data_5NQT # _model_server_result.job_id VlnJSAYN1gpNSzhZTWpFSQ _model_server_result.datetime_utc '2024-11-22 23:21:03' _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 5nqt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5NQT # _exptl.entry_id 5NQT _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.82 _cell.angle_gamma 90 _cell.entry_id 5NQT _cell.length_a 74.04 _cell.length_b 91.43 _cell.length_c 83.61 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NQT _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 D O1G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc2 D O2B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc3 E MG MG . A MG 502 1_555 G O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc4 E MG MG . A MG 502 1_555 G O HOH . A HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc5 E MG MG . A MG 502 1_555 G O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? # _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 174 n n PG O2G GTP sing 175 n n PG O3G GTP sing 176 n n PG O3B GTP sing 177 n n O2G HOG2 GTP sing 178 n n O3G HOG3 GTP sing 179 n n O3B PB GTP sing 180 n n PB O1B GTP doub 181 n n PB O2B GTP sing 182 n n PB O3A GTP sing 183 n n O2B HOB2 GTP sing 184 n n O3A PA GTP sing 185 n n PA O1A GTP doub 186 n n PA O2A GTP sing 187 n n PA O5' GTP sing 188 n n O2A HOA2 GTP sing 189 n n O5' C5' GTP sing 190 n n C5' C4' GTP sing 191 n n C5' H5' GTP sing 192 n n C5' "H5''" GTP sing 193 n n C4' O4' GTP sing 194 n n C4' C3' GTP sing 195 n n C4' H4' GTP sing 196 n n O4' C1' GTP sing 197 n n C3' O3' GTP sing 198 n n C3' C2' GTP sing 199 n n C3' H3' GTP sing 200 n n O3' HO3' GTP sing 201 n n C2' O2' GTP sing 202 n n C2' C1' GTP sing 203 n n C2' H2' GTP sing 204 n n O2' HO2' GTP sing 205 n n C1' N9 GTP sing 206 n n C1' H1' GTP sing 207 n n N9 C8 GTP sing 208 n y N9 C4 GTP sing 209 n y C8 N7 GTP doub 210 n y C8 H8 GTP sing 211 n n N7 C5 GTP sing 212 n y C5 C6 GTP sing 213 n n C5 C4 GTP doub 214 n y C6 O6 GTP doub 215 n n C6 N1 GTP sing 216 n n N1 C2 GTP sing 217 n n N1 HN1 GTP sing 218 n n C2 N2 GTP sing 219 n n C2 N3 GTP doub 220 n n N2 HN21 GTP sing 221 n n N2 HN22 GTP sing 222 n n N3 C4 GTP sing 223 n n # _atom_sites.entry_id 5NQT _atom_sites.fract_transf_matrix[1][1] 0.013506 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001615 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010937 _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] 0.012046 _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 D 4 GTP A 1 501 1 GTP GTP . E 5 MG A 1 502 503 MG MG . F 6 GDP B 1 501 1 GDP GDP . G 7 HOH A 1 601 65 HOH HOH . G 7 HOH A 2 602 60 HOH HOH . G 7 HOH A 3 603 2 HOH HOH . G 7 HOH A 4 604 59 HOH HOH . G 7 HOH A 5 605 37 HOH HOH . G 7 HOH A 6 606 25 HOH HOH . G 7 HOH A 7 607 20 HOH HOH . G 7 HOH A 8 608 15 HOH HOH . G 7 HOH A 9 609 34 HOH HOH . G 7 HOH A 10 610 69 HOH HOH . G 7 HOH A 11 611 73 HOH HOH . G 7 HOH A 12 612 68 HOH HOH . G 7 HOH A 13 613 11 HOH HOH . G 7 HOH A 14 614 44 HOH HOH . G 7 HOH A 15 615 4 HOH HOH . G 7 HOH A 16 616 3 HOH HOH . G 7 HOH A 17 617 1 HOH HOH . H 7 HOH B 1 601 43 HOH HOH . H 7 HOH B 2 602 29 HOH HOH . H 7 HOH B 3 603 1 HOH HOH . H 7 HOH B 4 604 5 HOH HOH . H 7 HOH B 5 605 42 HOH HOH . H 7 HOH B 6 606 81 HOH HOH . H 7 HOH B 7 607 5 HOH HOH . H 7 HOH B 8 608 2 HOH HOH . I 7 HOH F 1 201 9 HOH HOH . I 7 HOH F 2 202 19 HOH HOH . I 7 HOH F 3 203 6 HOH HOH . I 7 HOH F 4 204 30 HOH HOH . I 7 HOH F 5 205 4 HOH HOH . # 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 . . . D 4 103.922 23.486 23.675 1 52.85 ? PG GTP 501 A 1 HETATM 2 O O1G GTP . . . D 4 103.789 22.009 23.572 1 45.05 ? O1G GTP 501 A 1 HETATM 3 O O2G GTP . . . D 4 104.886 23.944 24.786 1 51.66 ? O2G GTP 501 A 1 HETATM 4 O O3G GTP . . . D 4 102.541 24.237 23.799 1 53.18 ? O3G GTP 501 A 1 HETATM 5 O O3B GTP . . . D 4 104.609 24.078 22.365 1 55.03 ? O3B GTP 501 A 1 HETATM 6 P PB GTP . . . D 4 105.323 23.334 21.157 1 52.61 ? PB GTP 501 A 1 HETATM 7 O O1B GTP . . . D 4 106.128 24.276 20.299 1 44.77 ? O1B GTP 501 A 1 HETATM 8 O O2B GTP . . . D 4 106.151 22.147 21.618 1 50.98 ? O2B GTP 501 A 1 HETATM 9 O O3A GTP . . . D 4 104.041 22.817 20.378 1 49.65 ? O3A GTP 501 A 1 HETATM 10 P PA GTP . . . D 4 103.987 22.341 18.857 1 53.93 ? PA GTP 501 A 1 HETATM 11 O O1A GTP . . . D 4 105.409 22.531 18.215 1 49.99 ? O1A GTP 501 A 1 HETATM 12 O O2A GTP . . . D 4 103.545 20.928 18.819 1 47.39 ? O2A GTP 501 A 1 HETATM 13 O O5' GTP . . . D 4 102.938 23.269 18.084 1 51.81 ? O5' GTP 501 A 1 HETATM 14 C C5' GTP . . . D 4 101.699 22.698 17.624 1 50.94 ? C5' GTP 501 A 1 HETATM 15 C C4' GTP . . . D 4 101.563 23.034 16.166 1 51.1 ? C4' GTP 501 A 1 HETATM 16 O O4' GTP . . . D 4 102.717 22.53 15.454 1 53.06 ? O4' GTP 501 A 1 HETATM 17 C C3' GTP . . . D 4 100.361 22.413 15.47 1 48.53 ? C3' GTP 501 A 1 HETATM 18 O O3' GTP . . . D 4 100.02 23.236 14.368 1 49.5 ? O3' GTP 501 A 1 HETATM 19 C C2' GTP . . . D 4 100.935 21.084 14.961 1 52.74 ? C2' GTP 501 A 1 HETATM 20 O O2' GTP . . . D 4 100.286 20.586 13.804 1 51.86 ? O2' GTP 501 A 1 HETATM 21 C C1' GTP . . . D 4 102.322 21.532 14.524 1 50.33 ? C1' GTP 501 A 1 HETATM 22 N N9 GTP . . . D 4 103.323 20.46 14.558 1 56.05 ? N9 GTP 501 A 1 HETATM 23 C C8 GTP . . . D 4 103.76 19.788 15.672 1 57.21 ? C8 GTP 501 A 1 HETATM 24 N N7 GTP . . . D 4 104.735 18.938 15.429 1 52.1 ? N7 GTP 501 A 1 HETATM 25 C C5 GTP . . . D 4 104.944 19.047 14.068 1 51.05 ? C5 GTP 501 A 1 HETATM 26 C C6 GTP . . . D 4 105.873 18.381 13.193 1 50.77 ? C6 GTP 501 A 1 HETATM 27 O O6 GTP . . . D 4 106.659 17.46 13.477 1 47.19 ? O6 GTP 501 A 1 HETATM 28 N N1 GTP . . . D 4 105.757 18.823 11.888 1 49.2 ? N1 GTP 501 A 1 HETATM 29 C C2 GTP . . . D 4 104.837 19.721 11.432 1 50.02 ? C2 GTP 501 A 1 HETATM 30 N N2 GTP . . . D 4 104.886 20.027 10.136 1 48.14 ? N2 GTP 501 A 1 HETATM 31 N N3 GTP . . . D 4 103.952 20.327 12.218 1 54.42 ? N3 GTP 501 A 1 HETATM 32 C C4 GTP . . . D 4 104.074 19.974 13.514 1 54.13 ? C4 GTP 501 A 1 HETATM 33 H H5' GTP . . . D 4 100.876 23.057 18.238 1 52.26 ? H5' GTP 501 A 1 HETATM 34 H "H5''" GTP . . . D 4 101.763 21.623 17.772 1 49.78 ? "H5''" GTP 501 A 1 HETATM 35 H H4' GTP . . . D 4 101.623 24.108 16 1 51.95 ? H4' GTP 501 A 1 HETATM 36 H H3' GTP . . . D 4 99.496 22.321 16.123 1 48.95 ? H3' GTP 501 A 1 HETATM 37 H HO3' GTP . . . D 4 99.557 24.029 14.743 1 51.23 ? HO3' GTP 501 A 1 HETATM 38 H H2' GTP . . . D 4 100.98 20.357 15.772 1 52.87 ? H2' GTP 501 A 1 HETATM 39 H HO2' GTP . . . D 4 99.324 20.806 13.922 1 52.09 ? HO2' GTP 501 A 1 HETATM 40 H H1' GTP . . . D 4 102.311 21.97 13.528 1 48.22 ? H1' GTP 501 A 1 HETATM 41 H H8 GTP . . . D 4 103.309 19.926 16.653 1 56.8 ? H8 GTP 501 A 1 HETATM 42 H HN1 GTP . . . D 4 106.449 18.467 11.241 1 50.2 ? HN1 GTP 501 A 1 HETATM 43 H HN21 GTP . . . D 4 104.22 20.683 9.745 1 48.37 ? HN21 GTP 501 A 1 HETATM 44 H HN22 GTP . . . D 4 105.587 19.65 9.505 1 48.24 ? HN22 GTP 501 A 1 # _model_server_stats.io_time_ms 86 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 27 _model_server_stats.element_count 44 #