data_8CYI # _model_server_result.job_id X8aMyc9mOvPjSC0qkN0Xpg _model_server_result.datetime_utc '2025-03-06 00:51:31' _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 8cyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":802}' # _entry.id 8CYI # _exptl.entry_id 8CYI _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 297.334 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXY-5'-METHYLTHIOADENOSINE" _entity.pdbx_number_of_molecules 1 _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 8CYI _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CYI _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 # _chem_comp.formula 'C11 H15 N5 O3 S' _chem_comp.formula_weight 297.334 _chem_comp.id MTA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 CS S5' MTA sing 235 n n CS HCS1 MTA sing 236 n n CS HCS2 MTA sing 237 n n CS HCS3 MTA sing 238 n n S5' C5' MTA sing 239 n n C5' C4' MTA sing 240 n n C5' "H5'1" MTA sing 241 n n C5' "H5'2" MTA sing 242 n n C4' O4' MTA sing 243 n n C4' C3' MTA sing 244 n n C4' H4' MTA sing 245 n n O4' C1' MTA sing 246 n n C2' O2' MTA sing 247 n n C2' C3' MTA sing 248 n n C2' C1' MTA sing 249 n n C2' H2' MTA sing 250 n n O2' HO2' MTA sing 251 n n C3' O3' MTA sing 252 n n C3' H3' MTA sing 253 n n O3' H3T MTA sing 254 n n C1' N9 MTA sing 255 n n C1' H1' MTA sing 256 n n N9 C8 MTA sing 257 n y N9 C4 MTA sing 258 n y C8 N7 MTA doub 259 n y C8 H8 MTA sing 260 n n N7 C5 MTA sing 261 n y C5 C6 MTA sing 262 n y C5 C4 MTA doub 263 n y C6 N6 MTA sing 264 n n C6 N1 MTA doub 265 n y N6 H61 MTA sing 266 n n N6 H62 MTA sing 267 n n N1 C2 MTA sing 268 n y C2 N3 MTA doub 269 n y C2 H2 MTA sing 270 n n N3 C4 MTA sing 271 n y # _atom_sites.entry_id 8CYI _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 P2R A 1 801 801 P2R P2R . D 4 MTA A 1 802 802 MTA MTA . # 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 C CS MTA . . . D 4 149.083 111.004 119.72 0 74.73 ? CS MTA 802 A 1 HETATM 2 S S5' MTA . . . D 4 148.18 112.3 120.543 0 74.73 ? S5' MTA 802 A 1 HETATM 3 C C5' MTA . . . D 4 148.285 111.697 122.239 0 74.73 ? C5' MTA 802 A 1 HETATM 4 C C4' MTA . . . D 4 147.233 110.644 122.483 0 74.73 ? C4' MTA 802 A 1 HETATM 5 O O4' MTA . . . D 4 147.372 110.127 123.783 0 74.73 ? O4' MTA 802 A 1 HETATM 6 C C2' MTA . . . D 4 145.259 110.978 123.857 0 74.73 ? C2' MTA 802 A 1 HETATM 7 O O2' MTA . . . D 4 143.937 110.668 123.824 0 74.73 ? O2' MTA 802 A 1 HETATM 8 C C3' MTA . . . D 4 145.809 111.267 122.458 0 74.73 ? C3' MTA 802 A 1 HETATM 9 O O3' MTA . . . D 4 145.055 110.602 121.529 0 74.73 ? O3' MTA 802 A 1 HETATM 10 C C1' MTA . . . D 4 146.088 109.727 124.169 0 74.73 ? C1' MTA 802 A 1 HETATM 11 N N9 MTA . . . D 4 146.086 109.4 125.556 0 74.73 ? N9 MTA 802 A 1 HETATM 12 C C8 MTA . . . D 4 146.627 110.168 126.619 0 74.73 ? C8 MTA 802 A 1 HETATM 13 N N7 MTA . . . D 4 146.466 109.561 127.809 0 74.73 ? N7 MTA 802 A 1 HETATM 14 C C5 MTA . . . D 4 145.808 108.374 127.497 0 74.73 ? C5 MTA 802 A 1 HETATM 15 C C6 MTA . . . D 4 145.377 107.341 128.317 0 74.73 ? C6 MTA 802 A 1 HETATM 16 N N6 MTA . . . D 4 145.565 107.375 129.636 0 74.73 ? N6 MTA 802 A 1 HETATM 17 N N1 MTA . . . D 4 144.74 106.251 127.776 0 74.73 ? N1 MTA 802 A 1 HETATM 18 C C2 MTA . . . D 4 144.58 106.28 126.422 0 74.73 ? C2 MTA 802 A 1 HETATM 19 N N3 MTA . . . D 4 144.944 107.205 125.511 0 74.73 ? N3 MTA 802 A 1 HETATM 20 C C4 MTA . . . D 4 145.566 108.254 126.119 0 74.73 ? C4 MTA 802 A 1 HETATM 21 H HCS1 MTA . . . D 4 149.116 111.218 118.653 1 74.73 ? HCS1 MTA 802 A 1 HETATM 22 H HCS2 MTA . . . D 4 150.094 110.965 120.123 1 74.73 ? HCS2 MTA 802 A 1 HETATM 23 H HCS3 MTA . . . D 4 148.578 110.055 119.893 1 74.73 ? HCS3 MTA 802 A 1 HETATM 24 H "H5'1" MTA . . . D 4 149.274 111.283 122.425 1 74.73 ? "H5'1" MTA 802 A 1 HETATM 25 H "H5'2" MTA . . . D 4 148.152 112.522 122.935 1 74.73 ? "H5'2" MTA 802 A 1 HETATM 26 H H4' MTA . . . D 4 147.357 109.887 121.71 1 74.73 ? H4' MTA 802 A 1 HETATM 27 H H2' MTA . . . D 4 145.33 111.802 124.565 1 74.73 ? H2' MTA 802 A 1 HETATM 28 H HO2' MTA . . . D 4 143.623 110.492 124.725 1 74.73 ? HO2' MTA 802 A 1 HETATM 29 H H3' MTA . . . D 4 145.803 112.327 122.21 1 74.73 ? H3' MTA 802 A 1 HETATM 30 H H3T MTA . . . D 4 144.163 110.982 121.504 1 74.73 ? H3T MTA 802 A 1 HETATM 31 H H1' MTA . . . D 4 145.706 108.839 123.667 1 74.73 ? H1' MTA 802 A 1 HETATM 32 H H8 MTA . . . D 4 147.111 111.127 126.488 1 74.73 ? H8 MTA 802 A 1 HETATM 33 H H61 MTA . . . D 4 145.24 106.606 130.215 1 74.73 ? H61 MTA 802 A 1 HETATM 34 H H62 MTA . . . D 4 146.033 108.17 130.062 1 74.73 ? H62 MTA 802 A 1 HETATM 35 H H2 MTA . . . D 4 144.076 105.416 126.01 1 74.73 ? H2 MTA 802 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #