data_8HPD # _model_server_result.job_id FYbDxn9sa9q-1i341TE49Q _model_server_result.datetime_utc '2024-11-25 02:46:25' _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 8hpd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":303}' # _entry.id 8HPD # _exptl.entry_id 8HPD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 600.87 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL _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 90 _cell.angle_gamma 90 _cell.entry_id 8HPD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8HPD _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? _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 ? 6 F N N ? 6 Y N N ? 6 RA 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 metalc ? metalc1 A O TRP 37 A TRP 11 1_555 G MG CHL . A CHL 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc2 A O VAL 134 A VAL 108 1_555 K MG CHL . A CHL 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? metalc ? metalc3 A OD1 ASN 198 A ASN 172 1_555 R MG CLA . A CLA 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? metalc ? metalc4 B O TRP 39 B TRP 11 1_555 Z MG CHL . B CHL 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc5 B OE2 GLU 81 B GLU 53 1_555 AA MG CHL . B CHL 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc6 B O VAL 136 B VAL 108 1_555 DA MG CHL . B CHL 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc7 B OE2 GLU 198 B GLU 170 1_555 IA MG CLA . B CLA 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? metalc ? metalc8 B OD1 ASN 201 B ASN 173 1_555 KA MG CLA . B CLA 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.932 ? metalc ? metalc9 C O TRP 41 C TRP 11 1_555 SA MG CHL . C CHL 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.912 ? metalc ? metalc10 C O ILE 138 C ILE 108 1_555 WA MG CHL . C CHL 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc11 C OD1 ASN 202 C ASN 172 1_555 DB MG CLA . C CLA 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? # _chem_comp.formula 'C40 H56 O4' _chem_comp.formula_weight 600.87 _chem_comp.id NEX _chem_comp.mon_nstd_flag . _chem_comp.name (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "(3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL;9'-CIS-NEOXANTHIN" # 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 C1 C2 NEX sing 882 n n C1 C6 NEX sing 883 n n C1 C16 NEX sing 884 n n C1 C17 NEX sing 885 n n C2 C3 NEX sing 886 n n C2 H21 NEX sing 887 n n C2 H22 NEX sing 888 n n C3 C4 NEX sing 889 n n C3 O3 NEX sing 890 n n C3 H3 NEX sing 891 n n C4 C5 NEX sing 892 n n C4 H41 NEX sing 893 n n C4 H42 NEX sing 894 n n C5 C6 NEX sing 895 n n C5 C18 NEX sing 896 n n C5 O4 NEX sing 897 n n C6 C7 NEX doub 898 n n C7 C8 NEX doub 899 n n C8 C9 NEX sing 900 n n C8 H8 NEX sing 901 n n C9 C10 NEX doub 902 e n C9 C19 NEX sing 903 n n C10 C11 NEX sing 904 n n C10 H10 NEX sing 905 n n C11 C12 NEX doub 906 e n C11 H11 NEX sing 907 n n C12 C13 NEX sing 908 n n C12 H12 NEX sing 909 n n C13 C14 NEX doub 910 e n C13 C20 NEX sing 911 n n C14 C15 NEX sing 912 n n C14 H14 NEX sing 913 n n C15 C35 NEX doub 914 e n C15 H15 NEX sing 915 n n C16 H161 NEX sing 916 n n C16 H162 NEX sing 917 n n C16 H163 NEX sing 918 n n C17 H171 NEX sing 919 n n C17 H172 NEX sing 920 n n C17 H173 NEX sing 921 n n C18 H181 NEX sing 922 n n C18 H182 NEX sing 923 n n C18 H183 NEX sing 924 n n C19 H191 NEX sing 925 n n C19 H192 NEX sing 926 n n C19 H193 NEX sing 927 n n C20 H201 NEX sing 928 n n C20 H202 NEX sing 929 n n C20 H203 NEX sing 930 n n O3 HO3 NEX sing 931 n n O4 HO4 NEX sing 932 n n C21 C22 NEX sing 933 n n C21 C26 NEX sing 934 n n C21 C36 NEX sing 935 n n C21 C37 NEX sing 936 n n C22 C23 NEX sing 937 n n C22 H221 NEX sing 938 n n C22 H222 NEX sing 939 n n C23 C24 NEX sing 940 n n C23 O23 NEX sing 941 n n C23 H23 NEX sing 942 n n C24 C25 NEX sing 943 n n C24 H241 NEX sing 944 n n C24 H242 NEX sing 945 n n C25 C26 NEX sing 946 n n C25 C38 NEX sing 947 n n C25 O24 NEX sing 948 n n C26 C27 NEX sing 949 n n C26 O24 NEX sing 950 n n C27 C28 NEX doub 951 e n C27 H27 NEX sing 952 n n C28 C29 NEX sing 953 n n C28 H28 NEX sing 954 n n C29 C30 NEX doub 955 z n C29 C39 NEX sing 956 n n C30 C31 NEX sing 957 n n C30 H30 NEX sing 958 n n C31 C32 NEX doub 959 e n C31 H31 NEX sing 960 n n C32 C33 NEX sing 961 n n C32 H32 NEX sing 962 n n C33 C34 NEX doub 963 e n C33 C40 NEX sing 964 n n C34 C35 NEX sing 965 n n C34 H34 NEX sing 966 n n C35 H35 NEX sing 967 n n C36 H361 NEX sing 968 n n C36 H362 NEX sing 969 n n C36 H363 NEX sing 970 n n C37 H371 NEX sing 971 n n C37 H372 NEX sing 972 n n C37 H373 NEX sing 973 n n C38 H381 NEX sing 974 n n C38 H382 NEX sing 975 n n C38 H383 NEX sing 976 n n C39 H391 NEX sing 977 n n C39 H392 NEX sing 978 n n C39 H393 NEX sing 979 n n C40 H401 NEX sing 980 n n C40 H402 NEX sing 981 n n C40 H403 NEX sing 982 n n O23 H1 NEX sing 983 n n # _atom_sites.entry_id 8HPD _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 4 0UR A 1 301 520 0UR 0UR . E 5 0IE A 1 302 521 0IE 0IE . F 6 NEX A 1 303 523 NEX NEX . G 7 CHL A 1 304 601 CHL CHL . H 7 CHL A 1 305 602 CHL CHL . I 8 CLA A 1 306 603 CLA CLA . J 8 CLA A 1 307 604 CLA CLA . K 7 CHL A 1 308 605 CHL CHL . L 7 CHL A 1 309 606 CHL CHL . M 7 CHL A 1 310 607 CHL CHL . N 7 CHL A 1 311 608 CHL CHL . O 7 CHL A 1 312 609 CHL CHL . P 8 CLA A 1 313 610 CLA CLA . Q 8 CLA A 1 314 611 CLA CLA . R 8 CLA A 1 315 612 CLA CLA . S 8 CLA A 1 316 613 CLA CLA . T 7 CHL A 1 317 614 CHL CHL . U 9 LHG A 1 318 630 LHG LHG . V 4 0UR B 1 301 520 0UR 0UR . W 5 0IE B 1 302 521 0IE 0IE . X 5 0IE B 1 303 522 0IE 0IE . Y 6 NEX B 1 304 523 NEX NEX . Z 7 CHL B 1 305 601 CHL CHL . AA 7 CHL B 1 306 602 CHL CHL . BA 8 CLA B 1 307 603 CLA CLA . CA 8 CLA B 1 308 604 CLA CLA . DA 7 CHL B 1 309 605 CHL CHL . EA 7 CHL B 1 310 606 CHL CHL . FA 7 CHL B 1 311 607 CHL CHL . GA 7 CHL B 1 312 608 CHL CHL . HA 7 CHL B 1 313 609 CHL CHL . IA 8 CLA B 1 314 610 CLA CLA . JA 8 CLA B 1 315 611 CLA CLA . KA 8 CLA B 1 316 612 CLA CLA . LA 8 CLA B 1 317 613 CLA CLA . MA 7 CHL B 1 318 614 CHL CHL . NA 9 LHG B 1 319 630 LHG LHG . OA 4 0UR C 1 301 520 0UR 0UR . PA 5 0IE C 1 302 521 0IE 0IE . QA 5 0IE C 1 303 522 0IE 0IE . RA 6 NEX C 1 304 523 NEX NEX . SA 7 CHL C 1 305 601 CHL CHL . TA 7 CHL C 1 306 602 CHL CHL . UA 8 CLA C 1 307 603 CLA CLA . VA 8 CLA C 1 308 604 CLA CLA . WA 7 CHL C 1 309 605 CHL CHL . XA 7 CHL C 1 310 606 CHL CHL . YA 7 CHL C 1 311 607 CHL CHL . ZA 7 CHL C 1 312 608 CHL CHL . AB 7 CHL C 1 313 609 CHL CHL . BB 8 CLA C 1 314 610 CLA CLA . CB 8 CLA C 1 315 611 CLA CLA . DB 8 CLA C 1 316 612 CLA CLA . EB 8 CLA C 1 317 613 CLA CLA . FB 7 CHL C 1 318 614 CHL CHL . GB 9 LHG C 1 319 630 LHG LHG . # 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 C1 NEX . . . F 6 143.834 157.81 101.582 1 74.33 ? C1 NEX 303 A 1 HETATM 2 C C2 NEX . . . F 6 144.801 156.705 101.113 1 74.95 ? C2 NEX 303 A 1 HETATM 3 C C3 NEX . . . F 6 146.302 156.902 101.351 1 76.09 ? C3 NEX 303 A 1 HETATM 4 C C4 NEX . . . F 6 146.552 157.264 102.83 1 75.63 ? C4 NEX 303 A 1 HETATM 5 C C5 NEX . . . F 6 145.718 158.413 103.427 1 75.11 ? C5 NEX 303 A 1 HETATM 6 C C6 NEX . . . F 6 144.2 158.171 103.069 1 73.95 ? C6 NEX 303 A 1 HETATM 7 C C7 NEX . . . F 6 143.215 158.211 104.057 1 70.03 ? C7 NEX 303 A 1 HETATM 8 C C8 NEX . . . F 6 142.245 158.224 105.029 1 64.52 ? C8 NEX 303 A 1 HETATM 9 C C9 NEX . . . F 6 141.644 157.05 105.665 1 61.29 ? C9 NEX 303 A 1 HETATM 10 C C10 NEX . . . F 6 140.724 157.279 106.626 1 57.78 ? C10 NEX 303 A 1 HETATM 11 C C11 NEX . . . F 6 140.273 156.36 107.622 1 52.95 ? C11 NEX 303 A 1 HETATM 12 C C12 NEX . . . F 6 139.368 156.741 108.545 1 48.62 ? C12 NEX 303 A 1 HETATM 13 C C13 NEX . . . F 6 138.831 155.978 109.644 1 45.47 ? C13 NEX 303 A 1 HETATM 14 C C14 NEX . . . F 6 137.974 156.611 110.473 1 41.99 ? C14 NEX 303 A 1 HETATM 15 C C15 NEX . . . F 6 137.392 156.092 111.667 1 39.14 ? C15 NEX 303 A 1 HETATM 16 C C16 NEX . . . F 6 142.399 157.252 101.438 1 73.79 ? C16 NEX 303 A 1 HETATM 17 C C17 NEX . . . F 6 143.957 159.054 100.688 1 74.21 ? C17 NEX 303 A 1 HETATM 18 C C18 NEX . . . F 6 145.979 158.456 104.948 1 75.53 ? C18 NEX 303 A 1 HETATM 19 C C19 NEX . . . F 6 142.352 155.737 105.489 1 60.53 ? C19 NEX 303 A 1 HETATM 20 C C20 NEX . . . F 6 139.309 154.565 109.828 1 43.64 ? C20 NEX 303 A 1 HETATM 21 O O3 NEX . . . F 6 146.981 155.693 101.046 1 78.89 ? O3 NEX 303 A 1 HETATM 22 O O4 NEX . . . F 6 146.142 159.65 102.869 1 75.73 ? O4 NEX 303 A 1 HETATM 23 C C21 NEX . . . F 6 130.319 159.993 120.505 1 22.1 ? C21 NEX 303 A 1 HETATM 24 C C22 NEX . . . F 6 128.952 160.561 120.959 1 20.76 ? C22 NEX 303 A 1 HETATM 25 C C23 NEX . . . F 6 127.776 160.411 119.995 1 20.94 ? C23 NEX 303 A 1 HETATM 26 C C24 NEX . . . F 6 127.522 158.982 119.502 1 22.03 ? C24 NEX 303 A 1 HETATM 27 C C25 NEX . . . F 6 128.776 158.209 119.173 1 22.06 ? C25 NEX 303 A 1 HETATM 28 C C26 NEX . . . F 6 130.158 158.672 119.639 1 22.7 ? C26 NEX 303 A 1 HETATM 29 C C27 NEX . . . F 6 131.246 157.652 119.791 1 23.34 ? C27 NEX 303 A 1 HETATM 30 C C28 NEX . . . F 6 132.186 157.31 118.901 1 23.77 ? C28 NEX 303 A 1 HETATM 31 C C29 NEX . . . F 6 133.175 156.218 119.027 1 24.3 ? C29 NEX 303 A 1 HETATM 32 C C30 NEX . . . F 6 134.035 155.992 118.013 1 26.28 ? C30 NEX 303 A 1 HETATM 33 C C31 NEX . . . F 6 134.174 156.745 116.798 1 26.36 ? C31 NEX 303 A 1 HETATM 34 C C32 NEX . . . F 6 134.989 156.324 115.81 1 27.74 ? C32 NEX 303 A 1 HETATM 35 C C33 NEX . . . F 6 135.306 157 114.558 1 31.09 ? C33 NEX 303 A 1 HETATM 36 C C34 NEX . . . F 6 136.116 156.363 113.684 1 33.88 ? C34 NEX 303 A 1 HETATM 37 C C35 NEX . . . F 6 136.579 156.853 112.422 1 36.23 ? C35 NEX 303 A 1 HETATM 38 C C36 NEX . . . F 6 131.138 159.732 121.767 1 21.27 ? C36 NEX 303 A 1 HETATM 39 C C37 NEX . . . F 6 131.041 161.056 119.674 1 19.7 ? C37 NEX 303 A 1 HETATM 40 C C38 NEX . . . F 6 128.491 156.773 118.842 1 21.2 ? C38 NEX 303 A 1 HETATM 41 C C39 NEX . . . F 6 133.147 155.388 120.257 1 24.71 ? C39 NEX 303 A 1 HETATM 42 C C40 NEX . . . F 6 134.73 158.351 114.329 1 29.97 ? C40 NEX 303 A 1 HETATM 43 O O23 NEX . . . F 6 126.594 160.934 120.573 1 20.49 ? O23 NEX 303 A 1 HETATM 44 O O24 NEX . . . F 6 129.689 158.878 118.279 1 23.2 ? O24 NEX 303 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 44 #