data_6RFD # _model_server_result.job_id pSVVzfIGRPZG7xckp8U84A _model_server_result.datetime_utc '2024-12-26 19:01:21' _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 6rfd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 6RFD # _exptl.entry_id 6RFD _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 2 _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 6RFD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RFD _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 PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,K _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 H N 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 F O2G GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc2 F O3B GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc3 F O1B GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc4 F O3A GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc5 F O1A GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc6 F O2A GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc7 H O2G GTP . a GTP 501 1_555 I MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc8 H O3B GTP . a GTP 501 1_555 I MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc9 H O1B GTP . a GTP 501 1_555 I MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc10 H O3A GTP . a GTP 501 1_555 I MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc11 H O1A GTP . a GTP 501 1_555 I MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc12 H O2A GTP . a GTP 501 1_555 I MG MG . a MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? # _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 6RFD _atom_sites.fract_transf_matrix[1][1] 0.01199 _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] 0.007494 _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] 0.00782 _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 F 4 GTP A 1 501 442 GTP GTP . G 5 MG A 1 502 443 MG MG . H 4 GTP a 1 501 442 GTP GTP . I 5 MG a 1 502 443 MG MG . J 6 GDP B 1 501 430 GDP GDP . K 6 GDP b 1 501 430 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 4 43.672 46.67 98.232 1 109.68 ? PG GTP 501 A 1 HETATM 2 O O1G GTP . . . F 4 43.902 45.803 99.419 1 109.68 ? O1G GTP 501 A 1 HETATM 3 O O2G GTP . . . F 4 44.906 46.85 97.357 1 109.68 ? O2G GTP 501 A 1 HETATM 4 O O3G GTP . . . F 4 43.147 48.055 98.576 1 109.68 ? O3G GTP 501 A 1 HETATM 5 O O3B GTP . . . F 4 42.567 46.041 97.278 1 109.68 ? O3B GTP 501 A 1 HETATM 6 P PB GTP . . . F 4 42.102 46.605 95.868 1 109.68 ? PB GTP 501 A 1 HETATM 7 O O1B GTP . . . F 4 42.835 47.852 95.608 1 109.68 ? O1B GTP 501 A 1 HETATM 8 O O2B GTP . . . F 4 40.612 46.866 95.917 1 109.68 ? O2B GTP 501 A 1 HETATM 9 O O3A GTP . . . F 4 42.428 45.532 94.74 1 109.68 ? O3A GTP 501 A 1 HETATM 10 P PA GTP . . . F 4 43.672 44.567 94.51 1 109.68 ? PA GTP 501 A 1 HETATM 11 O O1A GTP . . . F 4 44.55 44.614 95.691 1 109.68 ? O1A GTP 501 A 1 HETATM 12 O O2A GTP . . . F 4 44.426 45.104 93.31 1 109.68 ? O2A GTP 501 A 1 HETATM 13 O O5' GTP . . . F 4 43.166 43.107 94.159 1 109.68 ? O5' GTP 501 A 1 HETATM 14 C C5' GTP . . . F 4 43.737 41.898 94.699 1 109.68 ? C5' GTP 501 A 1 HETATM 15 C C4' GTP . . . F 4 43.889 40.886 93.591 1 109.68 ? C4' GTP 501 A 1 HETATM 16 O O4' GTP . . . F 4 44.976 41.273 92.721 1 109.68 ? O4' GTP 501 A 1 HETATM 17 C C3' GTP . . . F 4 44.187 39.457 94.044 1 109.68 ? C3' GTP 501 A 1 HETATM 18 O O3' GTP . . . F 4 43.434 38.52 93.286 1 109.68 ? O3' GTP 501 A 1 HETATM 19 C C2' GTP . . . F 4 45.687 39.318 93.783 1 109.68 ? C2' GTP 501 A 1 HETATM 20 O O2' GTP . . . F 4 46.057 37.976 93.495 1 109.68 ? O2' GTP 501 A 1 HETATM 21 C C1' GTP . . . F 4 45.846 40.175 92.537 1 109.68 ? C1' GTP 501 A 1 HETATM 22 N N9 GTP . . . F 4 47.207 40.69 92.365 1 109.68 ? N9 GTP 501 A 1 HETATM 23 C C8 GTP . . . F 4 47.845 41.601 93.159 1 109.68 ? C8 GTP 501 A 1 HETATM 24 N N7 GTP . . . F 4 49.064 41.869 92.762 1 109.68 ? N7 GTP 501 A 1 HETATM 25 C C5 GTP . . . F 4 49.236 41.084 91.636 1 109.68 ? C5 GTP 501 A 1 HETATM 26 C C6 GTP . . . F 4 50.347 40.941 90.762 1 109.68 ? C6 GTP 501 A 1 HETATM 27 O O6 GTP . . . F 4 51.43 41.514 90.838 1 109.68 ? O6 GTP 501 A 1 HETATM 28 N N1 GTP . . . F 4 50.1 40.048 89.743 1 109.68 ? N1 GTP 501 A 1 HETATM 29 C C2 GTP . . . F 4 48.933 39.363 89.568 1 109.68 ? C2 GTP 501 A 1 HETATM 30 N N2 GTP . . . F 4 48.864 38.545 88.52 1 109.68 ? N2 GTP 501 A 1 HETATM 31 N N3 GTP . . . F 4 47.885 39.485 90.38 1 109.68 ? N3 GTP 501 A 1 HETATM 32 C C4 GTP . . . F 4 48.103 40.354 91.38 1 109.68 ? C4 GTP 501 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #