDP sing 178 n n N1 HN1 GDP sing 179 n n C2 N2 GDP sing 180 n n C2 N3 GDP doub 181 n n N2 HN21 GDP sing 182 n n N2 HN22 GDP sing 183 n n N3 C4 GDP sing 184 n n # _atom_sites.entry_id 3DU7 _atom_sites.fract_transf_matrix[1][1] 0.003057 _atom_sites.fract_transf_matrix[1][2] 0.001765 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00353 _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] 0.018632 _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 F 4 MG A 1 500 500 MG MG . G 5 CN2 B 1 700 700 CN2 CN2 . H 6 HOS B 1 800 800 HOS HOS . I 4 MG C 1 501 501 MG MG . J 7 GTP D 1 600 600 GTP GTP . K 7 GTP D 1 601 601 GTP GTP . L 8 GDP D 1 602 602 GDP GDP . M 8 GDP D 1 603 603 GDP GDP . N 5 CN2 D 1 701 701 CN2 CN2 . O 6 HOS D 1 801 801 HOS HOS . # 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 . . . M 8 10.969 43.092 -1.221 1 98.97 ? PB GDP 603 D 1 HETATM 2 O O1B GDP . . . M 8 12.211 43.888 -1.057 1 98.97 ? O1B GDP 603 D 1 HETATM 3 O O2B GDP . . . M 8 11.286 41.613 -0.892 1 98.97 ? O2B GDP 603 D 1 HETATM 4 O O3B GDP . . . M 8 9.777 43.607 -0.368 1 98.97 ? O3B GDP 603 D 1 HETATM 5 O O3A GDP . . . M 8 10.479 43.342 -2.744 1 98.97 ? O3A GDP 603 D 1 HETATM 6 P PA GDP . . . M 8 11.278 42.981 -4.116 1 98.97 ? PA GDP 603 D 1 HETATM 7 O O1A GDP . . . M 8 12.634 42.49 -3.744 1 98.97 ? O1A GDP 603 D 1 HETATM 8 O O2A GDP . . . M 8 10.364 41.968 -4.905 1 98.97 ? O2A GDP 603 D 1 HETATM 9 O O5' GDP . . . M 8 11.475 44.387 -4.936 1 98.97 ? O5' GDP 603 D 1 HETATM 10 C C5' GDP . . . M 8 10.609 44.817 -5.988 1 98.97 ? C5' GDP 603 D 1 HETATM 11 C C4' GDP . . . M 8 11.367 45.491 -7.143 1 98.97 ? C4' GDP 603 D 1 HETATM 12 O O4' GDP . . . M 8 12.553 44.775 -7.413 1 98.97 ? O4' GDP 603 D 1 HETATM 13 C C3' GDP . . . M 8 10.591 45.518 -8.465 1 98.97 ? C3' GDP 603 D 1 HETATM 14 O O3' GDP . . . M 8 10.816 46.746 -9.145 1 98.97 ? O3' GDP 603 D 1 HETATM 15 C C2' GDP . . . M 8 11.133 44.369 -9.292 1 98.97 ? C2' GDP 603 D 1 HETATM 16 O O2' GDP . . . M 8 11.163 44.642 -10.682 1 98.97 ? O2' GDP 603 D 1 HETATM 17 C C1' GDP . . . M 8 12.534 44.267 -8.732 1 98.97 ? C1' GDP 603 D 1 HETATM 18 N N9 GDP . . . M 8 13.014 42.9 -8.714 1 98.97 ? N9 GDP 603 D 1 HETATM 19 C C8 GDP . . . M 8 12.522 41.793 -8.08 1 98.97 ? C8 GDP 603 D 1 HETATM 20 N N7 GDP . . . M 8 13.355 40.775 -8.37 1 98.97 ? N7 GDP 603 D 1 HETATM 21 C C5 GDP . . . M 8 14.338 41.257 -9.161 1 98.97 ? C5 GDP 603 D 1 HETATM 22 C C6 GDP . . . M 8 15.433 40.685 -9.753 1 98.97 ? C6 GDP 603 D 1 HETATM 23 O O6 GDP . . . M 8 15.512 39.461 -9.757 1 98.97 ? O6 GDP 603 D 1 HETATM 24 N N1 GDP . . . M 8 16.276 41.468 -10.526 1 98.97 ? N1 GDP 603 D 1 HETATM 25 C C2 GDP . . . M 8 16.034 42.809 -10.73 1 98.97 ? C2 GDP 603 D 1 HETATM 26 N N2 GDP . . . M 8 16.353 43.306 -11.912 1 98.97 ? N2 GDP 603 D 1 HETATM 27 N N3 GDP . . . M 8 14.946 43.362 -10.125 1 98.97 ? N3 GDP 603 D 1 HETATM 28 C C4 GDP . . . M 8 14.131 42.592 -9.381 1 98.97 ? C4 GDP 603 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 73 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #