data_5CK3 # _model_server_result.job_id YC881cftogKyn1rE_VKS2g _model_server_result.datetime_utc '2025-03-09 02:22:51' _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 5ck3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":401}' # _entry.id 5CK3 # _exptl.entry_id 5CK3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.23 _cell.angle_gamma 90 _cell.entry_id 5CK3 _cell.length_a 88.277 _cell.length_b 83.609 _cell.length_c 90.213 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CK3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I,J 1 1 C,D,K,L 2 1 E,F,M,N 3 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 ? 4 H N N ? 4 L N N ? 4 N N 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 B OG1 THR 24 B THR 64 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc2 B O HIS 65 B HIS 105 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.829 ? metalc ? metalc3 B OG SER 67 B SER 107 1_555 G MG MG . B MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc4 G MG MG . B MG 401 1_555 H O1B GTP . B GTP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc5 G MG MG . B MG 401 1_555 H O1G GTP . B GTP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc6 D OG1 THR 24 D THR 64 1_555 K MG MG . D MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc7 D OG SER 67 D SER 107 1_555 K MG MG . D MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc8 K MG MG . D MG 400 1_555 L O1G GTP . D GTP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc9 K MG MG . D MG 400 1_555 L O3G GTP . D GTP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? metalc ? metalc10 K MG MG . D MG 400 1_555 L O1B GTP . D GTP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc11 F OG1 THR 24 F THR 64 1_555 M MG MG . F MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc12 F OG SER 67 F SER 107 1_555 M MG MG . F MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc13 F OD1 ASP 106 F ASP 146 1_555 M MG MG . F MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc14 F OD2 ASP 106 F ASP 146 1_555 M MG MG . F MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc15 F O THR 107 F THR 147 1_555 M MG MG . F MG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc16 M MG MG . F MG 400 1_555 N O3G GTP . F GTP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc17 M MG MG . F MG 400 1_555 N O1B GTP . F GTP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PG O1G GTP doub 142 n n PG O2G GTP sing 143 n n PG O3G GTP sing 144 n n PG O3B GTP sing 145 n n O2G HOG2 GTP sing 146 n n O3G HOG3 GTP sing 147 n n O3B PB GTP sing 148 n n PB O1B GTP doub 149 n n PB O2B GTP sing 150 n n PB O3A GTP sing 151 n n O2B HOB2 GTP sing 152 n n O3A PA GTP sing 153 n n PA O1A GTP doub 154 n n PA O2A GTP sing 155 n n PA O5' GTP sing 156 n n O2A HOA2 GTP sing 157 n n O5' C5' GTP sing 158 n n C5' C4' GTP sing 159 n n C5' H5' GTP sing 160 n n C5' "H5''" GTP sing 161 n n C4' O4' GTP sing 162 n n C4' C3' GTP sing 163 n n C4' H4' GTP sing 164 n n O4' C1' GTP sing 165 n n C3' O3' GTP sing 166 n n C3' C2' GTP sing 167 n n C3' H3' GTP sing 168 n n O3' HO3' GTP sing 169 n n C2' O2' GTP sing 170 n n C2' C1' GTP sing 171 n n C2' H2' GTP sing 172 n n O2' HO2' GTP sing 173 n n C1' N9 GTP sing 174 n n C1' H1' GTP sing 175 n n N9 C8 GTP sing 176 n y N9 C4 GTP sing 177 n y C8 N7 GTP doub 178 n y C8 H8 GTP sing 179 n n N7 C5 GTP sing 180 n y C5 C6 GTP sing 181 n n C5 C4 GTP doub 182 n y C6 O6 GTP doub 183 n n C6 N1 GTP sing 184 n n N1 C2 GTP sing 185 n n N1 HN1 GTP sing 186 n n C2 N2 GTP sing 187 n n C2 N3 GTP doub 188 n n N2 HN21 GTP sing 189 n n N2 HN22 GTP sing 190 n n N3 C4 GTP sing 191 n n # _atom_sites.entry_id 5CK3 _atom_sites.fract_transf_matrix[1][1] 0.011328 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003084 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01196 _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] 0.011488 _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 G 3 MG B 1 401 400 MG MG . H 4 GTP B 1 402 401 GTP GTP . I 5 GOL B 1 403 1 GOL GOL . J 6 SO4 B 1 404 1 SO4 SO4 . K 3 MG D 1 400 400 MG MG . L 4 GTP D 1 401 401 GTP GTP . M 3 MG F 1 400 400 MG MG . N 4 GTP F 1 401 401 GTP GTP . # 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 PG GTP . . . N 4 52.708 5.968 153.716 1 105.97 ? PG GTP 401 F 1 HETATM 2 O O1G GTP . . . N 4 51.804 5.801 152.517 1 105.76 ? O1G GTP 401 F 1 HETATM 3 O O2G GTP . . . N 4 52.473 7.316 154.356 1 99.73 ? O2G GTP 401 F 1 HETATM 4 O O3G GTP . . . N 4 52.455 4.885 154.739 1 99.99 ? O3G GTP 401 F 1 HETATM 5 O O3B GTP . . . N 4 54.232 5.922 153.204 1 104.17 ? O3B GTP 401 F 1 HETATM 6 P PB GTP . . . N 4 55.069 4.556 153.327 1 108.41 ? PB GTP 401 F 1 HETATM 7 O O1B GTP . . . N 4 54.156 3.352 153.352 1 100.34 ? O1B GTP 401 F 1 HETATM 8 O O2B GTP . . . N 4 55.918 4.628 154.568 1 109.98 ? O2B GTP 401 F 1 HETATM 9 O O3A GTP . . . N 4 55.993 4.487 152.009 1 102.96 ? O3A GTP 401 F 1 HETATM 10 P PA GTP . . . N 4 55.366 4.292 150.54 1 95.08 ? PA GTP 401 F 1 HETATM 11 O O1A GTP . . . N 4 55.372 2.817 150.221 1 98.62 ? O1A GTP 401 F 1 HETATM 12 O O2A GTP . . . N 4 53.973 4.863 150.421 1 96.94 ? O2A GTP 401 F 1 HETATM 13 O O5' GTP . . . N 4 56.387 5.045 149.55 1 86.01 ? O5' GTP 401 F 1 HETATM 14 C C5' GTP . . . N 4 57.622 4.422 149.301 1 93.92 ? C5' GTP 401 F 1 HETATM 15 C C4' GTP . . . N 4 58.543 5.31 148.484 1 99.54 ? C4' GTP 401 F 1 HETATM 16 O O4' GTP . . . N 4 59.862 5.072 148.924 1 103.61 ? O4' GTP 401 F 1 HETATM 17 C C3' GTP . . . N 4 58.476 4.917 147.021 1 109.22 ? C3' GTP 401 F 1 HETATM 18 O O3' GTP . . . N 4 58.276 6.07 146.24 1 111.41 ? O3' GTP 401 F 1 HETATM 19 C C2' GTP . . . N 4 59.825 4.319 146.684 1 110.58 ? C2' GTP 401 F 1 HETATM 20 O O2' GTP . . . N 4 60.343 4.931 145.525 1 108.71 ? O2' GTP 401 F 1 HETATM 21 C C1' GTP . . . N 4 60.705 4.589 147.896 1 108.7 ? C1' GTP 401 F 1 HETATM 22 N N9 GTP . . . N 4 61.329 3.342 148.379 1 112.41 ? N9 GTP 401 F 1 HETATM 23 C C8 GTP . . . N 4 61.259 2.866 149.662 1 114.47 ? C8 GTP 401 F 1 HETATM 24 N N7 GTP . . . N 4 61.957 1.715 149.739 1 114.82 ? N7 GTP 401 F 1 HETATM 25 C C5 GTP . . . N 4 62.482 1.449 148.526 1 111.7 ? C5 GTP 401 F 1 HETATM 26 C C6 GTP . . . N 4 63.272 0.406 148.069 1 111.14 ? C6 GTP 401 F 1 HETATM 27 O O6 GTP . . . N 4 63.606 -0.488 148.841 1 111.11 ? O6 GTP 401 F 1 HETATM 28 N N1 GTP . . . N 4 63.676 0.38 146.753 1 117.19 ? N1 GTP 401 F 1 HETATM 29 C C2 GTP . . . N 4 63.289 1.394 145.901 1 119.17 ? C2 GTP 401 F 1 HETATM 30 N N2 GTP . . . N 4 63.677 1.37 144.628 1 121.78 ? N2 GTP 401 F 1 HETATM 31 N N3 GTP . . . N 4 62.503 2.432 146.365 1 115.92 ? N3 GTP 401 F 1 HETATM 32 C C4 GTP . . . N 4 62.102 2.463 147.659 1 112.07 ? C4 GTP 401 F 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #