data_3GEH # _model_server_result.job_id kTcWjEr-bjxKEITj7GglGw _model_server_result.datetime_utc '2024-12-21 14:25:14' _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 3geh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":460}' # _entry.id 3GEH # _exptl.entry_id 3GEH _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 3GEH _cell.length_a 124.279 _cell.length_b 124.279 _cell.length_c 174.701 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GEH _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 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,D,E _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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 87.3505 # _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 # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OE2 GLU 352 A GLU 349 1_555 D ZN ZN . A ZN 462 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc2 B O3B GDP . A GDP 460 1_555 E ZN ZN . A ZN 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? # _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 3GEH _atom_sites.fract_transf_matrix[1][1] 0.008046 _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] 0.008046 _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] 0.005724 _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 1 460 460 GDP GDP . C 3 FON A 1 461 461 FON FON . D 4 ZN A 1 462 462 ZN ZN . E 4 ZN A 1 463 463 ZN ZN . # 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 -45.185 24.928 34.134 1 93.54 ? PB GDP 460 A 1 HETATM 2 O O1B GDP . . . B 2 -44.929 25.662 32.841 1 93.45 ? O1B GDP 460 A 1 HETATM 3 O O2B GDP . . . B 2 -45.779 25.868 35.158 1 93.8 ? O2B GDP 460 A 1 HETATM 4 O O3B GDP . . . B 2 -43.885 24.399 34.692 1 93.89 ? O3B GDP 460 A 1 HETATM 5 O O3A GDP . . . B 2 -46.195 23.715 33.835 1 93.4 ? O3A GDP 460 A 1 HETATM 6 P PA GDP . . . B 2 -46.252 22.427 34.798 1 93.48 ? PA GDP 460 A 1 HETATM 7 O O1A GDP . . . B 2 -45.143 21.458 34.468 1 93.02 ? O1A GDP 460 A 1 HETATM 8 O O2A GDP . . . B 2 -46.186 22.854 36.245 1 93.56 ? O2A GDP 460 A 1 HETATM 9 O O5' GDP . . . B 2 -47.69 21.788 34.455 1 93.47 ? O5' GDP 460 A 1 HETATM 10 C C5' GDP . . . B 2 -48.888 22.445 34.871 1 93.08 ? C5' GDP 460 A 1 HETATM 11 C C4' GDP . . . B 2 -49.999 21.426 35.102 1 92.98 ? C4' GDP 460 A 1 HETATM 12 O O4' GDP . . . B 2 -50.429 20.877 33.853 1 92.66 ? O4' GDP 460 A 1 HETATM 13 C C3' GDP . . . B 2 -49.549 20.27 35.984 1 93.01 ? C3' GDP 460 A 1 HETATM 14 O O3' GDP . . . B 2 -50.379 20.199 37.146 1 93.56 ? O3' GDP 460 A 1 HETATM 15 C C2' GDP . . . B 2 -49.705 19.022 35.135 1 92.75 ? C2' GDP 460 A 1 HETATM 16 O O2' GDP . . . B 2 -50.39 17.986 35.843 1 93.28 ? O2' GDP 460 A 1 HETATM 17 C C1' GDP . . . B 2 -50.504 19.453 33.914 1 91.92 ? C1' GDP 460 A 1 HETATM 18 N N9 GDP . . . B 2 -49.901 18.859 32.698 1 91.6 ? N9 GDP 460 A 1 HETATM 19 C C8 GDP . . . B 2 -48.638 19.054 32.276 1 91.59 ? C8 GDP 460 A 1 HETATM 20 N N7 GDP . . . B 2 -48.388 18.367 31.134 1 91.54 ? N7 GDP 460 A 1 HETATM 21 C C5 GDP . . . B 2 -49.513 17.713 30.809 1 91.43 ? C5 GDP 460 A 1 HETATM 22 C C6 GDP . . . B 2 -49.932 16.802 29.72 1 91.63 ? C6 GDP 460 A 1 HETATM 23 O O6 GDP . . . B 2 -49.137 16.485 28.81 1 91.64 ? O6 GDP 460 A 1 HETATM 24 N N1 GDP . . . B 2 -51.189 16.338 29.74 1 91.53 ? N1 GDP 460 A 1 HETATM 25 C C2 GDP . . . B 2 -52.062 16.667 30.709 1 91.35 ? C2 GDP 460 A 1 HETATM 26 N N2 GDP . . . B 2 -53.309 16.15 30.649 1 91.47 ? N2 GDP 460 A 1 HETATM 27 N N3 GDP . . . B 2 -51.745 17.496 31.74 1 91.25 ? N3 GDP 460 A 1 HETATM 28 C C4 GDP . . . B 2 -50.509 18.039 31.841 1 91.32 ? C4 GDP 460 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 28 #