data_5EML # _model_server_result.job_id znoa6s9QMQV7Q8ue2YFh6Q _model_server_result.datetime_utc '2025-07-10 09:16:26' _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 5eml # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 5EML # _exptl.entry_id 5EML _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 5EML _cell.length_a 103.4 _cell.length_b 138.13 _cell.length_c 178.92 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EML _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 octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -138.13 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_545 x,-y-1,-z 1 0 0 0 -1 0 0 0 -1 0 -138.13 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 2.035 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _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 N CA SAM sing 347 n n N HN1 SAM sing 348 n n N HN2 SAM sing 349 n n CA C SAM sing 350 n n CA CB SAM sing 351 n n CA HA SAM sing 352 n n C O SAM doub 353 n n C OXT SAM sing 354 n n CB CG SAM sing 355 n n CB HB1 SAM sing 356 n n CB HB2 SAM sing 357 n n CG SD SAM sing 358 n n CG HG1 SAM sing 359 n n CG HG2 SAM sing 360 n n SD CE SAM sing 361 n n SD C5' SAM sing 362 n n CE HE1 SAM sing 363 n n CE HE2 SAM sing 364 n n CE HE3 SAM sing 365 n n C5' C4' SAM sing 366 n n C5' "H5'1" SAM sing 367 n n C5' "H5'2" SAM sing 368 n n C4' O4' SAM sing 369 n n C4' C3' SAM sing 370 n n C4' H4' SAM sing 371 n n O4' C1' SAM sing 372 n n C3' O3' SAM sing 373 n n C3' C2' SAM sing 374 n n C3' H3' SAM sing 375 n n O3' HO3' SAM sing 376 n n C2' O2' SAM sing 377 n n C2' C1' SAM sing 378 n n C2' H2' SAM sing 379 n n O2' HO2' SAM sing 380 n n C1' N9 SAM sing 381 n n C1' H1' SAM sing 382 n n N9 C8 SAM sing 383 n y N9 C4 SAM sing 384 n y C8 N7 SAM doub 385 n y C8 H8 SAM sing 386 n n N7 C5 SAM sing 387 n y C5 C6 SAM sing 388 n y C5 C4 SAM doub 389 n y C6 N6 SAM sing 390 n n C6 N1 SAM doub 391 n y N6 HN61 SAM sing 392 n n N6 HN62 SAM sing 393 n n N1 C2 SAM sing 394 n y C2 N3 SAM doub 395 n y C2 H2 SAM sing 396 n n N3 C4 SAM sing 397 n y # _atom_sites.entry_id 5EML _atom_sites.fract_transf_matrix[1][1] 0.009671 _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] 0.00724 _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] 0.005589 _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 SAM A 1 701 1 SAM SAM . D 4 5QK A 1 702 1 5QK EPZ . E 5 GOL A 1 703 1 GOL GOL . F 5 GOL B 1 401 2 GOL GOL . G 6 HOH A 1 801 109 HOH HOH . G 6 HOH A 2 802 22 HOH HOH . G 6 HOH A 3 803 64 HOH HOH . G 6 HOH A 4 804 60 HOH HOH . G 6 HOH A 5 805 46 HOH HOH . G 6 HOH A 6 806 104 HOH HOH . G 6 HOH A 7 807 53 HOH HOH . G 6 HOH A 8 808 117 HOH HOH . G 6 HOH A 9 809 54 HOH HOH . G 6 HOH A 10 810 9 HOH HOH . G 6 HOH A 11 811 12 HOH HOH . G 6 HOH A 12 812 6 HOH HOH . G 6 HOH A 13 813 34 HOH HOH . G 6 HOH A 14 814 44 HOH HOH . G 6 HOH A 15 815 74 HOH HOH . G 6 HOH A 16 816 65 HOH HOH . G 6 HOH A 17 817 66 HOH HOH . G 6 HOH A 18 818 131 HOH HOH . G 6 HOH A 19 819 71 HOH HOH . G 6 HOH A 20 820 80 HOH HOH . G 6 HOH A 21 821 10 HOH HOH . G 6 HOH A 22 822 19 HOH HOH . G 6 HOH A 23 823 49 HOH HOH . G 6 HOH A 24 824 26 HOH HOH . G 6 HOH A 25 825 91 HOH HOH . G 6 HOH A 26 826 67 HOH HOH . G 6 HOH A 27 827 61 HOH HOH . G 6 HOH A 28 828 11 HOH HOH . G 6 HOH A 29 829 15 HOH HOH . G 6 HOH A 30 830 28 HOH HOH . G 6 HOH A 31 831 8 HOH HOH . G 6 HOH A 32 832 130 HOH HOH . G 6 HOH A 33 833 2 HOH HOH . G 6 HOH A 34 834 96 HOH HOH . G 6 HOH A 35 835 55 HOH HOH . G 6 HOH A 36 836 4 HOH HOH . G 6 HOH A 37 837 81 HOH HOH . G 6 HOH A 38 838 20 HOH HOH . G 6 HOH A 39 839 103 HOH HOH . G 6 HOH A 40 840 21 HOH HOH . G 6 HOH A 41 841 78 HOH HOH . G 6 HOH A 42 842 122 HOH HOH . G 6 HOH A 43 843 135 HOH HOH . G 6 HOH A 44 844 42 HOH HOH . G 6 HOH A 45 845 119 HOH HOH . G 6 HOH A 46 846 70 HOH HOH . G 6 HOH A 47 847 39 HOH HOH . G 6 HOH A 48 848 121 HOH HOH . G 6 HOH A 49 849 56 HOH HOH . G 6 HOH A 50 850 98 HOH HOH . G 6 HOH A 51 851 138 HOH HOH . G 6 HOH A 52 852 88 HOH HOH . G 6 HOH A 53 853 59 HOH HOH . G 6 HOH A 54 854 29 HOH HOH . G 6 HOH A 55 855 1 HOH HOH . G 6 HOH A 56 856 17 HOH HOH . G 6 HOH A 57 857 5 HOH HOH . G 6 HOH A 58 858 41 HOH HOH . G 6 HOH A 59 859 101 HOH HOH . G 6 HOH A 60 860 36 HOH HOH . G 6 HOH A 61 861 87 HOH HOH . G 6 HOH A 62 862 47 HOH HOH . G 6 HOH A 63 863 43 HOH HOH . G 6 HOH A 64 864 79 HOH HOH . G 6 HOH A 65 865 48 HOH HOH . G 6 HOH A 66 866 30 HOH HOH . G 6 HOH A 67 867 89 HOH HOH . G 6 HOH A 68 868 75 HOH HOH . G 6 HOH A 69 869 95 HOH HOH . G 6 HOH A 70 870 108 HOH HOH . G 6 HOH A 71 871 136 HOH HOH . G 6 HOH A 72 872 127 HOH HOH . G 6 HOH A 73 873 33 HOH HOH . G 6 HOH A 74 874 90 HOH HOH . G 6 HOH A 75 875 18 HOH HOH . G 6 HOH A 76 876 110 HOH HOH . G 6 HOH A 77 877 92 HOH HOH . G 6 HOH A 78 878 85 HOH HOH . G 6 HOH A 79 879 50 HOH HOH . G 6 HOH A 80 880 112 HOH HOH . G 6 HOH A 81 881 38 HOH HOH . G 6 HOH A 82 882 77 HOH HOH . G 6 HOH A 83 883 35 HOH HOH . G 6 HOH A 84 884 116 HOH HOH . G 6 HOH A 85 885 83 HOH HOH . G 6 HOH A 86 886 86 HOH HOH . G 6 HOH A 87 887 51 HOH HOH . G 6 HOH A 88 888 99 HOH HOH . G 6 HOH A 89 889 106 HOH HOH . G 6 HOH A 90 890 133 HOH HOH . G 6 HOH A 91 891 23 HOH HOH . G 6 HOH A 92 892 73 HOH HOH . G 6 HOH A 93 893 105 HOH HOH . G 6 HOH A 94 894 32 HOH HOH . G 6 HOH A 95 895 129 HOH HOH . G 6 HOH A 96 896 25 HOH HOH . G 6 HOH A 97 897 118 HOH HOH . G 6 HOH A 98 898 72 HOH HOH . G 6 HOH A 99 899 84 HOH HOH . G 6 HOH A 100 900 139 HOH HOH . G 6 HOH A 101 901 107 HOH HOH . G 6 HOH A 102 902 97 HOH HOH . G 6 HOH A 103 903 128 HOH HOH . G 6 HOH A 104 904 111 HOH HOH . G 6 HOH A 105 905 114 HOH HOH . G 6 HOH A 106 906 102 HOH HOH . G 6 HOH A 107 907 62 HOH HOH . G 6 HOH A 108 908 52 HOH HOH . G 6 HOH A 109 909 126 HOH HOH . G 6 HOH A 110 910 100 HOH HOH . G 6 HOH A 111 911 125 HOH HOH . G 6 HOH A 112 912 115 HOH HOH . H 6 HOH B 1 501 57 HOH HOH . H 6 HOH B 2 502 123 HOH HOH . H 6 HOH B 3 503 14 HOH HOH . H 6 HOH B 4 504 45 HOH HOH . H 6 HOH B 5 505 7 HOH HOH . H 6 HOH B 6 506 63 HOH HOH . H 6 HOH B 7 507 134 HOH HOH . H 6 HOH B 8 508 58 HOH HOH . H 6 HOH B 9 509 69 HOH HOH . H 6 HOH B 10 510 40 HOH HOH . H 6 HOH B 11 511 93 HOH HOH . H 6 HOH B 12 512 13 HOH HOH . H 6 HOH B 13 513 76 HOH HOH . H 6 HOH B 14 514 16 HOH HOH . H 6 HOH B 15 515 31 HOH HOH . H 6 HOH B 16 516 3 HOH HOH . H 6 HOH B 17 517 140 HOH HOH . H 6 HOH B 18 518 27 HOH HOH . H 6 HOH B 19 519 120 HOH HOH . H 6 HOH B 20 520 24 HOH HOH . H 6 HOH B 21 521 68 HOH HOH . H 6 HOH B 22 522 132 HOH HOH . H 6 HOH B 23 523 94 HOH HOH . H 6 HOH B 24 524 82 HOH HOH . H 6 HOH B 25 525 37 HOH HOH . H 6 HOH B 26 526 124 HOH HOH . H 6 HOH B 27 527 113 HOH HOH . H 6 HOH B 28 528 137 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 N N SAM . . . C 3 23.478 -36.542 -7.192 1 42.46 ? N SAM 701 A 1 HETATM 2 C CA SAM . . . C 3 23.943 -37.679 -6.405 1 46.43 ? CA SAM 701 A 1 HETATM 3 C C SAM . . . C 3 24.982 -38.422 -7.205 1 44.52 ? C SAM 701 A 1 HETATM 4 O O SAM . . . C 3 25.802 -39.093 -6.528 1 42.87 ? O SAM 701 A 1 HETATM 5 O OXT SAM . . . C 3 24.948 -38.342 -8.475 1 39.37 ? OXT SAM 701 A 1 HETATM 6 C CB SAM . . . C 3 22.812 -38.627 -5.94 1 45.76 ? CB SAM 701 A 1 HETATM 7 C CG SAM . . . C 3 21.983 -39.275 -7.063 1 46.03 ? CG SAM 701 A 1 HETATM 8 S SD SAM . . . C 3 20.677 -40.147 -6.469 1 51.91 ? SD SAM 701 A 1 HETATM 9 C CE SAM . . . C 3 20.218 -41.305 -7.574 1 48.79 ? CE SAM 701 A 1 HETATM 10 C C5' SAM . . . C 3 19.35 -39.169 -6.224 1 43.2 ? C5' SAM 701 A 1 HETATM 11 C C4' SAM . . . C 3 19.393 -38.439 -4.876 1 38.13 ? C4' SAM 701 A 1 HETATM 12 O O4' SAM . . . C 3 18.263 -37.557 -4.818 1 37.13 ? O4' SAM 701 A 1 HETATM 13 C C3' SAM . . . C 3 19.245 -39.38 -3.688 1 37.58 ? C3' SAM 701 A 1 HETATM 14 O O3' SAM . . . C 3 20.289 -39.13 -2.729 1 34.68 ? O3' SAM 701 A 1 HETATM 15 C C2' SAM . . . C 3 17.846 -39.057 -3.16 1 33.74 ? C2' SAM 701 A 1 HETATM 16 O O2' SAM . . . C 3 17.721 -39.226 -1.761 1 34.1 ? O2' SAM 701 A 1 HETATM 17 C C1' SAM . . . C 3 17.64 -37.61 -3.524 1 34.87 ? C1' SAM 701 A 1 HETATM 18 N N9 SAM . . . C 3 16.224 -37.195 -3.708 1 34.32 ? N9 SAM 701 A 1 HETATM 19 C C8 SAM . . . C 3 15.329 -37.888 -4.427 1 33.49 ? C8 SAM 701 A 1 HETATM 20 N N7 SAM . . . C 3 14.129 -37.256 -4.463 1 34.39 ? N7 SAM 701 A 1 HETATM 21 C C5 SAM . . . C 3 14.244 -36.136 -3.759 1 31.95 ? C5 SAM 701 A 1 HETATM 22 C C6 SAM . . . C 3 13.326 -35.052 -3.432 1 32.95 ? C6 SAM 701 A 1 HETATM 23 N N6 SAM . . . C 3 12.046 -35.076 -3.885 1 38.43 ? N6 SAM 701 A 1 HETATM 24 N N1 SAM . . . C 3 13.805 -34.054 -2.665 1 34.68 ? N1 SAM 701 A 1 HETATM 25 C C2 SAM . . . C 3 15.1 -34.043 -2.242 1 33.83 ? C2 SAM 701 A 1 HETATM 26 N N3 SAM . . . C 3 15.995 -35.013 -2.513 1 32.65 ? N3 SAM 701 A 1 HETATM 27 C C4 SAM . . . C 3 15.631 -36.076 -3.272 1 32.31 ? C4 SAM 701 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #