data_8VEU # _model_server_result.job_id EHSn9sZYi6adI30oO05TrA _model_server_result.datetime_utc '2024-11-05 04:13:30' _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 8veu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 8VEU # _exptl.entry_id 8VEU _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 8VEU _cell.length_a 103.37 _cell.length_b 138.79 _cell.length_c 179.71 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8VEU _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z _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 2.029 _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 298 n n CS HCS1 MTA sing 299 n n CS HCS2 MTA sing 300 n n CS HCS3 MTA sing 301 n n S5' C5' MTA sing 302 n n C5' C4' MTA sing 303 n n C5' "H5'1" MTA sing 304 n n C5' "H5'2" MTA sing 305 n n C4' O4' MTA sing 306 n n C4' C3' MTA sing 307 n n C4' H4' MTA sing 308 n n O4' C1' MTA sing 309 n n C2' O2' MTA sing 310 n n C2' C3' MTA sing 311 n n C2' C1' MTA sing 312 n n C2' H2' MTA sing 313 n n O2' HO2' MTA sing 314 n n C3' O3' MTA sing 315 n n C3' H3' MTA sing 316 n n O3' H3T MTA sing 317 n n C1' N9 MTA sing 318 n n C1' H1' MTA sing 319 n n N9 C8 MTA sing 320 n y N9 C4 MTA sing 321 n y C8 N7 MTA doub 322 n y C8 H8 MTA sing 323 n n N7 C5 MTA sing 324 n y C5 C6 MTA sing 325 n y C5 C4 MTA doub 326 n y C6 N6 MTA sing 327 n n C6 N1 MTA doub 328 n y N6 H61 MTA sing 329 n n N6 H62 MTA sing 330 n n N1 C2 MTA sing 331 n y C2 N3 MTA doub 332 n y C2 H2 MTA sing 333 n n N3 C4 MTA sing 334 n y # _atom_sites.entry_id 8VEU _atom_sites.fract_transf_matrix[1][1] 0.009674 _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] 0.007205 _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] 0.005565 _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 A1AAT A 1 702 1 A1AAT LIG . E 5 EDO A 1 703 1 EDO EDO . F 5 EDO A 1 704 2 EDO EDO . G 5 EDO A 1 705 4 EDO EDO . H 5 EDO A 1 706 6 EDO EDO . I 5 EDO A 1 707 7 EDO EDO . J 5 EDO A 1 708 8 EDO EDO . K 5 EDO A 1 709 9 EDO EDO . L 5 EDO A 1 710 10 EDO EDO . M 5 EDO A 1 711 11 EDO EDO . N 5 EDO A 1 712 12 EDO EDO . O 5 EDO A 1 713 13 EDO EDO . P 5 EDO A 1 714 14 EDO EDO . Q 5 EDO A 1 715 15 EDO EDO . R 5 EDO A 1 716 16 EDO EDO . S 5 EDO A 1 717 17 EDO EDO . T 5 EDO A 1 718 18 EDO EDO . U 5 EDO A 1 719 19 EDO EDO . V 5 EDO B 1 401 3 EDO EDO . W 5 EDO B 1 402 5 EDO EDO . X 5 EDO B 1 403 20 EDO EDO . Y 6 HOH A 1 801 89 HOH HOH . Y 6 HOH A 2 802 32 HOH HOH . Y 6 HOH A 3 803 38 HOH HOH . Y 6 HOH A 4 804 12 HOH HOH . Y 6 HOH A 5 805 2 HOH HOH . Y 6 HOH A 6 806 17 HOH HOH . Y 6 HOH A 7 807 15 HOH HOH . Y 6 HOH A 8 808 37 HOH HOH . Y 6 HOH A 9 809 54 HOH HOH . Y 6 HOH A 10 810 52 HOH HOH . Y 6 HOH A 11 811 11 HOH HOH . Y 6 HOH A 12 812 39 HOH HOH . Y 6 HOH A 13 813 87 HOH HOH . Y 6 HOH A 14 814 78 HOH HOH . Y 6 HOH A 15 815 69 HOH HOH . Y 6 HOH A 16 816 20 HOH HOH . Y 6 HOH A 17 817 81 HOH HOH . Y 6 HOH A 18 818 85 HOH HOH . Y 6 HOH A 19 819 9 HOH HOH . Y 6 HOH A 20 820 4 HOH HOH . Y 6 HOH A 21 821 14 HOH HOH . Y 6 HOH A 22 822 43 HOH HOH . Y 6 HOH A 23 823 40 HOH HOH . Y 6 HOH A 24 824 76 HOH HOH . Y 6 HOH A 25 825 92 HOH HOH . Y 6 HOH A 26 826 28 HOH HOH . Y 6 HOH A 27 827 50 HOH HOH . Y 6 HOH A 28 828 72 HOH HOH . Y 6 HOH A 29 829 58 HOH HOH . Y 6 HOH A 30 830 33 HOH HOH . Y 6 HOH A 31 831 55 HOH HOH . Y 6 HOH A 32 832 23 HOH HOH . Y 6 HOH A 33 833 59 HOH HOH . Y 6 HOH A 34 