data_7NB8 # _model_server_result.job_id K1FAwZy68C7oeNbm6U8frw _model_server_result.datetime_utc '2025-07-15 09:06:24' _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 7nb8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 7NB8 # _exptl.entry_id 7NB8 _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 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 _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 metalc ? metalc1 A OD1 ASP 69 A ASP 69 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? metalc ? metalc2 A OD2 ASP 69 A ASP 69 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc3 A OD1 ASP 98 A ASP 98 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc4 A OD2 ASP 98 A ASP 98 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.823 ? metalc ? metalc5 D O1G GTP . A GTP 500 1_555 E MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc6 B OE1 GLN 11 B GLN 11 1_555 G MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? metalc ? metalc7 B OD2 ASP 67 B ASP 67 1_555 G MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.905 ? metalc ? metalc8 B OE1 GLU 69 B GLU 69 1_555 G MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.811 ? metalc ? metalc9 F O2G G2P . B G2P 500 1_555 G MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc10 F O2B G2P . B G2P 500 1_555 G MG MG . B MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? # _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 181 n n PG O2G GTP sing 182 n n PG O3G GTP sing 183 n n PG O3B GTP sing 184 n n O2G HOG2 GTP sing 185 n n O3G HOG3 GTP sing 186 n n O3B PB GTP sing 187 n n PB O1B GTP doub 188 n n PB O2B GTP sing 189 n n PB O3A GTP sing 190 n n O2B HOB2 GTP sing 191 n n O3A PA GTP sing 192 n n PA O1A GTP doub 193 n n PA O2A GTP sing 194 n n PA O5' GTP sing 195 n n O2A HOA2 GTP sing 196 n n O5' C5' GTP sing 197 n n C5' C4' GTP sing 198 n n C5' H5' GTP sing 199 n n C5' "H5''" GTP sing 200 n n C4' O4' GTP sing 201 n n C4' C3' GTP sing 202 n n C4' H4' GTP sing 203 n n O4' C1' GTP sing 204 n n C3' O3' GTP sing 205 n n C3' C2' GTP sing 206 n n C3' H3' GTP sing 207 n n O3' HO3' GTP sing 208 n n C2' O2' GTP sing 209 n n C2' C1' GTP sing 210 n n C2' H2' GTP sing 211 n n O2' HO2' GTP sing 212 n n C1' N9 GTP sing 213 n n C1' H1' GTP sing 214 n n N9 C8 GTP sing 215 n y N9 C4 GTP sing 216 n y C8 N7 GTP doub 217 n y C8 H8 GTP sing 218 n n N7 C5 GTP sing 219 n y C5 C6 GTP sing 220 n n C5 C4 GTP doub 221 n y C6 O6 GTP doub 222 n n C6 N1 GTP sing 223 n n N1 C2 GTP sing 224 n n N1 HN1 GTP sing 225 n n C2 N2 GTP sing 226 n n C2 N3 GTP doub 227 n n N2 HN21 GTP sing 228 n n N2 HN22 GTP sing 229 n n N3 C4 GTP sing 230 n n # _atom_sites.entry_id 7NB8 _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 GTP A 1 500 500 GTP GTP . E 5 MG A 1 501 501 MG MG . F 6 G2P B 1 500 500 G2P G2P . G 5 MG B 1 501 501 MG MG . # 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 4 205.808 224.477 307.322 1 20 ? PG GTP 500 A 1 HETATM 2 O O1G GTP . . . D 4 207.199 225.129 307.256 1 20 ? O1G GTP 500 A 1 HETATM 3 O O2G GTP . . . D 4 205.966 223.12 307.954 1 20 ? O2G GTP 500 A 1 HETATM 4 O O3G GTP . . . D 4 204.957 224.458 306.078 1 20 ? O3G GTP 500 A 1 HETATM 5 O O3B GTP . . . D 4 204.843 225.21 308.368 1 20 ? O3B GTP 500 A 1 HETATM 6 P PB GTP . . . D 4 205.408 226.11 309.554 1 20 ? PB GTP 500 A 1 HETATM 7 O O1B GTP . . . D 4 206.86 226.54 309.403 1 20 ? O1B GTP 500 A 1 HETATM 8 O O2B GTP . . . D 4 205.122 225.284 310.797 1 20 ? O2B GTP 500 A 1 HETATM 9 O O3A GTP . . . D 4 204.524 227.421 309.454 1 20 ? O3A GTP 500 A 1 HETATM 10 P PA GTP . . . D 4 205.206 228.843 309.29 1 20 ? PA GTP 500 A 1 HETATM 11 O O1A GTP . . . D 4 205.516 229 307.823 1 20 ? O1A GTP 500 A 1 HETATM 12 O O2A GTP . . . D 4 206.355 228.922 310.278 1 20 ? O2A GTP 500 A 1 HETATM 13 O O5' GTP . . . D 4 203.974 229.758 309.701 1 20 ? O5' GTP 500 A 1 HETATM 14 C C5' GTP . . . D 4 204.043 231.075 310.213 1 20 ? C5' GTP 500 A 1 HETATM 15 C C4' GTP . . . D 4 203.091 231.069 311.383 1 20 ? C4' GTP 500 A 1 HETATM 16 O O4' GTP . . . D 4 203.598 231.885 312.425 1 20 ? O4' GTP 500 A 1 HETATM 17 C C3' GTP . . . D 4 201.793 231.744 311.069 1 20 ? C3' GTP 500 A 1 HETATM 18 O O3' GTP . . . D 4 200.876 231.312 312.079 1 20 ? O3' GTP 500 A 1 HETATM 19 C C2' GTP . . . D 4 202.133 233.222 311.14 1 20 ? C2' GTP 500 A 1 HETATM 20 O O2' GTP . . . D 4 201.012 234.008 311.538 1 20 ? O2' GTP 500 A 1 HETATM 21 C C1' GTP . . . D 4 203.244 233.248 312.18 1 20 ? C1' GTP 500 A 1 HETATM 22 N N9 GTP . . . D 4 204.458 233.994 311.774 1 20 ? N9 GTP 500 A 1 HETATM 23 C C8 GTP . . . D 4 205.415 233.638 310.893 1 20 ? C8 GTP 500 A 1 HETATM 24 N N7 GTP . . . D 4 206.651 233.773 311.471 1 20 ? N7 GTP 500 A 1 HETATM 25 C C5 GTP . . . D 4 206.433 234.221 312.709 1 20 ? C5 GTP 500 A 1 HETATM 26 C C6 GTP . . . D 4 207.14 234.409 313.989 1 20 ? C6 GTP 500 A 1 HETATM 27 O O6 GTP . . . D 4 208.367 234.317 314.105 1 20 ? O6 GTP 500 A 1 HETATM 28 N N1 GTP . . . D 4 206.362 234.65 315.038 1 20 ? N1 GTP 500 A 1 HETATM 29 C C2 GTP . . . D 4 205.256 235.397 314.903 1 20 ? C2 GTP 500 A 1 HETATM 30 N N2 GTP . . . D 4 204.474 235.619 315.984 1 20 ? N2 GTP 500 A 1 HETATM 31 N N3 GTP . . . D 4 204.645 235.48 313.704 1 20 ? N3 GTP 500 A 1 HETATM 32 C C4 GTP . . . D 4 205.075 234.739 312.666 1 20 ? C4 GTP 500 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 32 #