data_5HZK # _model_server_result.job_id k-YVnG_cxYI2bK_D8TqTvQ _model_server_result.datetime_utc '2024-11-16 06:39:49' _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 5hzk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":201}' # _entry.id 5HZK # _exptl.entry_id 5HZK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 90 _cell.entry_id 5HZK _cell.length_a 112.37 _cell.length_b 119.08 _cell.length_c 131.08 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HZK _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F 1 1 C,D,G,H 2 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 ? 3 E N N ? 3 G 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 137 n n PB O2B GDP sing 138 n n PB O3B GDP sing 139 n n PB O3A GDP sing 140 n n O2B HOB2 GDP sing 141 n n O3B HOB3 GDP sing 142 n n O3A PA GDP sing 143 n n PA O1A GDP doub 144 n n PA O2A GDP sing 145 n n PA O5' GDP sing 146 n n O2A HOA2 GDP sing 147 n n O5' C5' GDP sing 148 n n C5' C4' GDP sing 149 n n C5' H5' GDP sing 150 n n C5' "H5''" GDP sing 151 n n C4' O4' GDP sing 152 n n C4' C3' GDP sing 153 n n C4' H4' GDP sing 154 n n O4' C1' GDP sing 155 n n C3' O3' GDP sing 156 n n C3' C2' GDP sing 157 n n C3' H3' GDP sing 158 n n O3' HO3' GDP sing 159 n n C2' O2' GDP sing 160 n n C2' C1' GDP sing 161 n n C2' H2' GDP sing 162 n n O2' HO2' GDP sing 163 n n C1' N9 GDP sing 164 n n C1' H1' GDP sing 165 n n N9 C8 GDP sing 166 n y N9 C4 GDP sing 167 n y C8 N7 GDP doub 168 n y C8 H8 GDP sing 169 n n N7 C5 GDP sing 170 n y C5 C6 GDP sing 171 n n C5 C4 GDP doub 172 n y C6 O6 GDP doub 173 n n C6 N1 GDP sing 174 n n N1 C2 GDP sing 175 n n N1 HN1 GDP sing 176 n n C2 N2 GDP sing 177 n n C2 N3 GDP doub 178 n n N2 HN21 GDP sing 179 n n N2 HN22 GDP sing 180 n n N3 C4 GDP sing 181 n n # _atom_sites.entry_id 5HZK _atom_sites.fract_transf_matrix[1][1] 0.008899 _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] 0.008398 _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] 0.007629 _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 E 3 GDP A 1 200 200 GDP GDP . F 4 FMN B 1 1801 1723 FMN FMN . G 3 GDP C 1 201 201 GDP GDP . H 4 FMN D 1 1801 1724 FMN FMN . # 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 . . . G 3 -34.822 -29.854 52.748 1 54.31 ? PB GDP 201 C 1 HETATM 2 O O1B GDP . . . G 3 -33.44 -30.327 52.357 1 53.04 ? O1B GDP 201 C 1 HETATM 3 O O2B GDP . . . G 3 -35.738 -31.041 52.913 1 52.19 -1 O2B GDP 201 C 1 HETATM 4 O O3B GDP . . . G 3 -34.739 -29.085 54.045 1 57.75 ? O3B GDP 201 C 1 HETATM 5 O O3A GDP . . . G 3 -35.419 -28.902 51.597 1 94.25 ? O3A GDP 201 C 1 HETATM 6 P PA GDP . . . G 3 -34.791 -27.448 51.316 1 54.94 ? PA GDP 201 C 1 HETATM 7 O O1A GDP . . . G 3 -33.288 -27.453 51.467 1 62.11 -1 O1A GDP 201 C 1 HETATM 8 O O2A GDP . . . G 3 -35.411 -26.425 52.234 1 47.88 ? O2A GDP 201 C 1 HETATM 9 O O5' GDP . . . G 3 -35.229 -27.177 49.79 1 83.01 ? O5' GDP 201 C 1 HETATM 10 C C5' GDP . . . G 3 -34.24 -27.001 48.779 1 81.89 ? C5' GDP 201 C 1 HETATM 11 C C4' GDP . . . G 3 -34.822 -26.186 47.634 1 77.26 ? C4' GDP 201 C 1 HETATM 12 O O4' GDP . . . G 3 -36.247 -26.291 47.629 1 72.03 ? O4' GDP 201 C 1 HETATM 13 C C3' GDP . . . G 3 -34.484 -24.713 47.79 1 80.45 ? C3' GDP 201 C 1 HETATM 14 O O3' GDP . . . G 3 -33.462 -24.337 46.863 1 84.1 ? O3' GDP 201 C 1 HETATM 15 C C2' GDP . . . G 3 -35.772 -23.967 47.501 1 82.61 ? C2' GDP 201 C 1 HETATM 16 O O2' GDP . . . G 3 -35.623 -23.132 46.348 1 91.6 ? O2' GDP 201 C 1 HETATM 17 C C1' GDP . . . G 3 -36.821 -25.039 47.244 1 77.55 ? C1' GDP 201 C 1 HETATM 18 N N9 GDP . . . G 3 -38.035 -24.73 48.04 1 76.01 ? N9 GDP 201 C 1 HETATM 19 C C8 GDP . . . G 3 -38.212 -24.977 49.352 1 71.19 ? C8 GDP 201 C 1 HETATM 20 N N7 GDP . . . G 3 -39.438 -24.563 49.764 1 70.48 ? N7 GDP 201 C 1 HETATM 21 C C5 GDP . . . G 3 -40.07 -24.037 48.697 1 71.77 ? C5 GDP 201 C 1 HETATM 22 C C6 GDP . . . G 3 -41.391 -23.419 48.428 1 67.92 ? C6 GDP 201 C 1 HETATM 23 O O6 GDP . . . G 3 -42.24 -23.286 49.335 1 66.95 ? O6 GDP 201 C 1 HETATM 24 N N1 GDP . . . G 3 -41.65 -23.004 47.181 1 69.97 ? N1 GDP 201 C 1 HETATM 25 C C2 GDP . . . G 3 -40.759 -23.132 46.18 1 71.14 ? C2 GDP 201 C 1 HETATM 26 N N2 GDP . . . G 3 -41.102 -22.687 44.947 1 65.7 ? N2 GDP 201 C 1 HETATM 27 N N3 GDP . . . G 3 -39.532 -23.688 46.353 1 77.48 ? N3 GDP 201 C 1 HETATM 28 C C4 GDP . . . G 3 -39.139 -24.15 47.565 1 77.57 ? C4 GDP 201 C 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #