data_5NM5 # _model_server_result.job_id FgRYAursYR0nQvtnkb_w9A _model_server_result.datetime_utc '2024-11-26 12:05:19' _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 5nm5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5NM5 # _exptl.entry_id 5NM5 _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 97.32 _cell.angle_gamma 90 _cell.entry_id 5NM5 _cell.length_a 72.92 _cell.length_b 85.02 _cell.length_c 84.34 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NM5 _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,J _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 O3G GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc2 D O2B GTP . A GTP 501 1_555 E MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc3 E MG MG . A MG 502 1_555 H O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc4 E MG MG . A MG 502 1_555 H O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc5 E MG MG . A MG 502 1_555 H O HOH . A HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc6 E MG MG . A MG 502 1_555 H O HOH . A HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? # _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 5NM5 _atom_sites.fract_transf_matrix[1][1] 0.013714 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001762 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011762 _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] 0.011954 _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 LOC B 1 502 1 LOC LOC . H 8 HOH A 1 601 38 HOH HOH . H 8 HOH A 2 602 7 HOH HOH . H 8 HOH A 3 603 8 HOH HOH . H 8 HOH A 4 604 13 HOH HOH . H 8 HOH A 5 605 41 HOH HOH . H 8 HOH A 6 606 25 HOH HOH . H 8 HOH A 7 607 18 HOH HOH . H 8 HOH A 8 608 10 HOH HOH . H 8 HOH A 9 609 12 HOH HOH . H 8 HOH A 10 610 29 HOH HOH . H 8 HOH A 11 611 11 HOH HOH . H 8 HOH A 12 612 26 HOH HOH . H 8 HOH A 13 613 33 HOH HOH . H 8 HOH A 14 614 48 HOH HOH . H 8 HOH A 15 615 30 HOH HOH . H 8 HOH A 16 616 3 HOH HOH . H 8 HOH A 17 617 32 HOH HOH . H 8 HOH A 18 618 30 HOH HOH . H 8 HOH A 19 619 10 HOH HOH . H 8 HOH A 20 620 7 HOH HOH . H 8 HOH A 21 621 39 HOH HOH . H 8 HOH A 22 622 41 HOH HOH . H 8 HOH A 23 623 27 HOH HOH . H 8 HOH A 24 624 33 HOH HOH . H 8 HOH A 25 625 4 HOH HOH . H 8 HOH A 26 626 28 HOH HOH . H 8 HOH A 27 627 20 HOH HOH . H 8 HOH A 28 628 40 HOH HOH . H 8 HOH A 29 629 43 HOH HOH . H 8 HOH A 30 630 47 HOH HOH . H 8 HOH A 31 631 50 HOH HOH . I 8 HOH B 1 601 37 HOH HOH . I 8 HOH B 2 602 22 HOH HOH . I 8 HOH B 3 603 36 HOH HOH . I 8 HOH B 4 604 2 HOH HOH . I 8 HOH B 5 605 12 HOH HOH . I 8 HOH B 6 606 6 HOH HOH . I 8 HOH B 7 607 11 HOH HOH . I 8 HOH B 8 608 53 HOH HOH . I 8 HOH B 9 609 16 HOH HOH . I 8 HOH B 10 610 38 HOH HOH . I 8 HOH B 11 611 8 HOH HOH . I 8 HOH B 12 612 1 HOH HOH . I 8 HOH B 13 613 23 HOH HOH . I 8 HOH B 14 614 14 HOH HOH . I 8 HOH B 15 615 37 HOH HOH . I 8 HOH B 16 616 22 HOH HOH . I 8 HOH B 17 617 26 HOH HOH . I 8 HOH B 18 618 46 HOH HOH . I 8 HOH B 19 619 49 HOH HOH . I 8 HOH B 20 620 15 HOH HOH . I 8 HOH B 21 621 18 HOH HOH . I 8 HOH B 22 622 45 HOH HOH . I 8 HOH B 23 623 2 HOH HOH . I 8 HOH B 24 624 52 HOH HOH . I 8 HOH B 25 625 44 HOH HOH . I 8 HOH B 26 626 32 HOH HOH . I 8 HOH B 27 627 5 HOH HOH . J 8 HOH F 1 201 35 HOH HOH . J 8 HOH F 2 202 21 HOH HOH . J 8 HOH F 3 203 23 HOH HOH . J 8 HOH F 4 204 24 HOH HOH . J 8 HOH F 5 205 36 HOH HOH . J 8 HOH F 6 206 51 HOH HOH . J 8 HOH F 7 207 9 HOH HOH . J 8 HOH F 8 208 13 HOH HOH . J 8 HOH F 9 209 3 HOH HOH . J 8 HOH F 10 210 35 HOH HOH . J 8 HOH F 11 211 17 HOH HOH . J 8 HOH F 12 212 42 HOH HOH . J 8 HOH F 13 213 34 HOH HOH . J 8 HOH F 14 214 19 HOH HOH . J 8 HOH F 15 215 29 HOH HOH . J 8 HOH F 16 216 31 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 98.928 24.221 24.672 1 57.48 ? PG GTP 501 A 1 HETATM 2 O O1G GTP . . . D 4 97.537 24.848 24.452 1 48.79 ? O1G GTP 501 A 1 HETATM 3 O O2G GTP . . . D 4 99.713 24.833 25.79 1 51.2 ? O2G GTP 501 A 1 HETATM 4 O O3G GTP . . . D 4 98.951 22.72 24.689 1 52.5 ? O3G GTP 501 A 1 HETATM 5 O O3B GTP . . . D 4 99.719 24.768 23.399 1 65.25 ? O3B GTP 501 A 1 HETATM 6 P PB GTP . . . D 4 100.422 23.99 22.202 1 62.9 ? PB GTP 501 A 1 HETATM 7 O O1B GTP . . . D 4 101.169 24.966 21.378 1 67.53 ? O1B GTP 501 A 1 HETATM 8 O O2B GTP . . . D 4 101.19 22.872 22.811 1 60.23 ? O2B GTP 501 A 1 HETATM 9 O O3A GTP . . . D 4 99.224 23.421 21.351 1 52.38 ? O3A GTP 501 A 1 HETATM 10 P PA GTP . . . D 4 99.077 22.667 19.97 1 57.29 ? PA GTP 501 A 1 HETATM 11 O O1A GTP . . . D 4 100.446 22.923 19.378 1 59.09 ? O1A GTP 501 A 1 HETATM 12 O O2A GTP . . . D 4 98.805 21.232 20.196 1 58.16 ? O2A GTP 501 A 1 HETATM 13 O O5' GTP . . . D 4 97.917 23.397 19.176 1 49.61 ? O5' GTP 501 A 1 HETATM 14 C C5' GTP . . . D 4 96.78 22.715 18.598 1 53.54 ? C5' GTP 501 A 1 HETATM 15 C C4' GTP . . . D 4 96.654 23.104 17.143 1 50.46 ? C4' GTP 501 A 1 HETATM 16 O O4' GTP . . . D 4 97.846 22.639 16.477 1 55.18 ? O4' GTP 501 A 1 HETATM 17 C C3' GTP . . . D 4 95.503 22.444 16.399 1 52.09 ? C3' GTP 501 A 1 HETATM 18 O O3' GTP . . . D 4 95.134 23.189 15.247 1 52.27 ? O3' GTP 501 A 1 HETATM 19 C C2' GTP . . . D 4 96.119 21.115 15.963 1 49.85 ? C2' GTP 501 A 1 HETATM 20 O O2' GTP . . . D 4 95.523 20.615 14.765 1 51.76 ? O2' GTP 501 A 1 HETATM 21 C C1' GTP . . . D 4 97.522 21.573 15.599 1 52.78 ? C1' GTP 501 A 1 HETATM 22 N N9 GTP . . . D 4 98.528 20.524 15.752 1 55.38 ? N9 GTP 501 A 1 HETATM 23 C C8 GTP . . . D 4 99.021 20.004 16.923 1 57.13 ? C8 GTP 501 A 1 HETATM 24 N N7 GTP . . . D 4 100.009 19.163 16.75 1 55.74 ? N7 GTP 501 A 1 HETATM 25 C C5 GTP . . . D 4 100.176 19.122 15.373 1 54.45 ? C5 GTP 501 A 1 HETATM 26 C C6 GTP . . . D 4 101.153 18.462 14.564 1 53.31 ? C6 GTP 501 A 1 HETATM 27 O O6 GTP . . . D 4 102.098 17.774 14.962 1 51.91 ? O6 GTP 501 A 1 HETATM 28 N N1 GTP . . . D 4 101.014 18.762 13.221 1 51.04 ? N1 GTP 501 A 1 HETATM 29 C C2 GTP . . . D 4 100.059 19.593 12.689 1 58.17 ? C2 GTP 501 A 1 HETATM 30 N N2 GTP . . . D 4 100.037 19.718 11.364 1 53.08 ? N2 GTP 501 A 1 HETATM 31 N N3 GTP . . . D 4 99.139 20.219 13.425 1 58.36 ? N3 GTP 501 A 1 HETATM 32 C C4 GTP . . . D 4 99.257 19.948 14.747 1 56.22 ? C4 GTP 501 A 1 HETATM 33 H H5' GTP . . . D 4 95.878 22.922 19.172 1 54.9 ? H5' GTP 501 A 1 HETATM 34 H "H5''" GTP . . . D 4 96.986 21.651 18.7 1 52.56 ? "H5''" GTP 501 A 1 HETATM 35 H H4' GTP . . . D 4 96.681 24.179 16.977 1 48.36 ? H4' GTP 501 A 1 HETATM 36 H H3' GTP . . . D 4 94.62 22.303 17.019 1 53.19 ? H3' GTP 501 A 1 HETATM 37 H HO3' GTP . . . D 4 94.897 24.1 15.56 1 53.92 ? HO3' GTP 501 A 1 HETATM 38 H H2' GTP . . . D 4 96.136 20.401 16.785 1 46.17 ? H2' GTP 501 A 1 HETATM 39 H HO2' GTP . . . D 4 94.771 21.219 14.526 1 50.89 ? HO2' GTP 501 A 1 HETATM 40 H H1' GTP . . . D 4 97.569 21.965 14.584 1 51.83 ? H1' GTP 501 A 1 HETATM 41 H H8 GTP . . . D 4 98.632 20.271 17.903 1 57.8 ? H8 GTP 501 A 1 HETATM 42 H HN1 GTP . . . D 4 101.697 18.339 12.605 1 52.2 ? HN1 GTP 501 A 1 HETATM 43 H HN21 GTP . . . D 4 99.36 20.332 10.924 1 52.39 ? HN21 GTP 501 A 1 HETATM 44 H HN22 GTP . . . D 4 100.649 19.186 10.754 1 54.06 ? HN22 GTP 501 A 1 # _model_server_stats.io_time_ms 145 _model_server_stats.parse_time_ms 60 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 1183 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 44 #