data_5VEA # _model_server_result.job_id P8a0ypSPACJje-sUJoQZKQ _model_server_result.datetime_utc '2024-11-14 06:22:00' _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 5vea # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":101}' # _entry.id 5VEA # _exptl.entry_id 5VEA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 909.077 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate' _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 120 _cell.entry_id 5VEA _cell.length_a 62.763 _cell.length_b 62.763 _cell.length_c 82.238 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VEA _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 27.412667 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C50 H64 N6 O10' _chem_comp.formula_weight 909.077 _chem_comp.id 3TL _chem_comp.mon_nstd_flag . _chem_comp.name 'benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-4,13-bis(1-methylethyl)-2,5,12,15,18-pentaoxo-20-phenyl-19-oxa-3,6,11,14,17-pentaazaicos-1-yl]carbamate' _chem_comp.type peptide-like _chem_comp.pdbx_synonyms 'TL-3, C2 symmetric inhibitor' # 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 C31 O8 3TL doub 1 n n C31 O9 3TL sing 2 n n C31 N4 3TL sing 3 n n O9 CA 3TL sing 4 n n CA C 3TL sing 5 n n CA HA1 3TL sing 6 n n CA HA2 3TL sing 7 n n C C13 3TL doub 8 n y C C17 3TL sing 9 n y C13 C14 3TL sing 10 n y C13 H13 3TL sing 11 n n C14 C15 3TL doub 12 n y C14 H14 3TL sing 13 n n C15 C16 3TL sing 14 n y C15 H15 3TL sing 15 n n C16 C17 3TL doub 16 n y C16 H16 3TL sing 17 n n C17 H17 3TL sing 18 n n N4 C18 3TL sing 19 n n N4 HN4 3TL sing 20 n n C18 C19 3TL sing 21 n n C18 C20 3TL sing 22 n n C18 H18 3TL sing 23 n n C19 O4 3TL doub 24 n n C19 N2 3TL sing 25 n n C20 H201 3TL sing 26 n n C20 H202 3TL sing 27 n n C20 H203 3TL sing 28 n n N2 C10 3TL sing 29 n n N2 HN2 3TL sing 30 n n C10 C11 3TL sing 31 n n C10 C12 3TL sing 32 n n C10 H10 3TL sing 33 n n C11 O2 3TL doub 34 n n C11 N1 3TL sing 35 n n C12 CG2 3TL sing 36 n n C12 CG1 3TL sing 37 n n C12 H12 3TL sing 38 n n CG2 HG21 3TL sing 39 n n CG2 HG22 3TL sing 40 n n CG2 HG23 3TL sing 41 n n CG1 HG11 3TL sing 42 n n CG1 HG12 3TL sing 43 n n CG1 HG13 3TL sing 44 n n C2 O1 3TL sing 45 n n C2 C1 3TL sing 46 n n C2 H2 3TL sing 47 n n C2 C52 3TL sing 48 n n O1 HO1 3TL sing 49 n n C1 N1 3TL sing 50 n n C1 C3 3TL sing 51 n n C1 H1 3TL sing 52 n n N1 HN1 3TL sing 53 n n C3 C4 3TL sing 54 n n C3 H31 3TL sing 55 n n C3 H32 3TL sing 56 n n C4 C5 3TL doub 57 n y C4 C9 3TL sing 58 n y C5 C6 3TL sing 59 n y C5 H5 3TL sing 60 n n C9 C8 3TL doub 61 n y C9 H9 3TL sing 62 n n C6 C7 3TL doub 63 n y C6 H6 3TL sing 64 n n C8 C7 3TL sing 65 n y C8 H8 3TL sing 66 n n C7 H7 3TL sing 67 n n N51 C51 3TL sing 68 n n N51 HN51 3TL sing 69 n n N51 C61 3TL sing 70 n n C51 C52 3TL sing 71 n n C51 C53 3TL sing 72 n n C51 H51 3TL sing 73 n n C52 O51 3TL sing 74 n n C52 H52 3TL sing 75 n n O51 HO51 3TL sing 76 n n C53 C54 3TL sing 77 n n C53 H531 3TL sing 78 n n C53 H532 3TL sing 79 n n C54 C55 3TL doub 80 n y C54 C59 3TL sing 81 n y C55 C56 3TL sing 82 n y C55 H55 3TL sing 83 n n C59 C58 3TL doub 84 n y C59 H59 3TL sing 85 n n C56 C57 3TL doub 86 n y C56 H56 3TL sing 87 n n C58 C57 3TL sing 88 n y C58 H58 3TL sing 89 n n C57 H57 3TL sing 90 n n N52 C60 3TL sing 91 n n N52 HN52 3TL sing 92 n n N52 C69 3TL sing 93 n n C60 C61 3TL sing 94 n n C60 C62 3TL sing 95 n n C60 H60 3TL sing 96 n n C61 O52 3TL doub 97 n n C62 CG6 3TL sing 98 n n C62 CG5 3TL sing 99 n n C62 H62 3TL sing 100 n n CG6 HG61 3TL sing 101 n n CG6 HG62 3TL sing 102 n n CG6 HG63 3TL sing 103 n n CG5 HG51 3TL sing 104 n n CG5 HG52 3TL sing 105 n n CG5 HG53 3TL sing 106 n n N54 C68 3TL sing 107 n n N54 HN54 3TL sing 108 n n N54 C81 3TL sing 109 n n C68 C69 3TL sing 110 n n C68 C70 3TL sing 111 n n C68 H68 3TL sing 112 n n C69 O54 3TL doub 113 n n C70 H701 3TL sing 114 n n C70 H702 3TL sing 115 n n C70 H703 3TL sing 116 n n C81 O58 3TL doub 117 n n C81 O59 3TL sing 118 n n O59 CA5 3TL sing 119 n n CA5 C50 3TL sing 120 n n CA5 HA51 3TL sing 121 n n CA5 HA52 3TL sing 122 n n C50 C63 3TL doub 123 n y C50 C67 3TL sing 124 n y C63 C64 3TL sing 125 n y C63 H63 3TL sing 126 n n C64 C65 3TL doub 127 n y C64 H64 3TL sing 128 n n C65 C66 3TL sing 129 n y C65 H65 3TL sing 130 n n C66 C67 3TL doub 131 n y C66 H66 3TL sing 132 n n C67 H67 3TL sing 133 n n # _atom_sites.entry_id 5VEA _atom_sites.fract_transf_matrix[1][1] 0.015933 _atom_sites.fract_transf_matrix[1][2] 0.009199 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018398 _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] 0.01216 _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 B 2 3TL A 1 101 200 3TL TL3 . C 3 9AY A 1 102 201 9AY 4G3 . D 4 DMS A 1 103 300 DMS DMS . E 4 DMS A 1 104 301 DMS DMS . F 4 DMS A 1 105 303 DMS DMS . G 5 HOH A 1 201 215 HOH HOH . G 5 HOH A 2 202 227 HOH HOH . G 5 HOH A 3 203 236 HOH HOH . G 5 HOH A 4 204 247 HOH HOH . G 5 HOH A 5 205 240 HOH HOH . G 5 HOH A 6 206 232 HOH HOH . G 5 HOH A 7 207 209 HOH HOH . G 5 HOH A 8 208 257 HOH HOH . G 5 HOH A 9 209 231 HOH HOH . G 5 HOH A 10 210 214 HOH HOH . G 5 HOH A 11 211 255 HOH HOH . G 5 HOH A 12 212 221 HOH HOH . G 5 HOH A 13 213 243 HOH HOH . G 5 HOH A 14 214 216 HOH HOH . G 5 HOH A 15 215 251 HOH HOH . G 5 HOH A 16 216 217 HOH HOH . G 5 HOH A 17 217 242 HOH HOH . G 5 HOH A 18 218 213 HOH HOH . G 5 HOH A 19 219 252 HOH HOH . G 5 HOH A 20 220 235 HOH HOH . G 5 HOH A 21 221 224 HOH HOH . G 5 HOH A 22 222 205 HOH HOH . G 5 HOH A 23 223 229 HOH HOH . G 5 HOH A 24 224 256 HOH HOH . G 5 HOH A 25 225 250 HOH HOH . G 5 HOH A 26 226 244 HOH HOH . G 5 HOH A 27 227 233 HOH HOH . G 5 HOH A 28 228 223 HOH HOH . G 5 HOH A 29 229 248 HOH HOH . G 5 HOH A 30 230 246 HOH HOH . G 5 HOH A 31 231 206 HOH HOH . G 5 HOH A 32 232 241 HOH HOH . G 5 HOH A 33 233 218 HOH HOH . G 5 HOH A 34 234 226 HOH HOH . G 5 HOH A 35 235 210 HOH HOH . G 5 HOH A 36 236 228 HOH HOH . G 5 HOH A 37 237 258 HOH HOH . G 5 HOH A 38 238 237 HOH HOH . G 5 HOH A 39 239 239 HOH HOH . G 5 HOH A 40 240 238 HOH HOH . G 5 HOH A 41 241 212 HOH HOH . G 5 HOH A 42 242 234 HOH HOH . G 5 HOH A 43 243 254 HOH HOH . G 5 HOH A 44 244 230 HOH HOH . G 5 HOH A 45 245 249 HOH HOH . G 5 HOH A 46 246 225 HOH HOH . G 5 HOH A 47 247 253 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 C31 3TL . . . B 2 11.814 11.707 5.606 1 26.16 ? C31 3TL 101 A 1 HETATM 2 O O8 3TL . . . B 2 10.894 10.865 5.887 1 30.6 ? O8 3TL 101 A 1 HETATM 3 O O9 3TL . . . B 2 12.021 11.538 4.29 1 28.47 ? O9 3TL 101 A 1 HETATM 4 C CA 3TL . . . B 2 11.716 10.354 3.492 1 30.26 ? CA 3TL 101 A 1 HETATM 5 C C 3TL . . . B 2 12.391 9.02 3.799 1 30.46 ? C 3TL 101 A 1 HETATM 6 C C13 3TL . . . B 2 11.966 7.925 3.066 1 27.31 ? C13 3TL 101 A 1 HETATM 7 C C14 3TL . . . B 2 12.564 6.668 3.271 1 23.01 ? C14 3TL 101 A 1 HETATM 8 C C15 3TL . . . B 2 13.537 6.649 4.231 1 27.47 ? C15 3TL 101 A 1 HETATM 9 C C16 3TL . . . B 2 13.902 7.748 5.033 1 32.23 ? C16 3TL 101 A 1 HETATM 10 C C17 3TL . . . B 2 13.352 9.016 4.774 1 31.31 ? C17 3TL 101 A 1 HETATM 11 N N4 3TL . . . B 2 12.58 12.515 6.318 1 24.11 ? N4 3TL 101 A 1 HETATM 12 C C18 3TL . . . B 2 12.249 12.528 7.728 1 24.08 ? C18 3TL 101 A 1 HETATM 13 C C19 3TL . . . B 2 11.606 13.835 8.17 1 22.55 ? C19 3TL 101 A 1 HETATM 14 O O4 3TL . . . B 2 12.145 14.936 7.835 1 20.04 ? O4 3TL 101 A 1 HETATM 15 C C20 3TL . . . B 2 13.595 12.14 8.364 1 20.44 ? C20 3TL 101 A 1 HETATM 16 N N2 3TL . . . B 2 10.58 13.82 8.923 1 24.85 ? N2 3TL 101 A 1 HETATM 17 C C10 3TL . . . B 2 9.727 14.81 9.572 1 22.94 ? C10 3TL 101 A 1 HETATM 18 C C11 3TL . . . B 2 9.651 14.634 11.047 1 21.63 ? C11 3TL 101 A 1 HETATM 19 O O2 3TL . . . B 2 8.788 13.803 11.534 1 24.25 ? O2 3TL 101 A 1 HETATM 20 C C12 3TL . . . B 2 8.497 15.125 8.73 1 25.73 ? C12 3TL 101 A 1 HETATM 21 C CG2 3TL . . . B 2 7.742 16.234 9.444 1 24.2 ? CG2 3TL 101 A 1 HETATM 22 C CG1 3TL . . . B 2 8.785 15.584 7.312 1 23.66 ? CG1 3TL 101 A 1 HETATM 23 C C2 3TL . . . B 2 10.736 16.148 14.249 1 37.3 ? C2 3TL 101 A 1 HETATM 24 O O1 3TL . . . B 2 11.142 17.314 13.512 1 46.06 ? O1 3TL 101 A 1 HETATM 25 C C1 3TL . . . B 2 10.825 14.97 13.33 1 33.95 ? C1 3TL 101 A 1 HETATM 26 N N1 3TL . . . B 2 10.461 15.286 11.902 1 25.98 ? N1 3TL 101 A 1 HETATM 27 C C3 3TL . . . B 2 12.161 14.37 13.795 1 34.81 ? C3 3TL 101 A 1 HETATM 28 C C4 3TL . . . B 2 12.377 12.987 13.281 1 35.56 ? C4 3TL 101 A 1 HETATM 29 C C5 3TL . . . B 2 13.186 12.614 12.221 1 40.71 ? C5 3TL 101 A 1 HETATM 30 C C9 3TL . . . B 2 11.703 12.114 14.106 1 37.68 ? C9 3TL 101 A 1 HETATM 31 C C6 3TL . . . B 2 13.275 11.267 11.901 1 38.76 ? C6 3TL 101 A 1 HETATM 32 C C8 3TL . . . B 2 11.776 10.768 13.812 1 39.02 ? C8 3TL 101 A 1 HETATM 33 C C7 3TL . . . B 2 12.533 10.422 12.708 1 39.19 ? C7 3TL 101 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 33 #