data_5HNY # _model_server_result.job_id j0m2fIyA70Gd-QcVY4YU_A _model_server_result.datetime_utc '2025-02-27 02:32:19' _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 5hny # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 5HNY # _exptl.entry_id 5HNY _exptl.method 'ELECTRON MICROSCOPY' # _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 ? # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 ? _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 covale ? covale1 C CG2 ILE 316 K ILE 316 1_555 C CG2 THR 331 K THR 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 C CB CYS 318 K CYS 318 1_555 C OG1 THR 328 K THR 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale3 C SG CYS 318 K CYS 318 1_555 C OG1 THR 328 K THR 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.632 ? metalc ? metalc1 D O1G GTP . A GTP 500 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc2 C OG1 THR 108 K THR 108 1_555 H MG MG . K MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? metalc ? metalc3 H MG MG . K MG 401 1_555 I O1B ANP . K ANP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc4 H MG MG . K MG 401 1_555 I O2G ANP . K ANP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? # _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 224 n n PG O2G GTP sing 225 n n PG O3G GTP sing 226 n n PG O3B GTP sing 227 n n O2G HOG2 GTP sing 228 n n O3G HOG3 GTP sing 229 n n O3B PB GTP sing 230 n n PB O1B GTP doub 231 n n PB O2B GTP sing 232 n n PB O3A GTP sing 233 n n O2B HOB2 GTP sing 234 n n O3A PA GTP sing 235 n n PA O1A GTP doub 236 n n PA O2A GTP sing 237 n n PA O5' GTP sing 238 n n O2A HOA2 GTP sing 239 n n O5' C5' GTP sing 240 n n C5' C4' GTP sing 241 n n C5' H5' GTP sing 242 n n C5' "H5''" GTP sing 243 n n C4' O4' GTP sing 244 n n C4' C3' GTP sing 245 n n C4' H4' GTP sing 246 n n O4' C1' GTP sing 247 n n C3' O3' GTP sing 248 n n C3' C2' GTP sing 249 n n C3' H3' GTP sing 250 n n O3' HO3' GTP sing 251 n n C2' O2' GTP sing 252 n n C2' C1' GTP sing 253 n n C2' H2' GTP sing 254 n n O2' HO2' GTP sing 255 n n C1' N9 GTP sing 256 n n C1' H1' GTP sing 257 n n N9 C8 GTP sing 258 n y N9 C4 GTP sing 259 n y C8 N7 GTP doub 260 n y C8 H8 GTP sing 261 n n N7 C5 GTP sing 262 n y C5 C6 GTP sing 263 n n C5 C4 GTP doub 264 n y C6 O6 GTP doub 265 n n C6 N1 GTP sing 266 n n N1 C2 GTP sing 267 n n N1 HN1 GTP sing 268 n n C2 N2 GTP sing 269 n n C2 N3 GTP doub 270 n n N2 HN21 GTP sing 271 n n N2 HN22 GTP sing 272 n n N3 C4 GTP sing 273 n n # _atom_sites.entry_id 5HNY _atom_sites.fract_transf_matrix[1][1] 0.001 _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] 0.001 _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] 0.001 _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 1 500 500 GTP GTP . E 5 MG A 1 501 501 MG MG . F 6 GDP B 1 600 600 GDP GDP . G 7 TA1 B 1 601 601 TA1 TA1 . H 5 MG K 1 401 350 MG MG . I 8 ANP K 1 402 351 ANP ANP . # 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 4 408.733 409.528 624.268 1 29.97 ? PG GTP 500 A 1 HETATM 2 O O1G GTP . . . D 4 409.553 410.58 623.551 1 28.7 ? O1G GTP 500 A 1 HETATM 3 O O2G GTP . . . D 4 409.209 408.101 623.963 1 34.97 ? O2G GTP 500 A 1 HETATM 4 O O3G GTP . . . D 4 407.273 409.529 623.827 1 32.1 ? O3G GTP 500 A 1 HETATM 5 O O3B GTP . . . D 4 408.883 409.948 625.865 1 35.17 ? O3B GTP 500 A 1 HETATM 6 P PB GTP . . . D 4 408.484 411.402 626.532 1 41.4 ? PB GTP 500 A 1 HETATM 7 O O1B GTP . . . D 4 409.679 412.185 626.812 1 41.17 ? O1B GTP 500 A 1 HETATM 8 O O2B GTP . . . D 4 407.546 411.073 627.682 1 42.02 ? O2B GTP 500 A 1 HETATM 9 O O3A GTP . . . D 4 407.561 412.058 625.502 1 39.24 ? O3A GTP 500 A 1 HETATM 10 P PA GTP . . . D 4 407.006 413.459 625.269 1 41.34 ? PA GTP 500 A 1 HETATM 11 O O1A GTP . . . D 4 406.185 413.414 624.026 1 43.37 ? O1A GTP 500 A 1 HETATM 12 O O2A GTP . . . D 4 408.066 414.484 625.305 1 44.48 ? O2A GTP 500 A 1 HETATM 13 O O5' GTP . . . D 4 405.953 413.659 626.519 1 34.27 ? O5' GTP 500 A 1 HETATM 14 C C5' GTP . . . D 4 405.31 414.922 626.498 1 25.47 ? C5' GTP 500 A 1 HETATM 15 C C4' GTP . . . D 4 404.33 415.178 627.598 1 17.26 ? C4' GTP 500 A 1 HETATM 16 O O4' GTP . . . D 4 404.999 415.74 628.757 1 18.2 ? O4' GTP 500 A 1 HETATM 17 C C3' GTP . . . D 4 403.356 416.235 627.13 1 18.14 ? C3' GTP 500 A 1 HETATM 18 O O3' GTP . . . D 4 402.136 416.103 627.826 1 19.98 ? O3' GTP 500 A 1 HETATM 19 C C2' GTP . . . D 4 404.102 417.519 627.46 1 17.5 ? C2' GTP 500 A 1 HETATM 20 O O2' GTP . . . D 4 403.164 418.579 627.661 1 19.33 ? O2' GTP 500 A 1 HETATM 21 C C1' GTP . . . D 4 404.873 417.169 628.743 1 18.43 ? C1' GTP 500 A 1 HETATM 22 N N9 GTP . . . D 4 406.222 417.749 628.852 1 9.96 ? N9 GTP 500 A 1 HETATM 23 C C8 GTP . . . D 4 407.267 417.582 627.975 1 11.6 ? C8 GTP 500 A 1 HETATM 24 N N7 GTP . . . D 4 408.351 418.216 628.331 1 7.31 ? N7 GTP 500 A 1 HETATM 25 C C5 GTP . . . D 4 408.009 418.852 629.499 1 2 ? C5 GTP 500 A 1 HETATM 26 C C6 GTP . . . D 4 408.757 419.686 630.328 1 3.48 ? C6 GTP 500 A 1 HETATM 27 O O6 GTP . . . D 4 409.93 420.015 630.169 1 2.56 ? O6 GTP 500 A 1 HETATM 28 N N1 GTP . . . D 4 408.039 420.143 631.456 1 2 ? N1 GTP 500 A 1 HETATM 29 C C2 GTP . . . D 4 406.728 419.827 631.733 1 2 ? C2 GTP 500 A 1 HETATM 30 N N2 GTP . . . D 4 406.215 420.346 632.81 1 2 ? N2 GTP 500 A 1 HETATM 31 N N3 GTP . . . D 4 405.994 419.039 630.945 1 2 ? N3 GTP 500 A 1 HETATM 32 C C4 GTP . . . D 4 406.683 418.575 629.851 1 3.56 ? C4 GTP 500 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 77 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 1188 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 32 #