data_5QD9 # _model_server_result.job_id e80LjI3gOp5E_l5hhXlejA _model_server_result.datetime_utc '2024-10-18 05:24:29' _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 5qd9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 5QD9 # _exptl.entry_id 5QD9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 529.754 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5S,8S,10R)-8-[(1R)-2-{[1-(3-tert-butylphenyl)cyclopropyl]amino}-1-hydroxyethyl]-4,5,10-trimethyl-1-oxa-4,7-diazacyclohexadecane-3,6-dione _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 104.31 _cell.angle_gamma 90 _cell.entry_id 5QD9 _cell.length_a 81.489 _cell.length_b 103.49 _cell.length_c 99.382 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5QD9 _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 ? monomeric 1 author_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 171 A CYS 155 1_555 A SG CYS 375 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf2 A SG CYS 233 A CYS 217 1_555 A SG CYS 398 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf3 A SG CYS 285 A CYS 269 1_555 A SG CYS 335 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf4 B SG CYS 171 B CYS 155 1_555 B SG CYS 375 B CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf5 B SG CYS 233 B CYS 217 1_555 B SG CYS 398 B CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf6 B SG CYS 285 B CYS 269 1_555 B SG CYS 335 B CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf7 C SG CYS 171 C CYS 155 1_555 C SG CYS 375 C CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf8 C SG CYS 233 C CYS 217 1_555 C SG CYS 398 C CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf9 C SG CYS 285 C CYS 269 1_555 C SG CYS 335 C CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? # _chem_comp.formula 'C31 H51 N3 O4' _chem_comp.formula_weight 529.754 _chem_comp.id E6Y _chem_comp.mon_nstd_flag . _chem_comp.name (5S,8S,10R)-8-[(1R)-2-{[1-(3-tert-butylphenyl)cyclopropyl]amino}-1-hydroxyethyl]-4,5,10-trimethyl-1-oxa-4,7-diazacyclohexadecane-3,6-dione _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 C73 C68 E6Y sing 83 n n C69 C68 E6Y sing 84 n n C68 C61 E6Y sing 85 n n C68 C77 E6Y sing 86 n n C62 C61 E6Y doub 87 n y C62 C64 E6Y sing 88 n y C61 C59 E6Y sing 89 n y C64 C66 E6Y doub 90 n y C59 C58 E6Y doub 91 n y C66 C58 E6Y sing 92 n y C58 C51 E6Y sing 93 n n C52 C51 E6Y sing 94 n n C52 C55 E6Y sing 95 n n C51 C55 E6Y sing 96 n n C51 N49 E6Y sing 97 n n N49 C46 E6Y sing 98 n n C46 C42 E6Y sing 99 n n O44 C42 E6Y sing 100 n n O81 C4 E6Y doub 101 n n C42 C7 E6Y sing 102 n n C38 C12 E6Y sing 103 n n C7 C9 E6Y sing 104 n n C7 N5 E6Y sing 105 n n C4 N5 E6Y sing 106 n n C4 C2 E6Y sing 107 n n C9 C12 E6Y sing 108 n n C82 C2 E6Y sing 109 n n C12 C14 E6Y sing 110 n n C2 N1 E6Y sing 111 n n C14 C17 E6Y sing 112 n n C86 N1 E6Y sing 113 n n N1 C36 E6Y sing 114 n n C17 C20 E6Y sing 115 n n C20 C23 E6Y sing 116 n n C36 O37 E6Y doub 117 n n C36 C33 E6Y sing 118 n n C33 O32 E6Y sing 119 n n C23 C26 E6Y sing 120 n n C29 O32 E6Y sing 121 n n C29 C26 E6Y sing 122 n n C2 H1 E6Y sing 123 n n C12 H2 E6Y sing 124 n n C14 H3 E6Y sing 125 n n C14 H4 E6Y sing 126 n n C17 H5 E6Y sing 127 n n C17 H6 E6Y sing 128 n n C20 H7 E6Y sing 129 n n C20 H8 E6Y sing 130 n n C23 H9 E6Y sing 131 n n C23 H10 E6Y sing 132 n n C26 H11 E6Y sing 133 n n C26 H12 E6Y sing 134 n n C29 H13 E6Y sing 135 n n C29 H14 E6Y sing 136 n n C33 H15 E6Y sing 137 n n C33 H16 E6Y sing 138 n n C38 H17 E6Y sing 139 n n C38 H18 E6Y sing 140 n n C38 H19 E6Y sing 141 n n C42 H20 E6Y sing 142 n n C46 H21 E6Y sing 143 n n C46 H22 E6Y sing 144 n n C52 H23 E6Y sing 145 n n C52 H24 E6Y sing 146 n n C55 H25 E6Y sing 147 n n C55 H26 E6Y sing 148 n n C59 H27 E6Y sing 149 n n C62 H28 E6Y sing 150 n n C64 H29 E6Y sing 151 n n C66 H30 E6Y sing 152 n n C69 H31 E6Y sing 153 n n C69 H32 E6Y sing 154 n n C69 H33 E6Y sing 155 n n C7 H34 E6Y sing 156 n n C73 H35 E6Y sing 157 n n C73 H36 E6Y sing 158 n n C73 H37 E6Y sing 159 n n C77 H38 E6Y sing 160 n n C77 H39 E6Y sing 161 n n C77 H40 E6Y sing 162 n n C82 H41 E6Y sing 163 n n C82 H42 E6Y sing 164 n n C82 H43 E6Y sing 165 n n C86 H44 E6Y sing 166 n n C86 H45 E6Y sing 167 n n C86 H46 E6Y sing 168 n n C9 H47 E6Y sing 169 n n C9 H48 E6Y sing 170 n n N49 H49 E6Y sing 171 n n N5 H51 E6Y sing 172 n n O44 H52 E6Y sing 173 n n # _atom_sites.entry_id 5QD9 _atom_sites.fract_transf_matrix[1][1] 0.012272 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00313 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009663 _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] 0.010384 _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 E6Y A 1 401 1 E6Y BMC . E 2 E6Y B 1 401 1 E6Y BMC . F 2 E6Y C 1 401 1 E6Y BMC . G 3 HOH A 1 501 48 HOH HOH . G 3 HOH A 2 502 47 HOH HOH . G 3 HOH A 3 503 45 HOH HOH . G 3 HOH A 4 504 57 HOH HOH . G 3 HOH A 5 505 46 HOH HOH . G 3 HOH A 6 506 33 HOH HOH . G 3 HOH A 7 507 26 HOH HOH . G 3 HOH A 8 508 28 HOH HOH . G 3 HOH A 9 509 38 HOH HOH . G 3 HOH A 10 510 22 HOH HOH . G 3 HOH A 11 511 19 HOH HOH . G 3 HOH A 12 512 29 HOH HOH . G 3 HOH A 13 513 52 HOH HOH . G 3 HOH A 14 514 7 HOH HOH . G 3 HOH A 15 515 8 HOH HOH . G 3 HOH A 16 516 51 HOH HOH . G 3 HOH A 17 517 21 HOH HOH . G 3 HOH A 18 518 56 HOH HOH . G 3 HOH A 19 519 50 HOH HOH . G 3 HOH A 20 520 10 HOH HOH . G 3 HOH A 21 521 5 HOH HOH . G 3 HOH A 22 522 55 HOH HOH . G 3 HOH A 23 523 43 HOH HOH . G 3 HOH A 24 524 14 HOH HOH . G 3 HOH A 25 525 23 HOH HOH . G 3 HOH A 26 526 18 HOH HOH . H 3 HOH B 1 501 9 HOH HOH . H 3 HOH B 2 502 6 HOH HOH . H 3 HOH B 3 503 35 HOH HOH . H 3 HOH B 4 504 15 HOH HOH . H 3 HOH B 5 505 1 HOH HOH . H 3 HOH B 6 506 40 HOH HOH . H 3 HOH B 7 507 37 HOH HOH . H 3 HOH B 8 508 30 HOH HOH . H 3 HOH B 9 509 2 HOH HOH . H 3 HOH B 10 510 4 HOH HOH . H 3 HOH B 11 511 25 HOH HOH . H 3 HOH B 12 512 39 HOH HOH . H 3 HOH B 13 513 11 HOH HOH . H 3 HOH B 14 514 17 HOH HOH . H 3 HOH B 15 515 59 HOH HOH . H 3 HOH B 16 516 60 HOH HOH . H 3 HOH B 17 517 36 HOH HOH . H 3 HOH B 18 518 13 HOH HOH . I 3 HOH C 1 501 24 HOH HOH . I 3 HOH C 2 502 41 HOH HOH . I 3 HOH C 3 503 31 HOH HOH . I 3 HOH C 4 504 53 HOH HOH . I 3 HOH C 5 505 34 HOH HOH . I 3 HOH C 6 506 32 HOH HOH . I 3 HOH C 7 507 44 HOH HOH . I 3 HOH C 8 508 16 HOH HOH . I 3 HOH C 9 509 42 HOH HOH . I 3 HOH C 10 510 54 HOH HOH . I 3 HOH C 11 511 12 HOH HOH . I 3 HOH C 12 512 3 HOH HOH . I 3 HOH C 13 513 61 HOH HOH . I 3 HOH C 14 514 27 HOH HOH . I 3 HOH C 15 515 58 HOH HOH . I 3 HOH C 16 516 20 HOH HOH . I 3 HOH C 17 517 49 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 C2 E6Y . . . D 2 27.328 5.705 16.209 1 44.52 ? C2 E6Y 401 A 1 HETATM 2 C C4 E6Y . . . D 2 28.388 5.952 15.126 1 48.31 ? C4 E6Y 401 A 1 HETATM 3 C C12 E6Y . . . D 2 31.196 8.387 15.79 1 49.11 ? C12 E6Y 401 A 1 HETATM 4 C C14 E6Y . . . D 2 32.224 9.265 16.527 1 47.96 ? C14 E6Y 401 A 1 HETATM 5 C C17 E6Y . . . D 2 31.626 10.408 17.351 1 41.59 ? C17 E6Y 401 A 1 HETATM 6 C C20 E6Y . . . D 2 30.581 9.966 18.344 1 39.01 ? C20 E6Y 401 A 1 HETATM 7 C C23 E6Y . . . D 2 31.114 9.075 19.46 1 46.23 ? C23 E6Y 401 A 1 HETATM 8 C C26 E6Y . . . D 2 30.127 8.815 20.551 1 48.11 ? C26 E6Y 401 A 1 HETATM 9 C C29 E6Y . . . D 2 28.729 9.051 20.096 1 61.57 ? C29 E6Y 401 A 1 HETATM 10 C C33 E6Y . . . D 2 26.862 7.806 19.335 1 53.38 ? C33 E6Y 401 A 1 HETATM 11 C C36 E6Y . . . D 2 26.919 6.63 18.399 1 59.11 ? C36 E6Y 401 A 1 HETATM 12 C C38 E6Y . . . D 2 30.593 9.12 14.601 1 45.22 ? C38 E6Y 401 A 1 HETATM 13 C C42 E6Y . . . D 2 31.531 4.785 14.352 1 41.5 ? C42 E6Y 401 A 1 HETATM 14 C C46 E6Y . . . D 2 30.644 3.956 13.439 1 35.35 ? C46 E6Y 401 A 1 HETATM 15 C C51 E6Y . . . D 2 30.733 2.074 11.969 1 46.91 ? C51 E6Y 401 A 1 HETATM 16 C C52 E6Y . . . D 2 31.146 0.644 11.821 1 43.75 ? C52 E6Y 401 A 1 HETATM 17 C C55 E6Y . . . D 2 29.867 0.953 12.538 1 37.91 ? C55 E6Y 401 A 1 HETATM 18 C C58 E6Y . . . D 2 30.665 2.806 10.649 1 49.56 ? C58 E6Y 401 A 1 HETATM 19 C C59 E6Y . . . D 2 31.852 3.146 10.004 1 39.88 ? C59 E6Y 401 A 1 HETATM 20 C C61 E6Y . . . D 2 31.821 3.827 8.792 1 44.99 ? C61 E6Y 401 A 1 HETATM 21 C C62 E6Y . . . D 2 30.59 4.177 8.244 1 41.32 ? C62 E6Y 401 A 1 HETATM 22 C C64 E6Y . . . D 2 29.408 3.851 8.888 1 41.59 ? C64 E6Y 401 A 1 HETATM 23 C C66 E6Y . . . D 2 29.445 3.161 10.082 1 51.43 ? C66 E6Y 401 A 1 HETATM 24 C C68 E6Y . . . D 2 33.116 4.209 8.074 1 50.21 ? C68 E6Y 401 A 1 HETATM 25 C C69 E6Y . . . D 2 33.994 2.979 7.836 1 39.96 ? C69 E6Y 401 A 1 HETATM 26 C C7 E6Y . . . D 2 30.813 6.095 14.684 1 40.85 ? C7 E6Y 401 A 1 HETATM 27 C C73 E6Y . . . D 2 32.788 4.852 6.747 1 34.5 ? C73 E6Y 401 A 1 HETATM 28 C C77 E6Y . . . D 2 33.913 5.224 8.917 1 59.18 ? C77 E6Y 401 A 1 HETATM 29 C C82 E6Y . . . D 2 25.97 5.341 15.629 1 39.01 ? C82 E6Y 401 A 1 HETATM 30 C C86 E6Y . . . D 2 27.525 8.184 16.574 1 55.11 ? C86 E6Y 401 A 1 HETATM 31 C C9 E6Y . . . D 2 31.796 7.031 15.371 1 40.03 ? C9 E6Y 401 A 1 HETATM 32 N N1 E6Y . . . D 2 27.249 6.851 17.115 1 60.38 ? N1 E6Y 401 A 1 HETATM 33 N N49 E6Y . . . D 2 31.459 2.821 12.986 1 44.41 ? N49 E6Y 401 A 1 HETATM 34 N N5 E6Y . . . D 2 29.659 5.867 15.547 1 40.77 ? N5 E6Y 401 A 1 HETATM 35 O O32 E6Y . . . D 2 28.035 7.822 20.122 1 66.14 ? O32 E6Y 401 A 1 HETATM 36 O O37 E6Y . . . D 2 26.707 5.504 18.827 1 59.72 ? O37 E6Y 401 A 1 HETATM 37 O O44 E6Y . . . D 2 32.767 5.054 13.676 1 36.91 ? O44 E6Y 401 A 1 HETATM 38 O O81 E6Y . . . D 2 28.072 6.21 13.966 1 58.51 ? O81 E6Y 401 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 38 #