data_5SYF # _model_server_result.job_id u8ZuSBYr_DyV6DB84rj80Q _model_server_result.datetime_utc '2025-07-03 23:00:57' _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 5syf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 5SYF # _exptl.entry_id 5SYF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 24.305 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM ION' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 130-meric 130 'representative helical assembly' 1 ? pentameric 5 'helical asymmetric unit' 2 ? pentameric 5 'helical asymmetric unit, std helical frame' 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F 1 (1-26) A,B,C,D,E,F 2 14 A,B,C,D,E,F 3 H # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] H 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'helical symmetry operation' ? ? -0.971134 -0.238533 0 0.238533 -0.971134 0 0 0 1 746.8677 585.61908 -56.88 3 'helical symmetry operation' ? ? -0.971134 -0.238533 0 0.238533 -0.971134 0 0 0 1 746.8677 585.61908 24.62 4 'helical symmetry operation' ? ? -0.748956 -0.66262 0 0.66262 -0.748956 0 0 0 1 815.11261 367.18146 -47.4 5 'helical symmetry operation' ? ? -0.748956 -0.66262 0 0.66262 -0.748956 0 0 0 1 815.11261 367.18146 34.1 6 'helical symmetry operation' ? ? -0.355107 -0.934826 0 0.934826 -0.355107 0 0 0 1 773.99723 142.05507 -37.92 7 'helical symmetry operation' ? ? -0.355107 -0.934826 0 0.934826 -0.355107 0 0 0 1 773.99723 142.05507 43.58 8 'helical symmetry operation' ? ? 0.120137 -0.992757 0 0.992757 0.120137 0 0 0 1 632.94573 -38.15823 -28.44 9 'helical symmetry operation' ? ? 0.120137 -0.992757 0 0.992757 0.120137 0 0 0 1 632.94573 -38.15823 53.06 10 'helical symmetry operation' ? ? 0.567844 -0.823136 0 0.823136 0.567844 0 0 0 1 424.28891 -132.15128 -18.96 11 'helical symmetry operation' ? ? 0.567844 -0.823136 0 0.823136 0.567844 0 0 0 1 424.28891 -132.15128 62.54 12 'helical symmetry operation' ? ? 0.885394 -0.464842 0 0.464842 0.885394 0 0 0 1 195.85357 -118.37966 -9.48 13 'helical symmetry operation' ? ? 0.885394 -0.464842 0 0.464842 0.885394 0 0 0 1 195.85357 -118.37966 72.02 14 'helical symmetry operation' ? ? 1 0 0 0 1 0 0 0 1 0 0 81.5 15 'helical symmetry operation' ? ? 0.885394 0.464842 0 -0.464842 0.885394 0 0 0 1 -118.37966 195.85357 9.48 16 'helical symmetry operation' ? ? 0.885394 0.464842 0 -0.464842 0.885394 0 0 0 1 -118.37966 195.85357 90.98 17 'helical symmetry operation' ? ? 0.567844 0.823136 0 -0.823136 0.567844 0 0 0 1 -132.15128 424.28891 18.96 18 'helical symmetry operation' ? ? 0.567844 0.823136 0 -0.823136 0.567844 0 0 0 1 -132.15128 424.28891 100.46 19 'helical symmetry operation' ? ? 0.120137 0.992757 0 -0.992757 0.120137 0 0 0 1 -38.15823 632.94573 28.44 20 'helical symmetry operation' ? ? 0.120137 0.992757 0 -0.992757 0.120137 0 0 0 1 -38.15823 632.94573 109.94 21 'helical symmetry operation' ? ? -0.355107 0.934826 0 -0.934826 -0.355107 0 0 0 1 142.05507 773.99723 37.92 22 'helical symmetry operation' ? ? -0.355107 0.934826 0 -0.934826 -0.355107 0 0 0 1 142.05507 773.99723 119.42 23 'helical symmetry operation' ? ? -0.748956 0.66262 0 -0.66262 -0.748956 0 0 0 1 367.18146 815.11261 47.4 24 'helical symmetry operation' ? ? -0.748956 0.66262 0 -0.66262 -0.748956 0 0 0 1 367.18146 815.11261 128.9 25 'helical symmetry operation' ? ? -0.971134 0.238533 0 -0.238533 -0.971134 0 0 0 1 585.61908 746.8677 56.88 26 'helical symmetry operation' ? ? -0.971134 0.238533 0 -0.238533 -0.971134 0 0 0 1 585.61908 746.8677 138.38 # _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 OE2 GLU 71 A GLU 71 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc2 C O3G GTP . A GTP 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc3 C O1B GTP . A GTP 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.742 ? # _chem_comp.formula 'Mg 2' _chem_comp.formula_weight 24.305 _chem_comp.id MG _chem_comp.mon_nstd_flag . _chem_comp.name 'MAGNESIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5SYF _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 C 3 GTP A 1 501 1 GTP GTP . D 4 MG A 1 502 2 MG MG . E 5 GDP B 1 501 1 GDP GDP . F 6 TA1 B 1 502 1 TA1 TA1 . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MG _atom_site.label_atom_id MG _atom_site.label_comp_id MG _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 4 _atom_site.Cartn_x 320.775 _atom_site.Cartn_y 446.13 _atom_site.Cartn_z 347.806 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 17.53 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 502 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #