data_3J8Y # _model_server_result.job_id PbpSzOCWx2rLd7ZDRMHDFw _model_server_result.datetime_utc '2024-10-20 19:31:29' _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 3j8y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":600}' # _entry.id 3J8Y # _exptl.entry_id 3J8Y _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.18 _entity.id 6 _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 90 _cell.angle_gamma 90 _cell.entry_id 3J8Y _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3J8Y _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _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 _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 6 _struct_asym.id F _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 OG1 THR 92 K THR 92 1_555 E MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc2 A OG SER 202 K SER 202 1_555 E MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc3 D O3G ATP . K ATP 501 1_555 E MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.737 ? metalc ? metalc4 D O2B ATP . K ATP 501 1_555 E MG MG . K MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.803 ? # _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 223 n n PG O2G GTP sing 224 n n PG O3G GTP sing 225 n n PG O3B GTP sing 226 n n O2G HOG2 GTP sing 227 n n O3G HOG3 GTP sing 228 n n O3B PB GTP sing 229 n n PB O1B GTP doub 230 n n PB O2B GTP sing 231 n n PB O3A GTP sing 232 n n O2B HOB2 GTP sing 233 n n O3A PA GTP sing 234 n n PA O1A GTP doub 235 n n PA O2A GTP sing 236 n n PA O5' GTP sing 237 n n O2A HOA2 GTP sing 238 n n O5' C5' GTP sing 239 n n C5' C4' GTP sing 240 n n C5' H5' GTP sing 241 n n C5' "H5''" GTP sing 242 n n C4' O4' GTP sing 243 n n C4' C3' GTP sing 244 n n C4' H4' GTP sing 245 n n O4' C1' GTP sing 246 n n C3' O3' GTP sing 247 n n C3' C2' GTP sing 248 n n C3' H3' GTP sing 249 n n O3' HO3' GTP sing 250 n n C2' O2' GTP sing 251 n n C2' C1' GTP sing 252 n n C2' H2' GTP sing 253 n n O2' HO2' GTP sing 254 n n C1' N9 GTP sing 255 n n C1' H1' GTP sing 256 n n N9 C8 GTP sing 257 n y N9 C4 GTP sing 258 n y C8 N7 GTP doub 259 n y C8 H8 GTP sing 260 n n N7 C5 GTP sing 261 n y C5 C6 GTP sing 262 n n C5 C4 GTP doub 263 n y C6 O6 GTP doub 264 n n C6 N1 GTP sing 265 n n N1 C2 GTP sing 266 n n N1 HN1 GTP sing 267 n n C2 N2 GTP sing 268 n n C2 N3 GTP doub 269 n n N2 HN21 GTP sing 270 n n N2 HN22 GTP sing 271 n n N3 C4 GTP sing 272 n n # _atom_sites.entry_id 3J8Y _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 ATP K 1 501 501 ATP ATP . E 5 MG K 1 502 500 MG MG . F 6 GTP A 1 600 600 GTP GTP . G 7 GDP B 1 501 501 GDP GDP . # 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 . . . F 6 -47.454 108.163 -31.917 1 0 ? PG GTP 600 A 1 HETATM 2 O O1G GTP . . . F 6 -46.349 108.911 -32.474 1 0 ? O1G GTP 600 A 1 HETATM 3 O O2G GTP . . . F 6 -46.941 106.892 -31.234 1 0 ? O2G GTP 600 A 1 HETATM 4 O O3G GTP . . . F 6 -48.262 109.035 -30.958 1 0 ? O3G GTP 600 A 1 HETATM 5 O O3B GTP . . . F 6 -48.539 107.787 -33.022 1 0 ? O3B GTP 600 A 1 HETATM 6 P PB GTP . . . F 6 -47.971 107.2 -34.374 1 0 ? PB GTP 600 A 1 HETATM 7 O O1B GTP . . . F 6 -47.575 108.429 -35.151 1 0 ? O1B GTP 600 A 1 HETATM 8 O O2B GTP . . . F 6 -46.947 106.078 -34.126 1 0 ? O2B GTP 600 A 1 HETATM 9 O O3A GTP . . . F 6 -49.497 106.811 -34.719 1 0 ? O3A GTP 600 A 1 HETATM 10 P PA GTP . . . F 6 -49.383 105.907 -35.856 1 0 ? PA GTP 600 A 1 HETATM 11 O O1A GTP . . . F 6 -48.949 106.576 -37.12 1 0 ? O1A GTP 600 A 1 HETATM 12 O O2A GTP . . . F 6 -48.726 104.634 -35.46 1 0 ? O2A GTP 600 A 1 HETATM 13 O O5' GTP . . . F 6 -50.887 105.607 -36.049 1 0 ? O5' GTP 600 A 1 HETATM 14 C C5' GTP . . . F 6 -51.648 104.719 -35.2 1 0 ? C5' GTP 600 A 1 HETATM 15 C C4' GTP . . . F 6 -52.882 104.236 -35.877 1 0 ? C4' GTP 600 A 1 HETATM 16 O O4' GTP . . . F 6 -52.621 103.088 -36.751 1 0 ? O4' GTP 600 A 1 HETATM 17 C C3' GTP . . . F 6 -53.663 103.676 -34.756 1 0 ? C3' GTP 600 A 1 HETATM 18 O O3' GTP . . . F 6 -55.068 103.662 -35.057 1 0 ? O3' GTP 600 A 1 HETATM 19 C C2' GTP . . . F 6 -53.033 102.22 -34.54 1 0 ? C2' GTP 600 A 1 HETATM 20 O O2' GTP . . . F 6 -53.885 101.236 -34.008 1 0 ? O2' GTP 600 A 1 HETATM 21 C C1' GTP . . . F 6 -52.726 101.902 -35.991 1 0 ? C1' GTP 600 A 1 HETATM 22 N N9 GTP . . . F 6 -51.712 100.924 -36.224 1 0 ? N9 GTP 600 A 1 HETATM 23 C C8 GTP . . . F 6 -50.836 100.295 -35.381 1 0 ? C8 GTP 600 A 1 HETATM 24 N N7 GTP . . . F 6 -50.074 99.37 -35.933 1 0 ? N7 GTP 600 A 1 HETATM 25 C C5 GTP . . . F 6 -50.411 99.572 -37.262 1 0 ? C5 GTP 600 A 1 HETATM 26 C C6 GTP . . . F 6 -49.916 98.895 -38.375 1 0 ? C6 GTP 600 A 1 HETATM 27 O O6 GTP . . . F 6 -48.946 98.206 -38.433 1 0 ? O6 GTP 600 A 1 HETATM 28 N N1 GTP . . . F 6 -50.651 99.135 -39.537 1 0 ? N1 GTP 600 A 1 HETATM 29 C C2 GTP . . . F 6 -51.68 100.02 -39.561 1 0 ? C2 GTP 600 A 1 HETATM 30 N N2 GTP . . . F 6 -52.418 99.909 -40.681 1 0 ? N2 GTP 600 A 1 HETATM 31 N N3 GTP . . . F 6 -52.17 100.668 -38.557 1 0 ? N3 GTP 600 A 1 HETATM 32 C C4 GTP . . . F 6 -51.489 100.41 -37.412 1 0 ? C4 GTP 600 A 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 30 _model_server_stats.element_count 32 #