data_8X4O # _model_server_result.job_id 7NpTZt7gCYywLbk6nlhBYA _model_server_result.datetime_utc '2024-11-25 20:12:51' _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 8x4o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 8X4O # _exptl.entry_id 8X4O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.334 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-DEOXY-5'-METHYLTHIOADENOSINE" _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 120 _cell.entry_id 8X4O _cell.length_a 125.539 _cell.length_b 125.539 _cell.length_c 37.14 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8X4O _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F 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 A ND1 HIS 231 A HIS 231 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc2 A NE2 HIS 286 A HIS 286 1_555 G ZN ZN . B ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc3 D ZN ZN . A ZN 302 3_555 B NE2 HIS 286 B HIS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc4 I O HOH . A HOH 405 1_555 G ZN ZN . B ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc5 B ND1 HIS 231 B HIS 231 1_555 G ZN ZN . B ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? # _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 233 n n CS HCS1 MTA sing 234 n n CS HCS2 MTA sing 235 n n CS HCS3 MTA sing 236 n n S5' C5' MTA sing 237 n n C5' C4' MTA sing 238 n n C5' "H5'1" MTA sing 239 n n C5' "H5'2" MTA sing 240 n n C4' O4' MTA sing 241 n n C4' C3' MTA sing 242 n n C4' H4' MTA sing 243 n n O4' C1' MTA sing 244 n n C2' O2' MTA sing 245 n n C2' C3' MTA sing 246 n n C2' C1' MTA sing 247 n n C2' H2' MTA sing 248 n n O2' HO2' MTA sing 249 n n C3' O3' MTA sing 250 n n C3' H3' MTA sing 251 n n O3' H3T MTA sing 252 n n C1' N9 MTA sing 253 n n C1' H1' MTA sing 254 n n N9 C8 MTA sing 255 n y N9 C4 MTA sing 256 n y C8 N7 MTA doub 257 n y C8 H8 MTA sing 258 n n N7 C5 MTA sing 259 n y C5 C6 MTA sing 260 n y C5 C4 MTA doub 261 n y C6 N6 MTA sing 262 n n C6 N1 MTA doub 263 n y N6 H61 MTA sing 264 n n N6 H62 MTA sing 265 n n N1 C2 MTA sing 266 n y C2 N3 MTA doub 267 n y C2 H2 MTA sing 268 n n N3 C4 MTA sing 269 n y # _atom_sites.entry_id 8X4O _atom_sites.fract_transf_matrix[1][1] 0.007966 _atom_sites.fract_transf_matrix[1][2] 0.004599 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009198 _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] 0.026925 _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 2 MTA A 1 301 1 MTA MTA . D 3 ZN A 1 302 3 ZN ZN . E 4 EDO A 1 303 5 EDO EDO . F 2 MTA B 1 301 2 MTA MTA . G 3 ZN B 1 302 4 ZN ZN . H 4 EDO B 1 303 6 EDO EDO . I 5 HOH A 1 401 19 HOH HOH . I 5 HOH A 2 402 20 HOH HOH . I 5 HOH A 3 403 4 HOH HOH . I 5 HOH A 4 404 8 HOH HOH . I 5 HOH A 5 405 7 HOH HOH . I 5 HOH A 6 406 1 HOH HOH . I 5 HOH A 7 407 3 HOH HOH . I 5 HOH A 8 408 2 HOH HOH . J 5 HOH B 1 401 21 HOH HOH . J 5 HOH B 2 402 15 HOH HOH . J 5 HOH B 3 403 16 HOH HOH . J 5 HOH B 4 404 18 HOH HOH . J 5 HOH B 5 405 14 HOH HOH . J 5 HOH B 6 406 6 HOH HOH . J 5 HOH B 7 407 5 HOH HOH . J 5 HOH B 8 408 13 HOH HOH . J 5 HOH B 9 409 12 HOH HOH . J 5 HOH B 10 410 11 HOH HOH . J 5 HOH B 11 411 17 HOH HOH . J 5 HOH B 12 412 10 HOH HOH . J 5 HOH B 13 413 9 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 C CS MTA . . . C 2 53.325 -11.115 -1.535 1 113.45 ? CS MTA 301 A 1 HETATM 2 S S5' MTA . . . C 2 53.695 -9.785 -2.683 1 110.22 ? S5' MTA 301 A 1 HETATM 3 C C5' MTA . . . C 2 53.738 -10.648 -4.274 1 103.71 ? C5' MTA 301 A 1 HETATM 4 C C4' MTA . . . C 2 54.583 -11.903 -4.271 1 113.67 ? C4' MTA 301 A 1 HETATM 5 O O4' MTA . . . C 2 53.998 -12.862 -5.186 1 110.63 ? O4' MTA 301 A 1 HETATM 6 C C2' MTA . . . C 2 55.938 -12.069 -6.222 1 119.67 ? C2' MTA 301 A 1 HETATM 7 O O2' MTA . . . C 2 57.175 -12.437 -6.804 1 117.48 ? O2' MTA 301 A 1 HETATM 8 C C3' MTA . . . C 2 56.033 -11.715 -4.735 1 121 ? C3' MTA 301 A 1 HETATM 9 O O3' MTA . . . C 2 56.911 -12.596 -4.039 1 124.26 ? O3' MTA 301 A 1 HETATM 10 C C1' MTA . . . C 2 54.95 -13.232 -6.154 1 99.42 ? C1' MTA 301 A 1 HETATM 11 N N9 MTA . . . C 2 54.262 -13.488 -7.412 1 83.24 ? N9 MTA 301 A 1 HETATM 12 C C8 MTA . . . C 2 53.801 -12.566 -8.322 1 80.04 ? C8 MTA 301 A 1 HETATM 13 N N7 MTA . . . C 2 53.263 -13.106 -9.387 1 73.55 ? N7 MTA 301 A 1 HETATM 14 C C5 MTA . . . C 2 53.384 -14.469 -9.167 1 69.03 ? C5 MTA 301 A 1 HETATM 15 C C6 MTA . . . C 2 53.01 -15.582 -9.935 1 73.08 ? C6 MTA 301 A 1 HETATM 16 N N6 MTA . . . C 2 52.415 -15.486 -11.12 1 86.4 ? N6 MTA 301 A 1 HETATM 17 N N1 MTA . . . C 2 53.28 -16.81 -9.429 1 77.33 ? N1 MTA 301 A 1 HETATM 18 C C2 MTA . . . C 2 53.892 -16.895 -8.239 1 76.66 ? C2 MTA 301 A 1 HETATM 19 N N3 MTA . . . C 2 54.283 -15.918 -7.426 1 73.04 ? N3 MTA 301 A 1 HETATM 20 C C4 MTA . . . C 2 54.003 -14.717 -7.957 1 74.95 ? C4 MTA 301 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #