data_7RKP # _model_server_result.job_id hlGZoIf3iZRPza4S6_7KHw _model_server_result.datetime_utc '2024-11-26 00:32:02' _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 7rkp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 7RKP # _exptl.entry_id 7RKP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 421.446 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (5R)-5-hydroxy-16,21-dioxa-3,8,28-triazatetracyclo[20.3.1.1~2,6~.1~11,15~]octacosa-1(26),2,6(28),11(27),12,14,22,24-octaene-4,7-dione _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 90 _cell.entry_id 7RKP _cell.length_a 89.69 _cell.length_b 89.69 _cell.length_c 133.156 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RKP _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall 'I 4 2' _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 89.69 89.69 0 3 'crystal symmetry operation' 3_655 -y+1,x,z 0 -1 0 1 0 0 0 0 1 89.69 0 0 4 'crystal symmetry operation' 4_565 y,-x+1,z 0 1 0 -1 0 0 0 0 1 0 89.69 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A NE2 HIS 61 A HIS 41 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc2 A OE2 GLU 81 A GLU 80 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc3 A OD2 ASP 109 A ASP 108 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc4 A OD1 ASP 109 A ASP 108 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc5 A OE2 GLU 120 A GLU 119 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc6 A O ILE 121 A ILE 120 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc7 C O4 5Y1 . A 5Y1 402 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc8 C O5 5Y1 . A 5Y1 402 1_555 D MN MN . A MN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc9 C O1 5Y1 . A 5Y1 402 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.719 ? metalc ? metalc10 C O4 5Y1 . A 5Y1 402 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc11 E MN MN . A MN 404 1_555 I O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc12 E MN MN . A MN 404 1_555 I O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? # _chem_comp.formula 'C23 H23 N3 O5' _chem_comp.formula_weight 421.446 _chem_comp.id 5Y1 _chem_comp.mon_nstd_flag . _chem_comp.name (5R)-5-hydroxy-16,21-dioxa-3,8,28-triazatetracyclo[20.3.1.1~2,6~.1~11,15~]octacosa-1(26),2,6(28),11(27),12,14,22,24-octaene-4,7-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 O5 C23 5Y1 doub 1 n n O4 C22 5Y1 sing 2 n n C23 C22 5Y1 sing 3 n n C23 N3 5Y1 sing 4 n n C22 C10 5Y1 sing 5 n n N3 C11 5Y1 doub 6 n n O1 C1 5Y1 doub 7 n n C10 C1 5Y1 sing 8 n n C10 N2 5Y1 doub 9 n n C11 N2 5Y1 sing 10 n n C11 C12 5Y1 sing 11 n n C1 N1 5Y1 sing 12 n n C21 C12 5Y1 doub 13 n y C21 C16 5Y1 sing 14 n y C12 C13 5Y1 sing 15 n y C17 O2 5Y1 sing 16 n n C17 C18 5Y1 sing 17 n n O2 C16 5Y1 sing 18 n n C16 C15 5Y1 doub 19 n y C13 C14 5Y1 doub 20 n y N1 C2 5Y1 sing 21 n n C18 C19 5Y1 sing 22 n n C15 C14 5Y1 sing 23 n y C2 C3 5Y1 sing 24 n n C19 C20 5Y1 sing 25 n n C20 O3 5Y1 sing 26 n n C3 C4 5Y1 sing 27 n n C5 C4 5Y1 doub 28 n y C5 C6 5Y1 sing 29 n y C4 C9 5Y1 sing 30 n y O3 C6 5Y1 sing 31 n n C6 C7 5Y1 doub 32 n y C9 C8 5Y1 doub 33 n y C7 C8 5Y1 sing 34 n y C3 H1 5Y1 sing 35 n n C3 H2 5Y1 sing 36 n n C2 H3 5Y1 sing 37 n n C2 H4 5Y1 sing 38 n n C13 H5 5Y1 sing 39 n n C14 H6 5Y1 sing 40 n n C15 H7 5Y1 sing 41 n n C17 H8 5Y1 sing 42 n n C17 H9 5Y1 sing 43 n n C18 H10 5Y1 sing 44 n n C18 H11 5Y1 sing 45 n n C19 H12 5Y1 sing 46 n n C19 H13 5Y1 sing 47 n n C20 H14 5Y1 sing 48 n n C20 H15 5Y1 sing 49 n n C21 H16 5Y1 sing 50 n n C22 H17 5Y1 sing 51 n n C5 H18 5Y1 sing 52 n n C7 H19 5Y1 sing 53 n n C8 H20 5Y1 sing 54 n n C9 H21 5Y1 sing 55 n n N1 H22 5Y1 sing 56 n n O4 H23 5Y1 sing 57 n n # _atom_sites.entry_id 7RKP _atom_sites.fract_transf_matrix[1][1] 0.01115 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01115 _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] 0.00751 _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 QQ4 A 1 401 401 QQ4 PVP . C 3 5Y1 A 1 402 402 5Y1 C21 . D 4 MN A 1 403 301 MN MN . E 4 MN A 1 404 302 MN MN . F 5 SO4 A 1 405 1 SO4 SO4 . G 5 SO4 A 1 406 2 SO4 SO4 . H 5 SO4 A 1 407 3 SO4 SO4 . I 6 HOH A 1 501 5 HOH HOH . I 6 HOH A 2 502 3 HOH HOH . I 6 HOH A 3 503 1 HOH HOH . I 6 HOH A 4 504 2 HOH HOH . I 6 HOH A 5 505 4 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 C6 5Y1 . . . C 3 10.523 40.192 -11.416 1 116.28 ? C6 5Y1 402 A 1 HETATM 2 C C4 5Y1 . . . C 3 12.628 41.245 -11.898 1 109.89 ? C4 5Y1 402 A 1 HETATM 3 C C3 5Y1 . . . C 3 13.453 42.231 -12.722 1 99.82 ? C3 5Y1 402 A 1 HETATM 4 C C2 5Y1 . . . C 3 13.226 41.931 -14.201 1 102.69 ? C2 5Y1 402 A 1 HETATM 5 C C1 5Y1 . . . C 3 14.901 42.061 -16.17 1 73.88 ? C1 5Y1 402 A 1 HETATM 6 C C10 5Y1 . . . C 3 14.733 40.624 -16.688 1 82.92 ? C10 5Y1 402 A 1 HETATM 7 C C11 5Y1 . . . C 3 13.753 38.515 -16.635 1 97.91 ? C11 5Y1 402 A 1 HETATM 8 C C12 5Y1 . . . C 3 12.758 37.559 -15.982 1 122.95 ? C12 5Y1 402 A 1 HETATM 9 C C13 5Y1 . . . C 3 13.225 36.432 -15.327 1 136.45 ? C13 5Y1 402 A 1 HETATM 10 C C14 5Y1 . . . C 3 12.33 35.559 -14.725 1 141.41 ? C14 5Y1 402 A 1 HETATM 11 C C15 5Y1 . . . C 3 10.968 35.823 -14.777 1 140.83 ? C15 5Y1 402 A 1 HETATM 12 C C16 5Y1 . . . C 3 10.502 36.954 -15.427 1 136.05 ? C16 5Y1 402 A 1 HETATM 13 C C17 5Y1 . . . C 3 8.772 38.547 -15.655 1 139.04 ? C17 5Y1 402 A 1 HETATM 14 C C18 5Y1 . . . C 3 7.531 38.864 -14.823 1 132.27 ? C18 5Y1 402 A 1 HETATM 15 C C19 5Y1 . . . C 3 7.905 39.84 -13.71 1 128.5 ? C19 5Y1 402 A 1 HETATM 16 C C20 5Y1 . . . C 3 8.886 39.171 -12.748 1 118.65 ? C20 5Y1 402 A 1 HETATM 17 C C21 5Y1 . . . C 3 11.399 37.822 -16.028 1 125.16 ? C21 5Y1 402 A 1 HETATM 18 C C22 5Y1 . . . C 3 15.492 40.217 -17.737 1 71.93 ? C22 5Y1 402 A 1 HETATM 19 C C23 5Y1 . . . C 3 15.373 38.956 -18.223 1 81.09 ? C23 5Y1 402 A 1 HETATM 20 C C5 5Y1 . . . C 3 11.276 41.089 -12.161 1 114.56 ? C5 5Y1 402 A 1 HETATM 21 C C7 5Y1 . . . C 3 11.127 39.452 -10.408 1 116.31 ? C7 5Y1 402 A 1 HETATM 22 C C8 5Y1 . . . C 3 12.479 39.61 -10.148 1 103.48 ? C8 5Y1 402 A 1 HETATM 23 C C9 5Y1 . . . C 3 13.226 40.505 -10.894 1 100.64 ? C9 5Y1 402 A 1 HETATM 24 N N1 5Y1 . . . C 3 14.199 42.632 -15.022 1 73.74 ? N1 5Y1 402 A 1 HETATM 25 N N2 5Y1 . . . C 3 13.878 39.77 -16.154 1 96.02 ? N2 5Y1 402 A 1 HETATM 26 N N3 5Y1 . . . C 3 14.514 38.113 -17.677 1 87.84 ? N3 5Y1 402 A 1 HETATM 27 O O1 5Y1 . . . C 3 15.666 42.763 -16.739 1 70.2 ? O1 5Y1 402 A 1 HETATM 28 O O2 5Y1 . . . C 3 9.125 37.205 -15.47 1 139.4 ? O2 5Y1 402 A 1 HETATM 29 O O3 5Y1 . . . C 3 9.158 40.033 -11.68 1 115.95 ? O3 5Y1 402 A 1 HETATM 30 O O4 5Y1 . . . C 3 16.405 41.105 -18.322 1 66.05 ? O4 5Y1 402 A 1 HETATM 31 O O5 5Y1 . . . C 3 16.042 38.61 -19.139 1 57.87 ? O5 5Y1 402 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #