data_8B9P # _model_server_result.job_id Zvxr6SY4-V5-PNAn5ROQfg _model_server_result.datetime_utc '2024-11-21 21:02:24' _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 8b9p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":101}' # _entry.id 8B9P # _exptl.entry_id 8B9P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 492.002 _entity.id 3 _entity.src_method nat _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 99.93 _cell.angle_gamma 90 _cell.entry_id 8B9P _cell.length_a 73.885 _cell.length_b 76.757 _cell.length_c 115.049 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8B9P _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,C,E,G,I 1 1 B,D,F,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 ? 3 E N N ? 3 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 disulf ? disulf1 A SG CYS 116 A CYS 133 1_555 A SG CYS 124 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 327 A CYS 344 1_555 A SG CYS 344 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 A SG CYS 513 A CYS 530 1_555 A SG CYS 525 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 B SG CYS 116 B CYS 133 1_555 B SG CYS 124 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 B SG CYS 327 B CYS 344 1_555 B SG CYS 344 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 B SG CYS 513 B CYS 530 1_555 B SG CYS 525 B CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 C SG CYS 2 C CYS 2 1_555 E C11 LFI . C LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? covale ? covale2 C SG CYS 7 C CYS 7 1_555 E C12 LFI . C LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.696 ? covale ? covale3 C SG CYS 16 C CYS 16 1_555 E C10 LFI . C LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.616 ? covale ? covale4 C C ALA 17 C ALA 17 1_555 C N NH2 18 C NH2 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale5 D SG CYS 2 D CYS 2 1_555 F C12 LFI . D LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.657 ? covale ? covale6 D SG CYS 7 D CYS 7 1_555 F C10 LFI . D LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.831 ? covale ? covale7 D SG CYS 16 D CYS 16 1_555 F C11 LFI . D LFI 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.817 ? covale ? covale8 D C ALA 17 D ALA 17 1_555 D N NH2 18 D NH2 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _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 8B9P _atom_sites.fract_transf_matrix[1][1] 0.013535 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002371 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013028 _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] 0.008824 _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 LFI C 1 101 101 LFI TAT . F 3 LFI D 1 101 101 LFI TAT . G 4 HOH A 1 701 3 HOH HOH . G 4 HOH A 2 702 38 HOH HOH . G 4 HOH A 3 703 10 HOH HOH . G 4 HOH A 4 704 8 HOH HOH . G 4 HOH A 5 705 31 HOH HOH . G 4 HOH A 6 706 37 HOH HOH . G 4 HOH A 7 707 32 HOH HOH . G 4 HOH A 8 708 23 HOH HOH . G 4 HOH A 9 709 2 HOH HOH . G 4 HOH A 10 710 35 HOH HOH . G 4 HOH A 11 711 40 HOH HOH . G 4 HOH A 12 712 12 HOH HOH . G 4 HOH A 13 713 55 HOH HOH . G 4 HOH A 14 714 25 HOH HOH . G 4 HOH A 15 715 27 HOH HOH . G 4 HOH A 16 716 29 HOH HOH . G 4 HOH A 17 717 30 HOH HOH . G 4 HOH A 18 718 33 HOH HOH . G 4 HOH A 19 719 56 HOH HOH . G 4 HOH A 20 720 5 HOH HOH . G 4 HOH A 21 721 18 HOH HOH . G 4 HOH A 22 722 41 HOH HOH . G 4 HOH A 23 723 4 HOH HOH . G 4 HOH A 24 724 46 HOH HOH . G 4 HOH A 25 725 57 HOH HOH . G 4 HOH A 26 726 49 HOH HOH . G 4 HOH A 27 727 54 HOH HOH . G 4 HOH A 28 728 42 HOH HOH . G 4 HOH A 29 729 53 HOH HOH . G 4 HOH A 30 730 48 HOH HOH . G 4 HOH A 31 731 34 HOH HOH . G 4 HOH A 32 732 7 HOH HOH . G 4 HOH A 33 733 52 HOH HOH . G 4 HOH A 34 734 47 HOH HOH . G 4 HOH A 35 735 22 HOH HOH . G 4 HOH A 36 736 58 HOH HOH . G 4 HOH A 37 737 11 HOH HOH . G 4 HOH A 38 738 6 HOH HOH . G 4 HOH A 39 739 9 HOH HOH . G 4 HOH A 40 740 51 HOH HOH . G 4 HOH A 41 741 45 HOH HOH . H 4 HOH B 1 701 24 HOH HOH . H 4 HOH B 2 702 15 HOH HOH . H 4 HOH B 3 703 39 HOH HOH . H 4 HOH B 4 704 60 HOH HOH . H 4 HOH B 5 705 19 HOH HOH . H 4 HOH B 6 706 28 HOH HOH . H 4 HOH B 7 707 64 HOH HOH . H 4 HOH B 8 708 44 HOH HOH . H 4 HOH B 9 709 36 HOH HOH . H 4 HOH B 10 710 63 HOH HOH . H 4 HOH B 11 711 17 HOH HOH . H 4 HOH B 12 712 16 HOH HOH . H 4 HOH B 13 713 59 HOH HOH . H 4 HOH B 14 714 43 HOH HOH . H 4 HOH B 15 715 50 HOH HOH . H 4 HOH B 16 716 62 HOH HOH . H 4 HOH B 17 717 14 HOH HOH . H 4 HOH B 18 718 13 HOH HOH . H 4 HOH B 19 719 61 HOH HOH . I 4 HOH C 1 201 1 HOH HOH . I 4 HOH C 2 202 26 HOH HOH . I 4 HOH C 3 203 21 HOH HOH . I 4 HOH C 4 204 20 HOH HOH . J 4 HOH D 1 201 65 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 . . . F 3 -20.494 15.328 16.133 1 68.61 ? C10 LFI 101 D 1 HETATM 2 C C11 LFI . . . F 3 -15.891 20.863 16.629 1 88.82 ? C11 LFI 101 D 1 HETATM 3 C C12 LFI . . . F 3 -17.533 16.954 23.721 1 73.85 ? C12 LFI 101 D 1 HETATM 4 C C1 LFI . . . F 3 -17.424 15.677 19.498 1 67.02 ? C1 LFI 101 D 1 HETATM 5 C C2 LFI . . . F 3 -16.187 17.713 19.082 1 70.41 ? C2 LFI 101 D 1 HETATM 6 C C3 LFI . . . F 3 -17.636 16.819 17.401 1 69.93 ? C3 LFI 101 D 1 HETATM 7 C C4 LFI . . . F 3 -19.678 15.798 18.472 1 65.24 ? C4 LFI 101 D 1 HETATM 8 C C5 LFI . . . F 3 -17.576 19.316 17.707 1 83 ? C5 LFI 101 D 1 HETATM 9 C C6 LFI . . . F 3 -17.2 17.41 21.296 1 63.73 ? C6 LFI 101 D 1 HETATM 10 C C7 LFI . . . F 3 -17.817 16.499 22.308 1 70.36 ? C7 LFI 101 D 1 HETATM 11 C C8 LFI . . . F 3 -20.556 16.252 17.327 1 69.89 ? C8 LFI 101 D 1 HETATM 12 C C9 LFI . . . F 3 -16.631 20.487 17.907 1 87.64 ? C9 LFI 101 D 1 HETATM 13 N N1 LFI . . . F 3 -18.351 16.046 18.426 1 65.24 ? N1 LFI 101 D 1 HETATM 14 N N2 LFI . . . F 3 -16.929 16.932 20.07 1 69.58 ? N2 LFI 101 D 1 HETATM 15 N N3 LFI . . . F 3 -17.159 18.065 18.033 1 76.08 ? N3 LFI 101 D 1 HETATM 16 O O1 LFI . . . F 3 -16.986 18.582 21.57 1 62.5 ? O1 LFI 101 D 1 HETATM 17 O O2 LFI . . . F 3 -20.195 15.265 19.448 1 66.59 ? O2 LFI 101 D 1 HETATM 18 O O3 LFI . . . F 3 -18.702 19.53 17.261 1 73.07 ? O3 LFI 101 D 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 18 #