data_8C0P # _model_server_result.job_id pYbCKLswtw6EIs4QOP39pA _model_server_result.datetime_utc '2025-07-08 04:47:18' _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 8c0p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 8C0P # _exptl.entry_id 8C0P _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'Triple mutant K369A K370A K372A and acylated-serine 389 with the boronic inhibitor' _entity.formula_weight 451.171 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '[1-[[2,4-bis(trifluoromethyl)phenyl]methyl]benzimidazol-2-yl]sulfanylmethyl-$l^{3}-oxidanyl-bis(oxidanyl)boron' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation 'K369A K370A K372A' _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 108.092 _cell.angle_gamma 90 _cell.entry_id 8C0P _cell.length_a 46.904 _cell.length_b 106.78 _cell.length_c 56.278 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8C0P _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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 1 1 B,D,F 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 ? 2 C N N ? 2 D 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 covale ? covale1 A OG SER 58 A SER 389 1_555 C B SZI . A SZI 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 B OG SER 58 B SER 389 1_555 D B SZI . B SZI 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _chem_comp.formula 'C17 H14 B F6 N2 O3 S' _chem_comp.formula_weight 451.171 _chem_comp.id SZI _chem_comp.mon_nstd_flag . _chem_comp.name '[1-[[2,4-bis(trifluoromethyl)phenyl]methyl]benzimidazol-2-yl]sulfanylmethyl-$l^{3}-oxidanyl-bis(oxidanyl)boron' _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 C04 C03 SZI doub 277 n y C04 C05 SZI sing 278 n y C03 C02 SZI sing 279 n y C05 C06 SZI doub 280 n y F01 C15 SZI sing 281 n n C02 C01 SZI doub 282 n y C06 C01 SZI sing 283 n y C06 N02 SZI sing 284 n y C01 N01 SZI sing 285 n y C07 N02 SZI sing 286 n n C07 C08 SZI sing 287 n n N02 C10 SZI sing 288 n y C15 F03 SZI sing 289 n n C15 C09 SZI sing 290 n n C15 F02 SZI sing 291 n n C08 C09 SZI doub 292 n y C08 C14 SZI sing 293 n y C09 C11 SZI sing 294 n y C10 N01 SZI doub 295 n y C10 S01 SZI sing 296 n n C14 C13 SZI doub 297 n y C11 C12 SZI doub 298 n y C13 C12 SZI sing 299 n y C12 C16 SZI sing 300 n n F19 C16 SZI sing 301 n n S01 C17 SZI sing 302 n n C16 F18 SZI sing 303 n n C16 F17 SZI sing 304 n n C17 B SZI sing 305 n n O1 B SZI sing 306 n n B O2 SZI sing 307 n n O2 H1 SZI sing 308 n n C11 H2 SZI sing 309 n n O1 H3 SZI sing 310 n n C02 H4 SZI sing 311 n n C03 H5 SZI sing 312 n n C04 H6 SZI sing 313 n n C05 H7 SZI sing 314 n n C07 H8 SZI sing 315 n n C07 H9 SZI sing 316 n n C13 H10 SZI sing 317 n n C14 H11 SZI sing 318 n n C17 H12 SZI sing 319 n n C17 H13 SZI sing 320 n n B O3 SZI sing 321 n n O3 H15 SZI sing 322 n n # _atom_sites.entry_id 8C0P _atom_sites.fract_transf_matrix[1][1] 0.02132 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006965 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009365 _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] 0.018693 _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 2 SZI A 1 601 389 SZI 163 . D 2 SZI B 1 601 389 SZI 163 . E 3 HOH A 1 701 69 HOH HOH . E 3 HOH A 2 702 65 HOH HOH . E 3 HOH A 3 703 61 HOH HOH . E 3 HOH A 4 704 54 HOH HOH . E 3 HOH A 5 705 75 HOH HOH . E 3 HOH A 6 706 6 HOH HOH . E 3 HOH A 7 707 16 HOH HOH . E 3 HOH A 8 708 23 HOH HOH . E 3 HOH A 9 709 4 HOH HOH . E 3 HOH A 10 710 68 HOH HOH . E 3 HOH A 11 711 35 HOH HOH . E 3 HOH A 12 712 41 HOH HOH . E 3 HOH A 13 713 74 HOH HOH . E 3 HOH A 14 714 31 HOH HOH . E 3 HOH A 15 715 50 HOH HOH . E 3 HOH A 16 716 18 HOH HOH . E 3 HOH A 17 717 60 HOH HOH . E 3 HOH A 18 718 36 HOH HOH . E 3 HOH A 19 719 53 HOH HOH . E 3 HOH A 20 720 85 HOH HOH . E 3 HOH A 21 721 3 HOH HOH . E 3 HOH A 22 722 24 HOH HOH . E 3 HOH A 23 723 1 HOH HOH . E 3 HOH A 24 724 30 HOH HOH . E 3 HOH A 25 725 79 HOH HOH . E 3 HOH A 26 726 2 HOH HOH . E 3 HOH A 27 727 52 HOH HOH . E 3 HOH A 28 728 13 HOH HOH . E 3 HOH A 29 729 57 HOH HOH . E 3 HOH A 30 730 37 HOH HOH . E 3 HOH A 31 731 71 HOH HOH . E 3 HOH A 32 732 83 HOH HOH . E 3 HOH A 33 733 77 HOH HOH . E 3 HOH A 34 734 55 HOH HOH . E 3 HOH A 35 735 47 HOH HOH . E 3 HOH A 36 736 80 HOH HOH . E 3 HOH A 37 737 46 HOH HOH . E 3 HOH A 38 738 45 HOH HOH . E 3 HOH A 39 739 51 HOH HOH . E 3 HOH A 40 740 58 HOH HOH . E 3 HOH A 41 741 59 HOH HOH . E 3 HOH A 42 742 39 HOH HOH . E 3 HOH A 43 743 17 HOH HOH . E 3 HOH A 44 744 25 HOH HOH . E 3 HOH A 45 745 38 HOH HOH . E 3 HOH A 46 746 33 HOH HOH . E 3 HOH A 47 747 12 HOH HOH . E 3 HOH A 48 748 11 HOH HOH . E 3 HOH A 49 749 66 HOH HOH . E 3 HOH A 50 750 19 HOH HOH . E 3 HOH A 51 751 84 HOH HOH . E 3 HOH A 52 752 70 HOH HOH . E 3 HOH A 53 753 72 HOH HOH . E 3 HOH A 54 754 86 HOH HOH . E 3 HOH A 55 755 15 HOH HOH . E 3 HOH A 56 756 78 HOH HOH . E 3 HOH A 57 757 26 HOH HOH . E 3 HOH A 58 758 56 HOH HOH . F 3 HOH B 1 701 44 HOH HOH . F 3 HOH B 2 702 34 HOH HOH . F 3 HOH B 3 703 5 HOH HOH . F 3 HOH B 4 704 63 HOH HOH . F 3 HOH B 5 705 9 HOH HOH . F 3 HOH B 6 706 8 HOH HOH . F 3 HOH B 7 707 87 HOH HOH . F 3 HOH B 8 708 62 HOH HOH . F 3 HOH B 9 709 10 HOH HOH . F 3 HOH B 10 710 81 HOH HOH . F 3 HOH B 11 711 7 HOH HOH . F 3 HOH B 12 712 28 HOH HOH . F 3 HOH B 13 713 29 HOH HOH . F 3 HOH B 14 714 14 HOH HOH . F 3 HOH B 15 715 49 HOH HOH . F 3 HOH B 16 716 73 HOH HOH . F 3 HOH B 17 717 43 HOH HOH . F 3 HOH B 18 718 42 HOH HOH . F 3 HOH B 19 719 64 HOH HOH . F 3 HOH B 20 720 48 HOH HOH . F 3 HOH B 21 721 21 HOH HOH . F 3 HOH B 22 722 40 HOH HOH . F 3 HOH B 23 723 32 HOH HOH . F 3 HOH B 24 724 82 HOH HOH . F 3 HOH B 25 725 22 HOH HOH . F 3 HOH B 26 726 67 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 O O2 SZI . . . D 2 37.757 -14.282 34.143 1 29.63 0 O2 SZI 601 B 1 HETATM 2 C C10 SZI . . . D 2 39.676 -10.808 36.453 1 44.29 0 C10 SZI 601 B 1 HETATM 3 C C11 SZI . . . D 2 41.472 -7.643 32.439 1 71.72 0 C11 SZI 601 B 1 HETATM 4 C C12 SZI . . . D 2 40.569 -6.695 32.922 1 73.34 0 C12 SZI 601 B 1 HETATM 5 O O1 SZI . . . D 2 37.505 -12.543 32.705 1 34.77 0 O1 SZI 601 B 1 HETATM 6 C C01 SZI . . . D 2 39.886 -10.088 38.506 1 46.27 0 C01 SZI 601 B 1 HETATM 7 N N01 SZI . . . D 2 39.045 -10.761 37.6 1 44.92 0 N01 SZI 601 B 1 HETATM 8 S S01 SZI . . . D 2 39.129 -11.495 34.905 1 45.65 0 S01 SZI 601 B 1 HETATM 9 C C02 SZI . . . D 2 39.746 -9.747 39.856 1 45.55 0 C02 SZI 601 B 1 HETATM 10 N N02 SZI . . . D 2 40.909 -10.186 36.554 1 48.31 0 N02 SZI 601 B 1 HETATM 11 C C03 SZI . . . D 2 40.765 -9.061 40.529 1 45.95 0 C03 SZI 601 B 1 HETATM 12 C C04 SZI . . . D 2 41.945 -8.686 39.876 1 46.15 0 C04 SZI 601 B 1 HETATM 13 C C05 SZI . . . D 2 42.106 -9.01 38.526 1 48.56 0 C05 SZI 601 B 1 HETATM 14 C C06 SZI . . . D 2 41.076 -9.711 37.856 1 48.93 0 C06 SZI 601 B 1 HETATM 15 C C07 SZI . . . D 2 41.883 -9.986 35.466 1 52.68 0 C07 SZI 601 B 1 HETATM 16 C C08 SZI . . . D 2 41.461 -8.852 34.538 1 60.36 0 C08 SZI 601 B 1 HETATM 17 C C09 SZI . . . D 2 41.934 -8.721 33.213 1 71.07 0 C09 SZI 601 B 1 HETATM 18 C C13 SZI . . . D 2 40.117 -6.841 34.224 1 68.55 0 C13 SZI 601 B 1 HETATM 19 C C14 SZI . . . D 2 40.551 -7.896 35.012 1 64.8 0 C14 SZI 601 B 1 HETATM 20 C C15 SZI . . . D 2 42.895 -9.723 32.615 1 78.38 0 C15 SZI 601 B 1 HETATM 21 C C16 SZI . . . D 2 40.12 -5.558 32.03 1 77.87 0 C16 SZI 601 B 1 HETATM 22 C C17 SZI . . . D 2 37.397 -11.991 35.109 1 36.44 0 C17 SZI 601 B 1 HETATM 23 B B SZI . . . D 2 37.03 -13.036 33.996 1 34.67 0 B SZI 601 B 1 HETATM 24 F F01 SZI . . . D 2 43.801 -10.174 33.484 1 81.55 0 F01 SZI 601 B 1 HETATM 25 F F02 SZI . . . D 2 42.239 -10.787 32.142 1 80.73 0 F02 SZI 601 B 1 HETATM 26 F F03 SZI . . . D 2 43.622 -9.278 31.588 1 86.8 0 F03 SZI 601 B 1 HETATM 27 F F17 SZI . . . D 2 39.326 -5.947 31.025 1 81.16 0 F17 SZI 601 B 1 HETATM 28 F F18 SZI . . . D 2 39.38 -4.62 32.634 1 74.93 0 F18 SZI 601 B 1 HETATM 29 F F19 SZI . . . D 2 41.184 -4.938 31.504 1 75.87 0 F19 SZI 601 B 1 # _model_server_stats.io_time_ms 132 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #