data_3KYR # _model_server_result.job_id Sc9shIT7KoG49nbab8VBQw _model_server_result.datetime_utc '2024-10-19 16:42:11' _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 3kyr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 3KYR # _exptl.entry_id 3KYR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 722.791 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[[(2S)-2-[[[(2S)-2-[[(2S)-2-[[(2S)-2-azanyl-3-(1H-1,2,3,4-tetrazol-5-ylcarbonylamino)propanoyl]amino]-3-methyl-butanoyl]amino]-4-methyl-pentanoyl]amino]methyl]-2-hydroxy-4-phenyl-butanoyl]amino]benzoic acid' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.9 _cell.angle_gamma 90 _cell.entry_id 3KYR _cell.length_a 81.762 _cell.length_b 102.774 _cell.length_c 101.427 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KYR _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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,G 1 1 B,E,H 2 1 C,F,I 3 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 D N N ? 2 E N N ? 2 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 175 A CYS 155 1_555 A SG CYS 379 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf2 A SG CYS 237 A CYS 217 1_555 A SG CYS 402 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf3 A SG CYS 289 A CYS 269 1_555 A SG CYS 339 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf4 B SG CYS 175 B CYS 155 1_555 B SG CYS 379 B CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? disulf ? disulf5 B SG CYS 237 B CYS 217 1_555 B SG CYS 402 B CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? disulf ? disulf6 B SG CYS 289 B CYS 269 1_555 B SG CYS 339 B CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf7 C SG CYS 175 C CYS 155 1_555 C SG CYS 379 C CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf8 C SG CYS 237 C CYS 217 1_555 C SG CYS 402 C CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? disulf ? disulf9 C SG CYS 289 C CYS 269 1_555 C SG CYS 339 C CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? # _chem_comp.formula 'C34 H46 N10 O8' _chem_comp.formula_weight 722.791 _chem_comp.id 038 _chem_comp.mon_nstd_flag . _chem_comp.name '3-[[(2S)-2-[[[(2S)-2-[[(2S)-2-[[(2S)-2-azanyl-3-(1H-1,2,3,4-tetrazol-5-ylcarbonylamino)propanoyl]amino]-3-methyl-butanoyl]amino]-4-methyl-pentanoyl]amino]methyl]-2-hydroxy-4-phenyl-butanoyl]amino]benzoic acid' _chem_comp.type peptide-like _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 O1 C7 038 doub 1 n n O2 C4 038 doub 2 n n N3 C6 038 sing 3 n n N3 C7 038 sing 4 n n N3 HN3 038 sing 5 n n C4 C5 038 sing 6 n n N7 N6 038 sing 7 n y N7 C8 038 doub 8 n y C5 C6 038 sing 9 n n C5 N8 038 sing 10 n n C5 H5 038 sing 11 n n N6 N5 038 doub 12 n y C6 H6 038 sing 13 n n C6 H6A 038 sing 14 n n N5 N4 038 sing 15 n y C7 C8 038 sing 16 n n N4 C8 038 sing 17 n y N4 HN4 038 sing 18 n n N8 HN8 038 sing 19 n n N8 HN8A 038 sing 20 n n N2 C3 038 sing 21 n n N2 HN2 038 sing 22 n n C3 C2 038 sing 23 n n C3 C9 038 sing 24 n n C3 H3 038 sing 25 n n C2 O3 038 doub 26 n n C9 C10 038 sing 27 n n C9 C11 038 sing 28 n n C9 H9 038 sing 29 n n C10 H10 038 sing 30 n n C10 H10A 038 sing 31 n n C10 H10B 038 sing 32 n n C11 H11 038 sing 33 n n C11 H11A 038 sing 34 n n C11 H11B 038 sing 35 n n N1 C1 038 sing 36 n n N1 HN1 038 sing 37 n n C1 C19 038 sing 38 n n C1 C12 038 sing 39 n n C1 H1 038 sing 40 n n C19 O4 038 doub 41 n n C12 C13 038 sing 42 n n C12 H12 038 sing 43 n n C12 H12A 038 sing 44 n n C13 C14 038 sing 45 n n C13 C18 038 sing 46 n n C13 H13 038 sing 47 n n C14 H14 038 sing 48 n n C14 H14A 038 sing 49 n n C14 H14B 038 sing 50 n n C18 H18 038 sing 51 n n C18 H18A 038 sing 52 n n C18 H18B 038 sing 53 n n O5 C20 038 sing 54 n n O5 HO5 038 sing 55 n n O6 C29 038 doub 56 n n N9 C21 038 sing 57 n n N9 HN9 038 sing 58 n n C20 C21 038 sing 59 n n C20 C22 038 sing 60 n n C20 C29 038 sing 61 n n C21 H21 038 sing 62 n n C21 H21A 038 sing 63 n n C22 C52 038 sing 64 n n C22 H22 038 sing 65 n n C22 H22A 038 sing 66 n n C23 C24 038 doub 67 n y C23 C28 038 sing 68 n y C23 C52 038 sing 69 n n C24 C25 038 sing 70 n y C24 H24 038 sing 71 n n C25 C26 038 doub 72 n y C25 H25 038 sing 73 n n C26 C27 038 sing 74 n y C26 H26 038 sing 75 n n C27 C28 038 doub 76 n y C27 H27 038 sing 77 n n C28 H28 038 sing 78 n n C52 H52 038 sing 79 n n C52 H52A 038 sing 80 n n C36 O8 038 doub 81 n n C36 O7 038 sing 82 n n C36 C34 038 sing 83 n n O7 HO7 038 sing 84 n n C34 C33 038 sing 85 n y C34 C35 038 doub 86 n y C33 C30 038 doub 87 n y C33 H33 038 sing 88 n n C30 C31 038 sing 89 n y C30 N10 038 sing 90 n n C31 C32 038 doub 91 n y C31 H31 038 sing 92 n n C32 C35 038 sing 93 n y C32 H32 038 sing 94 n n C35 H35 038 sing 95 n n N10 HN10 038 sing 96 n n C4 N2 038 sing 97 n n C2 N1 038 sing 98 n n C19 N9 038 sing 99 n n C29 N10 038 sing 100 n n # _atom_sites.entry_id 3KYR _atom_sites.fract_transf_matrix[1][1] 0.012231 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002802 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00973 _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] 0.010115 _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 D 2 038 A 1 500 500 038 038 . E 2 038 B 1 500 500 038 038 . F 2 038 C 1 500 500 038 038 . G 3 HOH A 1 386 2 HOH HOH . G 3 HOH A 2 387 12 HOH HOH . G 3 HOH A 3 388 19 HOH HOH . G 3 HOH A 4 389 20 HOH HOH . G 3 HOH A 5 390 22 HOH HOH . G 3 HOH A 6 391 25 HOH HOH . G 3 HOH A 7 392 26 HOH HOH . G 3 HOH A 8 393 27 HOH HOH . G 3 HOH A 9 394 29 HOH HOH . G 3 HOH A 10 395 30 HOH HOH . G 3 HOH A 11 396 31 HOH HOH . G 3 HOH A 12 397 35 HOH HOH . G 3 HOH A 13 398 37 HOH HOH . G 3 HOH A 14 399 38 HOH HOH . G 3 HOH A 15 400 45 HOH HOH . G 3 HOH A 16 401 51 HOH HOH . G 3 HOH A 17 402 54 HOH HOH . G 3 HOH A 18 403 56 HOH HOH . G 3 HOH A 19 404 58 HOH HOH . G 3 HOH A 20 405 61 HOH HOH . G 3 HOH A 21 406 65 HOH HOH . G 3 HOH A 22 407 66 HOH HOH . G 3 HOH A 23 408 69 HOH HOH . G 3 HOH A 24 409 75 HOH HOH . H 3 HOH B 1 386 5 HOH HOH . H 3 HOH B 2 387 7 HOH HOH . H 3 HOH B 3 388 8 HOH HOH . H 3 HOH B 4 389 13 HOH HOH . H 3 HOH B 5 390 14 HOH HOH . H 3 HOH B 6 391 18 HOH HOH . H 3 HOH B 7 392 21 HOH HOH . H 3 HOH B 8 393 28 HOH HOH . H 3 HOH B 9 394 32 HOH HOH . H 3 HOH B 10 395 34 HOH HOH . H 3 HOH B 11 396 36 HOH HOH . H 3 HOH B 12 397 41 HOH HOH . H 3 HOH B 13 398 43 HOH HOH . H 3 HOH B 14 399 47 HOH HOH . H 3 HOH B 15 400 48 HOH HOH . H 3 HOH B 16 401 49 HOH HOH . H 3 HOH B 17 402 50 HOH HOH . H 3 HOH B 18 403 57 HOH HOH . H 3 HOH B 19 404 59 HOH HOH . H 3 HOH B 20 405 62 HOH HOH . H 3 HOH B 21 406 63 HOH HOH . H 3 HOH B 22 407 68 HOH HOH . H 3 HOH B 23 408 71 HOH HOH . H 3 HOH B 24 409 73 HOH HOH . H 3 HOH B 25 410 74 HOH HOH . H 3 HOH B 26 411 77 HOH HOH . I 3 HOH C 1 386 1 HOH HOH . I 3 HOH C 2 387 3 HOH HOH . I 3 HOH C 3 388 4 HOH HOH . I 3 HOH C 4 389 6 HOH HOH . I 3 HOH C 5 390 9 HOH HOH . I 3 HOH C 6 391 10 HOH HOH . I 3 HOH C 7 392 11 HOH HOH . I 3 HOH C 8 393 15 HOH HOH . I 3 HOH C 9 394 16 HOH HOH . I 3 HOH C 10 395 17 HOH HOH . I 3 HOH C 11 396 23 HOH HOH . I 3 HOH C 12 397 24 HOH HOH . I 3 HOH C 13 398 33 HOH HOH . I 3 HOH C 14 399 39 HOH HOH . I 3 HOH C 15 400 40 HOH HOH . I 3 HOH C 16 401 42 HOH HOH . I 3 HOH C 17 402 44 HOH HOH . I 3 HOH C 18 403 46 HOH HOH . I 3 HOH C 19 404 53 HOH HOH . I 3 HOH C 20 405 55 HOH HOH . I 3 HOH C 21 406 60 HOH HOH . I 3 HOH C 22 407 64 HOH HOH . I 3 HOH C 23 408 67 HOH HOH . I 3 HOH C 24 409 70 HOH HOH . I 3 HOH C 25 410 72 HOH HOH . I 3 HOH C 26 411 76 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 O1 038 . . . D 2 41.425 12.206 36.947 1 21.96 ? O1 038 500 A 1 HETATM 2 O O2 038 . . . D 2 39.454 15.217 38.298 1 17.78 ? O2 038 500 A 1 HETATM 3 N N3 038 . . . D 2 39.375 11.842 37.801 1 20.12 ? N3 038 500 A 1 HETATM 4 C C4 038 . . . D 2 38.446 14.573 38.028 1 16.52 ? C4 038 500 A 1 HETATM 5 N N7 038 . . . D 2 42.665 11.117 39.177 1 20.04 ? N7 038 500 A 1 HETATM 6 C C5 038 . . . D 2 38.43 13.883 36.698 1 16.06 ? C5 038 500 A 1 HETATM 7 N N6 038 . . . D 2 42.852 10.492 40.428 1 21.79 ? N6 038 500 A 1 HETATM 8 C C6 038 . . . D 2 38.515 12.357 36.739 1 19.73 ? C6 038 500 A 1 HETATM 9 N N5 038 . . . D 2 41.681 10.211 40.949 1 20.22 ? N5 038 500 A 1 HETATM 10 C C7 038 . . . D 2 40.695 11.784 37.82 1 20.29 ? C7 038 500 A 1 HETATM 11 N N4 038 . . . D 2 40.706 10.666 40.056 1 20.55 ? N4 038 500 A 1 HETATM 12 C C8 038 . . . D 2 41.339 11.201 38.996 1 20.51 ? C8 038 500 A 1 HETATM 13 N N8 038 . . . D 2 39.499 14.437 35.907 1 13.64 ? N8 038 500 A 1 HETATM 14 N N2 038 . . . D 2 37.411 14.509 38.762 1 12.91 ? N2 038 500 A 1 HETATM 15 C C3 038 . . . D 2 37.393 15.173 40.046 1 13.28 ? C3 038 500 A 1 HETATM 16 C C2 038 . . . D 2 38.291 14.423 40.991 1 16.16 ? C2 038 500 A 1 HETATM 17 O O3 038 . . . D 2 38.336 13.208 40.921 1 16.96 ? O3 038 500 A 1 HETATM 18 C C9 038 . . . D 2 35.964 15.183 40.566 1 13.18 ? C9 038 500 A 1 HETATM 19 C C10 038 . . . D 2 35.412 13.787 40.888 1 10.55 ? C10 038 500 A 1 HETATM 20 C C11 038 . . . D 2 35.878 16.11 41.777 1 11.09 ? C11 038 500 A 1 HETATM 21 N N1 038 . . . D 2 39.046 15.111 41.858 1 18.11 ? N1 038 500 A 1 HETATM 22 C C1 038 . . . D 2 39.937 14.373 42.766 1 17.97 ? C1 038 500 A 1 HETATM 23 C C19 038 . . . D 2 39.252 14.149 44.061 1 18.2 ? C19 038 500 A 1 HETATM 24 O O4 038 . . . D 2 38.226 14.768 44.299 1 17.44 ? O4 038 500 A 1 HETATM 25 C C12 038 . . . D 2 41.146 15.266 42.985 1 16.9 ? C12 038 500 A 1 HETATM 26 C C13 038 . . . D 2 41.925 15.475 41.688 1 17.64 ? C13 038 500 A 1 HETATM 27 C C14 038 . . . D 2 42.576 14.179 41.193 1 16.46 ? C14 038 500 A 1 HETATM 28 C C18 038 . . . D 2 42.958 16.569 41.89 1 16.22 ? C18 038 500 A 1 HETATM 29 O O5 038 . . . D 2 41.549 12.369 46.949 1 16.43 ? O5 038 500 A 1 HETATM 30 O O6 038 . . . D 2 40.516 15.684 46.888 1 13.77 ? O6 038 500 A 1 HETATM 31 N N9 038 . . . D 2 39.809 13.266 44.888 1 20.23 ? N9 038 500 A 1 HETATM 32 C C20 038 . . . D 2 40.538 13.334 47.153 1 14.82 ? C20 038 500 A 1 HETATM 33 C C21 038 . . . D 2 39.369 12.906 46.245 1 18.13 ? C21 038 500 A 1 HETATM 34 C C22 038 . . . D 2 40.199 13.359 48.645 1 21.47 ? C22 038 500 A 1 HETATM 35 C C23 038 . . . D 2 40.715 13.783 51.043 1 36.17 ? C23 038 500 A 1 HETATM 36 C C24 038 . . . D 2 41.606 13.499 52.106 1 38.62 ? C24 038 500 A 1 HETATM 37 C C25 038 . . . D 2 41.119 13.338 53.42 1 40.39 ? C25 038 500 A 1 HETATM 38 C C26 038 . . . D 2 39.736 13.444 53.694 1 38.46 ? C26 038 500 A 1 HETATM 39 C C27 038 . . . D 2 38.839 13.714 52.644 1 39.63 ? C27 038 500 A 1 HETATM 40 C C28 038 . . . D 2 39.332 13.886 51.331 1 37.78 ? C28 038 500 A 1 HETATM 41 C C29 038 . . . D 2 41.152 14.654 46.787 1 13.08 ? C29 038 500 A 1 HETATM 42 C C52 038 . . . D 2 41.239 13.941 49.617 1 30.04 ? C52 038 500 A 1 HETATM 43 C C36 038 . . . D 2 43.017 19.461 45.735 1 14.73 ? C36 038 500 A 1 HETATM 44 O O8 038 . . . D 2 41.971 19.725 46.415 1 18.49 ? O8 038 500 A 1 HETATM 45 O O7 038 . . . D 2 43.667 20.345 45.111 1 16.37 ? O7 038 500 A 1 HETATM 46 C C34 038 . . . D 2 43.513 18.044 45.695 1 13.53 ? C34 038 500 A 1 HETATM 47 C C33 038 . . . D 2 42.667 16.992 46.113 1 11.03 ? C33 038 500 A 1 HETATM 48 C C30 038 . . . D 2 43.166 15.688 46.087 1 8.45 ? C30 038 500 A 1 HETATM 49 C C31 038 . . . D 2 44.48 15.449 45.665 1 11.16 ? C31 038 500 A 1 HETATM 50 C C32 038 . . . D 2 45.327 16.483 45.26 1 12.44 ? C32 038 500 A 1 HETATM 51 C C35 038 . . . D 2 44.836 17.807 45.276 1 12.97 ? C35 038 500 A 1 HETATM 52 N N10 038 . . . D 2 42.415 14.611 46.394 1 9.91 ? N10 038 500 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 52 #