data_8VEX # _model_server_result.job_id ia4r3IIuuoDBffgVsYclbw _model_server_result.datetime_utc '2025-07-08 15:53:27' _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 8vex # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 8VEX # _exptl.entry_id 8VEX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 297.334 _entity.id 3 _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 8VEX _cell.length_a 99.47 _cell.length_b 136.35 _cell.length_c 177.69 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VEX _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 216 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 208 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 255 _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 247 _struct_conn.ptnr2_symmetry 1_555 _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 2.045 _struct_conn.pdbx_value_order ? # _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 303 n n CS HCS1 MTA sing 304 n n CS HCS2 MTA sing 305 n n CS HCS3 MTA sing 306 n n S5' C5' MTA sing 307 n n C5' C4' MTA sing 308 n n C5' "H5'1" MTA sing 309 n n C5' "H5'2" MTA sing 310 n n C4' O4' MTA sing 311 n n C4' C3' MTA sing 312 n n C4' H4' MTA sing 313 n n O4' C1' MTA sing 314 n n C2' O2' MTA sing 315 n n C2' C3' MTA sing 316 n n C2' C1' MTA sing 317 n n C2' H2' MTA sing 318 n n O2' HO2' MTA sing 319 n n C3' O3' MTA sing 320 n n C3' H3' MTA sing 321 n n O3' H3T MTA sing 322 n n C1' N9 MTA sing 323 n n C1' H1' MTA sing 324 n n N9 C8 MTA sing 325 n y N9 C4 MTA sing 326 n y C8 N7 MTA doub 327 n y C8 H8 MTA sing 328 n n N7 C5 MTA sing 329 n y C5 C6 MTA sing 330 n y C5 C4 MTA doub 331 n y C6 N6 MTA sing 332 n n C6 N1 MTA doub 333 n y N6 H61 MTA sing 334 n n N6 H62 MTA sing 335 n n N1 C2 MTA sing 336 n y C2 N3 MTA doub 337 n y C2 H2 MTA sing 338 n n N3 C4 MTA sing 339 n y # _atom_sites.entry_id 8VEX _atom_sites.fract_transf_matrix[1][1] 0.010053 _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] 0.007334 _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] 0.005628 _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 MTA A 1 701 1 MTA MTA . D 4 A1AAR A 1 702 1 A1AAR LIG . E 5 CL A 1 703 1 CL CL . F 5 CL A 1 704 2 CL CL . G 6 GOL A 1 705 1 GOL GOL . H 7 HOH A 1 801 17 HOH HOH . H 7 HOH A 2 802 34 HOH HOH . H 7 HOH A 3 803 24 HOH HOH . H 7 HOH A 4 804 53 HOH HOH . H 7 HOH A 5 805 18 HOH HOH . H 7 HOH A 6 806 9 HOH HOH . H 7 HOH A 7 807 13 HOH HOH . H 7 HOH A 8 808 25 HOH HOH . H 7 HOH A 9 809 22 HOH HOH . H 7 HOH A 10 810 54 HOH HOH . H 7 HOH A 11 811 47 HOH HOH . H 7 HOH A 12 812 11 HOH HOH . H 7 HOH A 13 813 19 HOH HOH . H 7 HOH A 14 814 32 HOH HOH . H 7 HOH A 15 815 2 HOH HOH . H 7 HOH A 16 816 6 HOH HOH . H 7 HOH A 17 817 28 HOH HOH . H 7 HOH A 18 818 46 HOH HOH . H 7 HOH A 19 819 3 HOH HOH . H 7 HOH A 20 820 16 HOH HOH . H 7 HOH A 21 821 1 HOH HOH . H 7 HOH A 22 822 21 HOH HOH . H 7 HOH A 23 823 4 HOH HOH . H 7 HOH A 24 824 5 HOH HOH . H 7 HOH A 25 825 44 HOH HOH . H 7 HOH A 26 826 26 HOH HOH . H 7 HOH A 27 827 7 HOH HOH . H 7 HOH A 28 828 30 HOH HOH . H 7 HOH A 29 829 35 HOH HOH . H 7 HOH A 30 830 33 HOH HOH . H 7 HOH A 31 831 31 HOH HOH . H 7 HOH A 32 832 40 HOH HOH . H 7 HOH A 33 833 8 HOH HOH . H 7 HOH A 34 834 20 HOH HOH . H 7 HOH A 35 835 50 HOH HOH . H 7 HOH A 36 836 52 HOH HOH . H 7 HOH A 37 837 27 HOH HOH . H 7 HOH A 38 838 58 HOH HOH . H 7 HOH A 39 839 10 HOH HOH . H 7 HOH A 40 840 42 HOH HOH . H 7 HOH A 41 841 15 HOH HOH . H 7 HOH A 42 842 49 HOH HOH . H 7 HOH A 43 843 38 HOH HOH . H 7 HOH A 44 844 41 HOH HOH . H 7 HOH A 45 845 39 HOH HOH . H 7 HOH A 46 846 45 HOH HOH . H 7 HOH A 47 847 57 HOH HOH . H 7 HOH A 48 848 59 HOH HOH . H 7 HOH A 49 849 36 HOH HOH . H 7 HOH A 50 850 48 HOH HOH . H 7 HOH A 51 851 37 HOH HOH . H 7 HOH A 52 852 43 HOH HOH . H 7 HOH A 53 853 56 HOH HOH . H 7 HOH A 54 854 51 HOH HOH . I 7 HOH B 1 401 29 HOH HOH . I 7 HOH B 2 402 23 HOH HOH . I 7 HOH B 3 403 12 HOH HOH . I 7 HOH B 4 404 14 HOH HOH . I 7 HOH B 5 405 55 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 3 21.498 -38.202 -6.177 1 72.05 ? CS MTA 701 A 1 HETATM 2 S S5' MTA . . . C 3 20.183 -39.351 -6.475 1 71.83 ? S5' MTA 701 A 1 HETATM 3 C C5' MTA . . . C 3 18.69 -38.65 -5.815 1 71.15 ? C5' MTA 701 A 1 HETATM 4 C C4' MTA . . . C 3 18.866 -37.585 -4.714 1 70.61 ? C4' MTA 701 A 1 HETATM 5 O O4' MTA . . . C 3 17.853 -36.588 -4.829 1 68.06 ? O4' MTA 701 A 1 HETATM 6 C C2' MTA . . . C 3 17.475 -37.566 -2.715 1 68.12 ? C2' MTA 701 A 1 HETATM 7 O O2' MTA . . . C 3 17.581 -37.276 -1.316 1 78.41 ? O2' MTA 701 A 1 HETATM 8 C C3' MTA . . . C 3 18.767 -38.116 -3.284 1 69.58 ? C3' MTA 701 A 1 HETATM 9 O O3' MTA . . . C 3 19.885 -37.594 -2.556 1 65.89 ? O3' MTA 701 A 1 HETATM 10 C C1' MTA . . . C 3 17.277 -36.327 -3.558 1 65.14 ? C1' MTA 701 A 1 HETATM 11 N N9 MTA . . . C 3 15.849 -36.107 -3.732 1 59.54 ? N9 MTA 701 A 1 HETATM 12 C C8 MTA . . . C 3 15.003 -36.931 -4.351 1 59.18 ? C8 MTA 701 A 1 HETATM 13 N N7 MTA . . . C 3 13.747 -36.422 -4.319 1 59.41 ? N7 MTA 701 A 1 HETATM 14 C C5 MTA . . . C 3 13.803 -35.256 -3.67 1 56.93 ? C5 MTA 701 A 1 HETATM 15 C C6 MTA . . . C 3 12.848 -34.208 -3.284 1 56.57 ? C6 MTA 701 A 1 HETATM 16 N N6 MTA . . . C 3 11.547 -34.3 -3.596 1 57.48 ? N6 MTA 701 A 1 HETATM 17 N N1 MTA . . . C 3 13.315 -33.143 -2.614 1 59.61 ? N1 MTA 701 A 1 HETATM 18 C C2 MTA . . . C 3 14.623 -33.022 -2.288 1 64.8 ? C2 MTA 701 A 1 HETATM 19 N N3 MTA . . . C 3 15.555 -33.946 -2.605 1 62.41 ? N3 MTA 701 A 1 HETATM 20 C C4 MTA . . . C 3 15.2 -35.055 -3.285 1 58.98 ? C4 MTA 701 A 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #