data_3E22 # _model_server_result.job_id 3NnqsD60laZXLMK2jJsaPg _model_server_result.datetime_utc '2024-11-28 13:23:20' _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 3e22 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":600}' # _entry.id 3E22 # _exptl.entry_id 3E22 _exptl.method 'X-RAY DIFFRACTION' # _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 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 3E22 _cell.length_a 324.093 _cell.length_b 324.093 _cell.length_c 53.28 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3E22 _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 _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 ? 6 H N N ? 6 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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 3E22 _atom_sites.fract_transf_matrix[1][1] 0.003086 _atom_sites.fract_transf_matrix[1][2] 0.001781 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003563 _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] 0.018769 _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 GTP A 1 600 600 GTP GTP . G 5 MG A 1 601 601 MG MG . H 6 GDP B 1 600 600 GDP GDP . I 7 LOC B 1 700 700 LOC COL . J 8 TZT B 1 800 800 TZT TZT . K 4 GTP C 1 600 600 GTP GTP . L 5 MG C 1 601 601 MG MG . M 6 GDP D 1 600 600 GDP GDP . N 7 LOC D 1 700 700 LOC COL . # 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 6 281.902 -12.707 33.738 1 95.45 ? PB GDP 600 D 1 HETATM 2 O O1B GDP . . . M 6 280.789 -12.82 34.694 1 95.55 ? O1B GDP 600 D 1 HETATM 3 O O2B GDP . . . M 6 282.314 -11.238 33.652 1 95.39 ? O2B GDP 600 D 1 HETATM 4 O O3B GDP . . . M 6 283.13 -13.523 34.173 1 95.36 ? O3B GDP 600 D 1 HETATM 5 O O3A GDP . . . M 6 281.248 -13.212 32.356 1 95.36 ? O3A GDP 600 D 1 HETATM 6 P PA GDP . . . M 6 281.778 -12.695 30.932 1 95.3 ? PA GDP 600 D 1 HETATM 7 O O1A GDP . . . M 6 281.798 -11.221 30.962 1 95.44 ? O1A GDP 600 D 1 HETATM 8 O O2A GDP . . . M 6 283.162 -13.302 30.626 1 95.57 ? O2A GDP 600 D 1 HETATM 9 O O5' GDP . . . M 6 280.656 -13.082 29.848 1 95.27 ? O5' GDP 600 D 1 HETATM 10 C C5' GDP . . . M 6 280.585 -14.337 29.236 1 95.54 ? C5' GDP 600 D 1 HETATM 11 C C4' GDP . . . M 6 279.677 -14.242 28.015 1 95.64 ? C4' GDP 600 D 1 HETATM 12 O O4' GDP . . . M 6 279.239 -12.916 27.843 1 95.33 ? O4' GDP 600 D 1 HETATM 13 C C3' GDP . . . M 6 280.42 -14.633 26.739 1 95.76 ? C3' GDP 600 D 1 HETATM 14 O O3' GDP . . . M 6 279.96 -15.854 26.2 1 95.74 ? O3' GDP 600 D 1 HETATM 15 C C2' GDP . . . M 6 280.191 -13.526 25.737 1 95.66 ? C2' GDP 600 D 1 HETATM 16 O O2' GDP . . . M 6 279.272 -13.933 24.738 1 95.55 ? O2' GDP 600 D 1 HETATM 17 C C1' GDP . . . M 6 279.651 -12.387 26.589 1 95.54 ? C1' GDP 600 D 1 HETATM 18 N N9 GDP . . . M 6 280.692 -11.337 26.738 1 95.46 ? N9 GDP 600 D 1 HETATM 19 C C8 GDP . . . M 6 281.826 -11.367 27.505 1 95.28 ? C8 GDP 600 D 1 HETATM 20 N N7 GDP . . . M 6 282.485 -10.194 27.334 1 95.31 ? N7 GDP 600 D 1 HETATM 21 C C5 GDP . . . M 6 281.802 -9.418 26.474 1 95.3 ? C5 GDP 600 D 1 HETATM 22 C C6 GDP . . . M 6 282.017 -8.148 25.959 1 95.16 ? C6 GDP 600 D 1 HETATM 23 O O6 GDP . . . M 6 283.149 -7.696 25.994 1 95.19 ? O6 GDP 600 D 1 HETATM 24 N N1 GDP . . . M 6 281.112 -7.597 25.071 1 95.07 ? N1 GDP 600 D 1 HETATM 25 C C2 GDP . . . M 6 279.998 -8.305 24.693 1 95.13 ? C2 GDP 600 D 1 HETATM 26 N N2 GDP . . . M 6 279.307 -7.92 23.629 1 95.01 ? N2 GDP 600 D 1 HETATM 27 N N3 GDP . . . M 6 279.799 -9.566 25.215 1 95.45 ? N3 GDP 600 D 1 HETATM 28 C C4 GDP . . . M 6 280.678 -10.124 26.089 1 95.5 ? C4 GDP 600 D 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #