data_5M54 # _model_server_result.job_id -zdRjAOZ5YgptYN3XzIZsg _model_server_result.datetime_utc '2024-11-05 00:31:26' _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 5m54 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 5M54 # _exptl.entry_id 5M54 _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 ? # _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,L,M,N,O _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 J 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 . D GTP 501 1_555 G MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc2 F O2B GTP . D GTP 501 1_555 G MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc3 G MG MG . D MG 502 1_555 N O HOH . D HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc4 G MG MG . D MG 502 1_555 N O HOH . D HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? metalc ? metalc5 G MG MG . D MG 502 1_555 N O HOH . D HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc6 J O2G GTP . A GTP 501 1_555 K MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc7 J O3B GTP . A GTP 501 1_555 K MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc8 J O2B GTP . A GTP 501 1_555 K MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc9 K MG MG . A MG 502 1_555 O O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc10 K MG MG . A MG 502 1_555 O O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? # _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 5M54 _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 F 4 GTP D 1 501 501 GTP GTP . G 5 MG D 1 502 502 MG MG . H 6 GDP E 1 501 501 GDP GDP . I 7 TA1 E 1 502 502 TA1 TA1 . J 4 GTP A 1 501 501 GTP GTP . K 5 MG A 1 502 502 MG MG . L 6 GDP B 1 501 501 GDP GDP . M 7 TA1 B 1 502 502 TA1 TA1 . N 8 HOH D 1 601 602 HOH HOH . N 8 HOH D 2 602 601 HOH HOH . N 8 HOH D 3 603 603 HOH HOH . N 8 HOH D 4 604 604 HOH HOH . O 8 HOH A 1 601 602 HOH HOH . O 8 HOH A 2 602 601 HOH HOH . O 8 HOH A 3 603 603 HOH HOH . O 8 HOH A 4 604 604 HOH HOH . # 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 66.839 42.367 58.269 1 360.78 ? PG GTP 501 D 1 HETATM 2 O O1G GTP . . . F 4 65.385 42.69 58.618 1 360.78 ? O1G GTP 501 D 1 HETATM 3 O O2G GTP . . . F 4 67.777 43.438 58.684 1 360.78 ? O2G GTP 501 D 1 HETATM 4 O O3G GTP . . . F 4 67.192 41.006 58.849 1 360.78 ? O3G GTP 501 D 1 HETATM 5 O O3B GTP . . . F 4 66.925 42.174 56.691 1 360.78 ? O3B GTP 501 D 1 HETATM 6 P PB GTP . . . F 4 68.164 41.817 55.757 1 360.78 ? PB GTP 501 D 1 HETATM 7 O O1B GTP . . . F 4 67.653 41.236 54.452 1 360.78 ? O1B GTP 501 D 1 HETATM 8 O O2B GTP . . . F 4 68.97 43.024 55.492 1 360.78 ? O2B GTP 501 D 1 HETATM 9 O O3A GTP . . . F 4 69.072 40.716 56.462 1 360.78 ? O3A GTP 501 D 1 HETATM 10 P PA GTP . . . F 4 70.651 40.51 56.492 1 360.78 ? PA GTP 501 D 1 HETATM 11 O O1A GTP . . . F 4 71.288 41.67 55.732 1 360.78 ? O1A GTP 501 D 1 HETATM 12 O O2A GTP . . . F 4 71.127 40.517 57.892 1 360.78 ? O2A GTP 501 D 1 HETATM 13 O O5' GTP . . . F 4 70.996 39.17 55.706 1 360.78 ? O5' GTP 501 D 1 HETATM 14 C C5' GTP . . . F 4 72.142 38.338 55.98 1 360.78 ? C5' GTP 501 D 1 HETATM 15 C C4' GTP . . . F 4 72.686 37.817 54.675 1 360.78 ? C4' GTP 501 D 1 HETATM 16 O O4' GTP . . . F 4 73.107 38.928 53.849 1 360.78 ? O4' GTP 501 D 1 HETATM 17 C C3' GTP . . . F 4 73.902 36.895 54.801 1 360.78 ? C3' GTP 501 D 1 HETATM 18 O O3' GTP . . . F 4 73.849 35.835 53.853 1 360.78 ? O3' GTP 501 D 1 HETATM 19 C C2' GTP . . . F 4 75.071 37.843 54.531 1 360.78 ? C2' GTP 501 D 1 HETATM 20 O O2' GTP . . . F 4 76.208 37.166 54.006 1 360.78 ? O2' GTP 501 D 1 HETATM 21 C C1' GTP . . . F 4 74.462 38.764 53.481 1 360.78 ? C1' GTP 501 D 1 HETATM 22 N N9 GTP . . . F 4 75.094 40.092 53.41 1 360.78 ? N9 GTP 501 D 1 HETATM 23 C C8 GTP . . . F 4 74.825 41.193 54.18 1 360.78 ? C8 GTP 501 D 1 HETATM 24 N N7 GTP . . . F 4 75.522 42.251 53.832 1 360.78 ? N7 GTP 501 D 1 HETATM 25 C C5 GTP . . . F 4 76.303 41.814 52.774 1 360.78 ? C5 GTP 501 D 1 HETATM 26 C C6 GTP . . . F 4 77.275 42.493 51.965 1 360.78 ? C6 GTP 501 D 1 HETATM 27 O O6 GTP . . . F 4 77.616 43.671 52.042 1 360.78 ? O6 GTP 501 D 1 HETATM 28 N N1 GTP . . . F 4 77.838 41.666 51.017 1 360.78 ? N1 GTP 501 D 1 HETATM 29 C C2 GTP . . . F 4 77.528 40.346 50.839 1 360.78 ? C2 GTP 501 D 1 HETATM 30 N N2 GTP . . . F 4 78.177 39.697 49.872 1 360.78 ? N2 GTP 501 D 1 HETATM 31 N N3 GTP . . . F 4 76.626 39.701 51.576 1 360.78 ? N3 GTP 501 D 1 HETATM 32 C C4 GTP . . . F 4 76.056 40.484 52.511 1 360.78 ? C4 GTP 501 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #