data_5ND2 # _model_server_result.job_id ZdaGqFQfoveB4MY8WEN5NQ _model_server_result.datetime_utc '2024-11-04 23:20:30' _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 5nd2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":500}' # _entry.id 5ND2 # _exptl.entry_id 5ND2 _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 ? # _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 ? _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 146 C THR 166 1_555 E MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.704 ? metalc ? metalc2 D O3B ADP . C ADP 601 1_555 E MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc3 B OE1 GLN 11 A GLN 11 1_555 G MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.985 ? metalc ? metalc4 F O2G GTP . A GTP 500 1_555 G MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? # _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 218 n n PG O2G GTP sing 219 n n PG O3G GTP sing 220 n n PG O3B GTP sing 221 n n O2G HOG2 GTP sing 222 n n O3G HOG3 GTP sing 223 n n O3B PB GTP sing 224 n n PB O1B GTP doub 225 n n PB O2B GTP sing 226 n n PB O3A GTP sing 227 n n O2B HOB2 GTP sing 228 n n O3A PA GTP sing 229 n n PA O1A GTP doub 230 n n PA O2A GTP sing 231 n n PA O5' GTP sing 232 n n O2A HOA2 GTP sing 233 n n O5' C5' GTP sing 234 n n C5' C4' GTP sing 235 n n C5' H5' GTP sing 236 n n C5' "H5''" GTP sing 237 n n C4' O4' GTP sing 238 n n C4' C3' GTP sing 239 n n C4' H4' GTP sing 240 n n O4' C1' GTP sing 241 n n C3' O3' GTP sing 242 n n C3' C2' GTP sing 243 n n C3' H3' GTP sing 244 n n O3' HO3' GTP sing 245 n n C2' O2' GTP sing 246 n n C2' C1' GTP sing 247 n n C2' H2' GTP sing 248 n n O2' HO2' GTP sing 249 n n C1' N9 GTP sing 250 n n C1' H1' GTP sing 251 n n N9 C8 GTP sing 252 n y N9 C4 GTP sing 253 n y C8 N7 GTP doub 254 n y C8 H8 GTP sing 255 n n N7 C5 GTP sing 256 n y C5 C6 GTP sing 257 n n C5 C4 GTP doub 258 n y C6 O6 GTP doub 259 n n C6 N1 GTP sing 260 n n N1 C2 GTP sing 261 n n N1 HN1 GTP sing 262 n n C2 N2 GTP sing 263 n n C2 N3 GTP doub 264 n n N2 HN21 GTP sing 265 n n N2 HN22 GTP sing 266 n n N3 C4 GTP sing 267 n n # _atom_sites.entry_id 5ND2 _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 ADP C 1 601 504 ADP ADP . E 5 MG C 1 602 505 MG MG . F 6 GTP A 1 500 500 GTP GTP . G 5 MG A 1 501 501 MG MG . H 7 GDP B 1 600 600 GDP GDP . I 8 TA1 B 1 601 601 TA1 TA1 . # 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 6 222.526 218.529 307.211 1 1.67 ? PG GTP 500 A 1 HETATM 2 O O1G GTP . . . F 6 221.093 218.984 307.518 1 1.67 ? O1G GTP 500 A 1 HETATM 3 O O2G GTP . . . F 6 223.568 219.372 307.919 1 1.67 ? O2G GTP 500 A 1 HETATM 4 O O3G GTP . . . F 6 222.552 217.072 307.662 1 1.67 ? O3G GTP 500 A 1 HETATM 5 O O3B GTP . . . F 6 222.938 218.675 305.611 1 1.67 ? O3B GTP 500 A 1 HETATM 6 P PB GTP . . . F 6 224.397 218.295 304.943 1 1.67 ? PB GTP 500 A 1 HETATM 7 O O1B GTP . . . F 6 224.078 217.346 303.8 1 1.67 ? O1B GTP 500 A 1 HETATM 8 O O2B GTP . . . F 6 225.16 219.501 304.652 1 1.67 ? O2B GTP 500 A 1 HETATM 9 O O3A GTP . . . F 6 225.071 217.391 305.975 1 1.67 ? O3A GTP 500 A 1 HETATM 10 P PA GTP . . . F 6 226.482 216.859 306.206 1 1.67 ? PA GTP 500 A 1 HETATM 11 O O1A GTP . . . F 6 227.489 217.937 306.162 1 1.67 ? O1A GTP 500 A 1 HETATM 12 O O2A GTP . . . F 6 226.455 216.046 307.456 1 1.67 ? O2A GTP 500 A 1 HETATM 13 O O5' GTP . . . F 6 226.695 215.802 304.964 1 1.67 ? O5' GTP 500 A 1 HETATM 14 C C5' GTP . . . F 6 227.967 215.18 304.983 1 1.67 ? C5' GTP 500 A 1 HETATM 15 C C4' GTP . . . F 6 228.237 214.197 303.89 1 1.67 ? C4' GTP 500 A 1 HETATM 16 O O4' GTP . . . F 6 228.783 214.867 302.725 1 1.67 ? O4' GTP 500 A 1 HETATM 17 C C3' GTP . . . F 6 229.311 213.244 304.36 1 1.67 ? C3' GTP 500 A 1 HETATM 18 O O3' GTP . . . F 6 229.196 212.018 303.673 1 1.67 ? O3' GTP 500 A 1 HETATM 19 C C2' GTP . . . F 6 230.581 214.008 304.021 1 1.67 ? C2' GTP 500 A 1 HETATM 20 O O2' GTP . . . F 6 231.655 213.085 303.824 1 1.67 ? O2' GTP 500 A 1 HETATM 21 C C1' GTP . . . F 6 230.215 214.764 302.734 1 1.67 ? C1' GTP 500 A 1 HETATM 22 N N9 GTP . . . F 6 230.771 216.122 302.614 1 1.67 ? N9 GTP 500 A 1 HETATM 23 C C8 GTP . . . F 6 230.591 217.17 303.484 1 1.67 ? C8 GTP 500 A 1 HETATM 24 N N7 GTP . . . F 6 231.206 218.262 303.12 1 1.67 ? N7 GTP 500 A 1 HETATM 25 C C5 GTP . . . F 6 231.843 217.922 301.953 1 1.67 ? C5 GTP 500 A 1 HETATM 26 C C6 GTP . . . F 6 232.662 218.678 301.114 1 1.67 ? C6 GTP 500 A 1 HETATM 27 O O6 GTP . . . F 6 232.972 219.858 301.265 1 1.67 ? O6 GTP 500 A 1 HETATM 28 N N1 GTP . . . F 6 233.127 217.961 299.99 1 1.67 ? N1 GTP 500 A 1 HETATM 29 C C2 GTP . . . F 6 232.83 216.642 299.724 1 1.67 ? C2 GTP 500 A 1 HETATM 30 N N2 GTP . . . F 6 233.354 216.131 298.647 1 1.67 ? N2 GTP 500 A 1 HETATM 31 N N3 GTP . . . F 6 232.058 215.902 300.518 1 1.67 ? N3 GTP 500 A 1 HETATM 32 C C4 GTP . . . F 6 231.587 216.59 301.608 1 1.67 ? C4 GTP 500 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 1368 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 32 #