data_8YH3 # _model_server_result.job_id JQsIY1xReqEVrDI0j25ZJQ _model_server_result.datetime_utc '2024-11-28 08:28:04' _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 8yh3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":801}' # _entry.id 8YH3 # _exptl.entry_id 8YH3 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 281.268 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N-methyladenosine _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 8YH3 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8YH3 _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 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 _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 x,y,z _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 5 _struct_asym.id F _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 disulf ? disulf1 B SG CYS 108 R CYS 83 1_555 B SG CYS 190 R CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf2 D SG CYS 22 S CYS 22 1_555 D SG CYS 96 S CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? disulf ? disulf3 D SG CYS 159 S CYS 147 1_555 D SG CYS 229 S CYS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? # _chem_comp.formula 'C11 H15 N5 O4' _chem_comp.formula_weight 281.268 _chem_comp.id 6MD _chem_comp.mon_nstd_flag . _chem_comp.name N-methyladenosine _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 C2 N1 6MD doub 1 n y C2 N3 6MD sing 2 n y N1 C6 6MD sing 3 n y N3 C4 6MD doub 4 n y CZ N6 6MD sing 5 n n C6 N6 6MD sing 6 n n C6 C5 6MD doub 7 n y C4 C5 6MD sing 8 n y C4 N9 6MD sing 9 n y C4' O4' 6MD sing 10 n n C4' C5' 6MD sing 11 n n C4' C3' 6MD sing 12 n n O4' C1' 6MD sing 13 n n C5 N7 6MD sing 14 n y C5' O5' 6MD sing 15 n n O3' C3' 6MD sing 16 n n C1' N9 6MD sing 17 n n C1' C2' 6MD sing 18 n n N9 C8 6MD sing 19 n y C3' C2' 6MD sing 20 n n C2' O2' 6MD sing 21 n n N7 C8 6MD doub 22 n y O5' H1 6MD sing 23 n n C5' H2 6MD sing 24 n n C5' H3 6MD sing 25 n n C4' H4 6MD sing 26 n n C3' H5 6MD sing 27 n n O3' H6 6MD sing 28 n n C2' H7 6MD sing 29 n n O2' H8 6MD sing 30 n n C1' H9 6MD sing 31 n n C8 H10 6MD sing 32 n n N6 H11 6MD sing 33 n n C2 H12 6MD sing 34 n n CZ H13 6MD sing 35 n n CZ H14 6MD sing 36 n n CZ H15 6MD sing 37 n n # _atom_sites.entry_id 8YH3 _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 # _pdbx_nonpoly_scheme.asym_id F _pdbx_nonpoly_scheme.entity_id 5 _pdbx_nonpoly_scheme.mon_id 6MD _pdbx_nonpoly_scheme.pdb_strand_id R _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 801 _pdbx_nonpoly_scheme.auth_seq_num 301 _pdbx_nonpoly_scheme.pdb_mon_id 6MD _pdbx_nonpoly_scheme.auth_mon_id m6a _pdbx_nonpoly_scheme.pdb_ins_code . # 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 O O5' 6MD . . . F 5 118.177 111.949 84.313 1 20 ? O5' 6MD 801 R 1 HETATM 2 C C5' 6MD . . . F 5 118.487 110.945 85.234 1 20 ? C5' 6MD 801 R 1 HETATM 3 C C4' 6MD . . . F 5 119.95 110.634 85.141 1 20 ? C4' 6MD 801 R 1 HETATM 4 O O4' 6MD . . . F 5 120.189 109.929 83.921 1 20 ? O4' 6MD 801 R 1 HETATM 5 C C3' 6MD . . . F 5 120.863 111.851 85.158 1 20 ? C3' 6MD 801 R 1 HETATM 6 O O3' 6MD . . . F 5 121.68 111.78 86.316 1 20 ? O3' 6MD 801 R 1 HETATM 7 C C2' 6MD . . . F 5 121.71 111.743 83.887 1 20 ? C2' 6MD 801 R 1 HETATM 8 O O2' 6MD . . . F 5 123.064 111.464 84.197 1 20 ? O2' 6MD 801 R 1 HETATM 9 C C1' 6MD . . . F 5 121.213 110.511 83.164 1 20 ? C1' 6MD 801 R 1 HETATM 10 N N9 6MD . . . F 5 120.675 110.783 81.857 1 20 ? N9 6MD 801 R 1 HETATM 11 C C8 6MD . . . F 5 119.357 110.964 81.558 1 20 ? C8 6MD 801 R 1 HETATM 12 N N7 6MD . . . F 5 119.098 110.952 80.28 1 20 ? N7 6MD 801 R 1 HETATM 13 C C5 6MD . . . F 5 120.332 110.751 79.699 1 20 ? C5 6MD 801 R 1 HETATM 14 C C6 6MD . . . F 5 120.721 110.602 78.387 1 20 ? C6 6MD 801 R 1 HETATM 15 N N6 6MD . . . F 5 119.699 110.615 77.543 1 20 ? N6 6MD 801 R 1 HETATM 16 N N1 6MD . . . F 5 122.01 110.384 78.119 1 20 ? N1 6MD 801 R 1 HETATM 17 C C2 6MD . . . F 5 122.855 110.314 79.147 1 20 ? C2 6MD 801 R 1 HETATM 18 N N3 6MD . . . F 5 122.603 110.436 80.449 1 20 ? N3 6MD 801 R 1 HETATM 19 C C4 6MD . . . F 5 121.313 110.65 80.656 1 20 ? C4 6MD 801 R 1 HETATM 20 C CZ 6MD . . . F 5 119.854 110.491 76.118 1 20 ? CZ 6MD 801 R 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 20 #