834 86 HOH HOH . Y 6 HOH A 35 835 18 HOH HOH . Y 6 HOH A 36 836 51 HOH HOH . Y 6 HOH A 37 837 16 HOH HOH . Y 6 HOH A 38 838 70 HOH HOH . Y 6 HOH A 39 839 62 HOH HOH . Y 6 HOH A 40 840 75 HOH HOH . Y 6 HOH A 41 841 71 HOH HOH . Y 6 HOH A 42 842 6 HOH HOH . Y 6 HOH A 43 843 34 HOH HOH . Y 6 HOH A 44 844 5 HOH HOH . Y 6 HOH A 45 845 53 HOH HOH . Y 6 HOH A 46 846 48 HOH HOH . Y 6 HOH A 47 847 79 HOH HOH . Y 6 HOH A 48 848 44 HOH HOH . Y 6 HOH A 49 849 61 HOH HOH . Y 6 HOH A 50 850 10 HOH HOH . Y 6 HOH A 51 851 65 HOH HOH . Y 6 HOH A 52 852 57 HOH HOH . Y 6 HOH A 53 853 21 HOH HOH . Y 6 HOH A 54 854 29 HOH HOH . Y 6 HOH A 55 855 19 HOH HOH . Y 6 HOH A 56 856 41 HOH HOH . Y 6 HOH A 57 857 63 HOH HOH . Y 6 HOH A 58 858 7 HOH HOH . Y 6 HOH A 59 859 84 HOH HOH . Y 6 HOH A 60 860 35 HOH HOH . Y 6 HOH A 61 861 83 HOH HOH . Y 6 HOH A 62 862 24 HOH HOH . Y 6 HOH A 63 863 1 HOH HOH . Y 6 HOH A 64 864 56 HOH HOH . Y 6 HOH A 65 865 90 HOH HOH . Y 6 HOH A 66 866 91 HOH HOH . Y 6 HOH A 67 867 77 HOH HOH . Y 6 HOH A 68 868 47 HOH HOH . Y 6 HOH A 69 869 93 HOH HOH . Y 6 HOH A 70 870 64 HOH HOH . Y 6 HOH A 71 871 36 HOH HOH . Y 6 HOH A 72 872 88 HOH HOH . Y 6 HOH A 73 873 66 HOH HOH . Y 6 HOH A 74 874 74 HOH HOH . Y 6 HOH A 75 875 3 HOH HOH . Y 6 HOH A 76 876 8 HOH HOH . Y 6 HOH A 77 877 13 HOH HOH . Y 6 HOH A 78 878 67 HOH HOH . Y 6 HOH A 79 879 80 HOH HOH . Y 6 HOH A 80 880 73 HOH HOH . Y 6 HOH A 81 881 30 HOH HOH . Z 6 HOH B 1 501 22 HOH HOH . Z 6 HOH B 2 502 42 HOH HOH . Z 6 HOH B 3 503 31 HOH HOH . Z 6 HOH B 4 504 45 HOH HOH . Z 6 HOH B 5 505 25 HOH HOH . Z 6 HOH B 6 506 82 HOH HOH . Z 6 HOH B 7 507 26 HOH HOH . Z 6 HOH B 8 508 49 HOH HOH . Z 6 HOH B 9 509 68 HOH HOH . Z 6 HOH B 10 510 60 HOH HOH . Z 6 HOH B 11 511 27 HOH HOH . Z 6 HOH B 12 512 46 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 21.859 -39.238 -6.395 1 45.74 ? CS MTA 701 A 1 HETATM 2 S S5' MTA . . . C 3 20.394 -40.212 -6.482 1 47.96 ? S5' MTA 701 A 1 HETATM 3 C C5' MTA . . . C 3 19.043 -39.093 -6.394 1 45.94 ? C5' MTA 701 A 1 HETATM 4 C C4' MTA . . . C 3 19.047 -38.27 -5.103 1 46.89 ? C4' MTA 701 A 1 HETATM 5 O O4' MTA . . . C 3 17.899 -37.402 -5.104 1 46.62 ? O4' MTA 701 A 1 HETATM 6 C C2' MTA . . . C 3 17.544 -38.813 -3.29 1 45.02 ? C2' MTA 701 A 1 HETATM 7 O O2' MTA . . . C 3 17.497 -38.859 -1.864 1 45.68 ? O2' MTA 701 A 1 HETATM 8 C C3' MTA . . . C 3 18.929 -39.12 -3.835 1 46.26 ? C3' MTA 701 A 1 HETATM 9 O O3' MTA . . . C 3 19.957 -38.76 -2.906 1 45.41 ? O3' MTA 701 A 1 HETATM 10 C C1' MTA . . . C 3 17.289 -37.418 -3.823 1 42.69 ? C1' MTA 701 A 1 HETATM 11 N N9 MTA . . . C 3 15.878 -37.075 -3.972 1 38.47 ? N9 MTA 701 A 1 HETATM 12 C C8 MTA . . . C 3 14.952 -37.771 -4.616 1 40.73 ? C8 MTA 701 A 1 HETATM 13 N N7 MTA . . . C 3 13.737 -37.153 -4.542 1 40.46 ? N7 MTA 701 A 1 HETATM 14 C C5 MTA . . . C 3 13.9 -36.034 -3.845 1 39.39 ? C5 MTA 701 A 1 HETATM 15 C C6 MTA . . . C 3 13.038 -34.932 -3.41 1 40.83 ? C6 MTA 701 A 1 HETATM 16 N N6 MTA . . . C 3 11.723 -34.895 -3.72 1 42.97 ? N6 MTA 701 A 1 HETATM 17 N N1 MTA . . . C 3 13.605 -33.96 -2.688 1 43.02 ? N1 MTA 701 A 1 HETATM 18 C C2 MTA . . . C 3 14.915 -33.971 -2.362 1 44.62 ? C2 MTA 701 A 1 HETATM 19 N N3 MTA . . . C 3 15.759 -34.949 -2.729 1 43.45 ? N3 MTA 701 A 1 HETATM 20 C C4 MTA . . . C 3 15.313 -35.99 -3.469 1 41 ? C4 MTA 701 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #