data_8BYJ # _model_server_result.job_id Li4F4jK1ARBgsPf9amQt0g _model_server_result.datetime_utc '2024-11-22 12:24:12' _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 8byj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":101}' # _entry.id 8BYJ # _exptl.entry_id 8BYJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 492.002 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[3,5-bis(3-bromanylpropanoyl)-1,3,5-triazinan-1-yl]-3-bromanyl-propan-1-one _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 102.15 _cell.angle_gamma 90 _cell.entry_id 8BYJ _cell.length_a 78.784 _cell.length_b 75.958 _cell.length_c 114.905 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8BYJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,D,E,I,J,M 1 1 B,C,F,G,H,K,L 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 ? 5 H N N ? 5 I 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 disulf ? disulf1 A SG CYS 116 A CYS 133 1_555 A SG CYS 124 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf2 A SG CYS 327 A CYS 344 1_555 A SG CYS 344 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf3 A SG CYS 513 A CYS 530 1_555 A SG CYS 525 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf4 B SG CYS 116 B CYS 133 1_555 B SG CYS 124 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf5 B SG CYS 327 B CYS 344 1_555 B SG CYS 344 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 B SG CYS 513 B CYS 530 1_555 B SG CYS 525 B CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? covale ? covale1 C SG CYS 2 C CYS 1 1_555 H C11 LFI . C LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.789 ? covale ? covale2 C SG CYS 7 C CYS 6 1_555 H C12 LFI . C LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? covale ? covale3 C SG CYS 16 C CYS 15 1_555 H C10 LFI . C LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.791 ? covale ? covale4 C C ALA 17 C ALA 16 1_555 C N NH2 18 C NH2 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.231 ? covale ? covale5 D SG CYS 2 D CYS 1 1_555 I C10 LFI . D LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.827 ? covale ? covale6 D SG CYS 7 D CYS 6 1_555 I C11 LFI . D LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.753 ? covale ? covale7 D SG CYS 16 D CYS 15 1_555 I C12 LFI . D LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.804 ? covale ? covale8 D C ALA 17 D ALA 16 1_555 D N NH2 18 D NH2 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.243 ? metalc ? metalc1 A NE2 HIS 357 A HIS 374 1_555 E ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc2 A NE2 HIS 361 A HIS 378 1_555 E ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc3 A OE2 GLU 385 A GLU 402 1_555 E ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc4 E ZN ZN . A ZN 701 1_555 J O HOH . A HOH 870 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc5 B OH TYR 235 B TYR 252 1_555 G NA NA . B NA 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? metalc ? metalc6 B NE2 HIS 357 B HIS 374 1_555 F ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc7 B NE2 HIS 361 B HIS 378 1_555 F ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc8 B OE1 GLU 385 B GLU 402 1_555 F ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc9 F ZN ZN . B ZN 701 1_555 K O HOH . B HOH 815 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? # _chem_comp.formula 'C12 H18 Br3 N3 O3' _chem_comp.formula_weight 492.002 _chem_comp.id LFI _chem_comp.mon_nstd_flag . _chem_comp.name 1-[3,5-bis(3-bromanylpropanoyl)-1,3,5-triazinan-1-yl]-3-bromanyl-propan-1-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Chemical crosslinker' # 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 O1 C6 LFI doub 194 n n C8 C10 LFI sing 195 n n C8 C4 LFI sing 196 n n C1 N2 LFI sing 197 n n C1 N1 LFI sing 198 n n C6 N2 LFI sing 199 n n C6 C7 LFI sing 200 n n C4 N1 LFI sing 201 n n C4 O2 LFI doub 202 n n N2 C2 LFI sing 203 n n N1 C3 LFI sing 204 n n C7 C12 LFI sing 205 n n C3 N3 LFI sing 206 n n C2 N3 LFI sing 207 n n N3 C5 LFI sing 208 n n C5 O3 LFI doub 209 n n C5 C9 LFI sing 210 n n C9 C11 LFI sing 211 n n C10 H1 LFI sing 212 n n C10 H2 LFI sing 213 n n C11 H4 LFI sing 214 n n C11 H5 LFI sing 215 n n C12 H7 LFI sing 216 n n C12 H8 LFI sing 217 n n C1 H10 LFI sing 218 n n C1 H11 LFI sing 219 n n C2 H12 LFI sing 220 n n C2 H13 LFI sing 221 n n C3 H14 LFI sing 222 n n C3 H15 LFI sing 223 n n C7 H16 LFI sing 224 n n C7 H17 LFI sing 225 n n C8 H18 LFI sing 226 n n C8 H19 LFI sing 227 n n C9 H20 LFI sing 228 n n C9 H21 LFI sing 229 n n C10 BR1 LFI sing 230 n n C12 BR2 LFI sing 231 n n C11 BR3 LFI sing 232 n n # _atom_sites.entry_id 8BYJ _atom_sites.fract_transf_matrix[1][1] 0.012693 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002733 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013165 _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] 0.008902 _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 E 3 ZN A 1 701 1 ZN ZN . F 3 ZN B 1 701 2 ZN ZN . G 4 NA B 1 702 1 NA NA . H 5 LFI C 1 101 101 LFI TAT . I 5 LFI D 1 101 101 LFI TAT . J 6 HOH A 1 801 66 HOH HOH . J 6 HOH A 2 802 52 HOH HOH . J 6 HOH A 3 803 45 HOH HOH . J 6 HOH A 4 804 83 HOH HOH . J 6 HOH A 5 805 85 HOH HOH . J 6 HOH A 6 806 16 HOH HOH . J 6 HOH A 7 807 76 HOH HOH . J 6 HOH A 8 808 69 HOH HOH . J 6 HOH A 9 809 103 HOH HOH . J 6 HOH A 10 810 11 HOH HOH . J 6 HOH A 11 811 47 HOH HOH . J 6 HOH A 12 812 60 HOH HOH . J 6 HOH A 13 813 38 HOH HOH . J 6 HOH A 14 814 56 HOH HOH . J 6 HOH A 15 815 20 HOH HOH . J 6 HOH A 16 816 9 HOH HOH . J 6 HOH A 17 817 71 HOH HOH . J 6 HOH A 18 818 25 HOH HOH . J 6 HOH A 19 819 41 HOH HOH . J 6 HOH A 20 820 70 HOH HOH . J 6 HOH A 21 821 58 HOH HOH . J 6 HOH A 22 822 115 HOH HOH . J 6 HOH A 23 823 113 HOH HOH . J 6 HOH A 24 824 75 HOH HOH . J 6 HOH A 25 825 37 HOH HOH . J 6 HOH A 26 826 23 HOH HOH . J 6 HOH A 27 827 43 HOH HOH . J 6 HOH A 28 828 21 HOH HOH . J 6 HOH A 29 829 65 HOH HOH . J 6 HOH A 30 830 50 HOH HOH . J 6 HOH A 31 831 73 HOH HOH . J 6 HOH A 32 832 63 HOH HOH . J 6 HOH A 33 833 114 HOH HOH . J 6 HOH A 34 834 80 HOH HOH . J 6 HOH A 35 835 4 HOH HOH . J 6 HOH A 36 836 110 HOH HOH . J 6 HOH A 37 837 82 HOH HOH . J 6 HOH A 38 838 8 HOH HOH . J 6 HOH A 39 839 40 HOH HOH . J 6 HOH A 40 840 13 HOH HOH . J 6 HOH A 41 841 99 HOH HOH . J 6 HOH A 42 842 79 HOH HOH . J 6 HOH A 43 843 7 HOH HOH . J 6 HOH A 44 844 100 HOH HOH . J 6 HOH A 45 845 57 HOH HOH . J 6 HOH A 46 846 125 HOH HOH . J 6 HOH A 47 847 22 HOH HOH . J 6 HOH A 48 848 122 HOH HOH . J 6 HOH A 49 849 93 HOH HOH . J 6 HOH A 50 850 78 HOH HOH . J 6 HOH A 51 851 124 HOH HOH . J 6 HOH A 52 852 88 HOH HOH . J 6 HOH A 53 853 129 HOH HOH . J 6 HOH A 54 854 96 HOH HOH . J 6 HOH A 55 855 94 HOH HOH . J 6 HOH A 56 856 111 HOH HOH . J 6 HOH A 57 857 17 HOH HOH . J 6 HOH A 58 858 118 HOH HOH . J 6 HOH A 59 859 102 HOH HOH . J 6 HOH A 60 860 68 HOH HOH . J 6 HOH A 61 861 87 HOH HOH . J 6 HOH A 62 862 15 HOH HOH . J 6 HOH A 63 863 12 HOH HOH . J 6 HOH A 64 864 10 HOH HOH . J 6 HOH A 65 865 32 HOH HOH . J 6 HOH A 66 866 72 HOH HOH . J 6 HOH A 67 867 39 HOH HOH . J 6 HOH A 68 868 5 HOH HOH . J 6 HOH A 69 869 97 HOH HOH . J 6 HOH A 70 870 1 HOH HOH . J 6 HOH A 71 871 127 HOH HOH . J 6 HOH A 72 872 101 HOH HOH . J 6 HOH A 73 873 130 HOH HOH . J 6 HOH A 74 874 90 HOH HOH . J 6 HOH A 75 875 123 HOH HOH . J 6 HOH A 76 876 120 HOH HOH . K 6 HOH B 1 801 19 HOH HOH . K 6 HOH B 2 802 24 HOH HOH . K 6 HOH B 3 803 109 HOH HOH . K 6 HOH B 4 804 51 HOH HOH . K 6 HOH B 5 805 62 HOH HOH . K 6 HOH B 6 806 53 HOH HOH . K 6 HOH B 7 807 61 HOH HOH . K 6 HOH B 8 808 48 HOH HOH . K 6 HOH B 9 809 77 HOH HOH . K 6 HOH B 10 810 86 HOH HOH . K 6 HOH B 11 811 105 HOH HOH . K 6 HOH B 12 812 89 HOH HOH . K 6 HOH B 13 813 108 HOH HOH . K 6 HOH B 14 814 91 HOH HOH . K 6 HOH B 15 815 2 HOH HOH . K 6 HOH B 16 816 42 HOH HOH . K 6 HOH B 17 817 28 HOH HOH . K 6 HOH B 18 818 74 HOH HOH . K 6 HOH B 19 819 46 HOH HOH . K 6 HOH B 20 820 92 HOH HOH . K 6 HOH B 21 821 44 HOH HOH . K 6 HOH B 22 822 64 HOH HOH . K 6 HOH B 23 823 30 HOH HOH . K 6 HOH B 24 824 106 HOH HOH . K 6 HOH B 25 825 49 HOH HOH . K 6 HOH B 26 826 59 HOH HOH . K 6 HOH B 27 827 84 HOH HOH . K 6 HOH B 28 828 107 HOH HOH . K 6 HOH B 29 829 117 HOH HOH . K 6 HOH B 30 830 98 HOH HOH . K 6 HOH B 31 831 126 HOH HOH . K 6 HOH B 32 832 54 HOH HOH . K 6 HOH B 33 833 31 HOH HOH . K 6 HOH B 34 834 26 HOH HOH . K 6 HOH B 35 835 18 HOH HOH . K 6 HOH B 36 836 36 HOH HOH . K 6 HOH B 37 837 119 HOH HOH . K 6 HOH B 38 838 95 HOH HOH . K 6 HOH B 39 839 128 HOH HOH . K 6 HOH B 40 840 112 HOH HOH . K 6 HOH B 41 841 121 HOH HOH . K 6 HOH B 42 842 104 HOH HOH . K 6 HOH B 43 843 34 HOH HOH . K 6 HOH B 44 844 27 HOH HOH . K 6 HOH B 45 845 35 HOH HOH . K 6 HOH B 46 846 81 HOH HOH . K 6 HOH B 47 847 33 HOH HOH . L 6 HOH C 1 201 29 HOH HOH . M 6 HOH D 1 201 116 HOH HOH . M 6 HOH D 2 202 14 HOH HOH . M 6 HOH D 3 203 6 HOH HOH . M 6 HOH D 4 204 3 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 C10 LFI . . . I 5 -7.027 21.084 -48.866 1 60.69 ? C10 LFI 101 D 1 HETATM 2 C C11 LFI . . . I 5 -11.363 15.446 -52.69 1 51.82 ? C11 LFI 101 D 1 HETATM 3 C C12 LFI . . . I 5 -4.377 13.984 -52.312 1 56.01 ? C12 LFI 101 D 1 HETATM 4 C C1 LFI . . . I 5 -7.005 17.073 -51.255 1 57.71 ? C1 LFI 101 D 1 HETATM 5 C C2 LFI . . . I 5 -7.495 15.248 -49.696 1 46.84 ? C2 LFI 101 D 1 HETATM 6 C C3 LFI . . . I 5 -8.837 17.282 -49.645 1 47.75 ? C3 LFI 101 D 1 HETATM 7 C C4 LFI . . . I 5 -7.638 19.3 -50.475 1 72.02 ? C4 LFI 101 D 1 HETATM 8 C C5 LFI . . . I 5 -9.685 15.3 -50.834 1 51.91 ? C5 LFI 101 D 1 HETATM 9 C C6 LFI . . . I 5 -5.186 15.594 -50.549 1 63.07 ? C6 LFI 101 D 1 HETATM 10 C C7 LFI . . . I 5 -4.885 14.168 -50.895 1 63.34 ? C7 LFI 101 D 1 HETATM 11 C C8 LFI . . . I 5 -6.533 19.909 -49.677 1 60.39 ? C8 LFI 101 D 1 HETATM 12 C C9 LFI . . . I 5 -10.589 16.195 -51.631 1 52.96 ? C9 LFI 101 D 1 HETATM 13 N N1 LFI . . . I 5 -7.815 17.969 -50.431 1 59.5 ? N1 LFI 101 D 1 HETATM 14 N N2 LFI . . . I 5 -6.48 15.949 -50.48 1 55.24 ? N2 LFI 101 D 1 HETATM 15 N N3 LFI . . . I 5 -8.748 15.89 -50.073 1 48.16 ? N3 LFI 101 D 1 HETATM 16 O O1 LFI . . . I 5 -4.288 16.413 -50.392 1 64.47 ? O1 LFI 101 D 1 HETATM 17 O O2 LFI . . . I 5 -8.335 19.999 -51.198 1 75.97 ? O2 LFI 101 D 1 HETATM 18 O O3 LFI . . . I 5 -9.736 14.083 -50.955 1 54.95 ? O3 LFI 101 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 432 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 18 #