data_8IX1
#
_model_server_result.job_id            Mj4SN7hmBsPYRFfP4QB3Fg 
_model_server_result.datetime_utc      '2025-09-05 22:54:53' 
_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          8ix1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"S","auth_seq_id":616}' 
#
_entry.id    8IX1 
#
_exptl.entry_id    8IX1 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              600.87 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-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            8IX1 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8IX1 
_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,HB 
_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
? 5 S N N 
? 5 NA N N 
? 5 QA 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 OE2 GLU 52 G GLU 65 1_555 E MG CLA . G CLA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc2 A O HIS 107 G HIS 120 1_555 H MG CHL . G CHL 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.768 ? 
metalc ? metalc3 A OE2 GLU 126 G GLU 139 1_555 K MG CHL . G CHL 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? 
metalc ? metalc4 A OE2 GLU 167 G GLU 180 1_555 L MG CLA . G CLA 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? 
metalc ? metalc5 B OE1 GLU 52 N GLU 65 1_555 Y MG CLA . N CLA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
metalc ? metalc6 B OD1 ASN 170 N ASN 183 1_555 IA MG CLA . N CLA 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? 
metalc ? metalc7 HA MG CLA . N CLA 312 1_555 PA O4 LHG . N LHG 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? 
metalc ? metalc8 C OE1 GLU 52 Y GLU 65 1_555 SA MG CLA . Y CLA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
metalc ? metalc9 C OE2 GLU 126 Y GLU 139 1_555 YA MG CHL . Y CHL 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? 
metalc ? metalc10 AB MG CLA . Y CLA 610 1_555 HB O4 LHG . Y LHG 617 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? 
#
_chem_comp.formula           'C40 H56 O4' 
_chem_comp.formula_weight    600.87 
_chem_comp.id                XAT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     VIOLAXANTHIN 
#
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 XAT sing 987 n n 
C1 C6 XAT sing 988 n n 
C1 C16 XAT sing 989 n n 
C1 C17 XAT sing 990 n n 
C2 C3 XAT sing 991 n n 
C2 H21 XAT sing 992 n n 
C2 H22 XAT sing 993 n n 
C3 C4 XAT sing 994 n n 
C3 O3 XAT sing 995 n n 
C3 H3 XAT sing 996 n n 
C4 C5 XAT sing 997 n n 
C4 H41 XAT sing 998 n n 
C4 H42 XAT sing 999 n n 
C5 C6 XAT sing 1000 n n 
C5 C18 XAT sing 1001 n n 
C5 O4 XAT sing 1002 n n 
C6 C7 XAT sing 1003 n n 
C6 O4 XAT sing 1004 n n 
C7 C8 XAT doub 1005 e n 
C7 H7 XAT sing 1006 n n 
C8 C9 XAT sing 1007 n n 
C8 H8 XAT sing 1008 n n 
C9 C10 XAT doub 1009 e n 
C9 C19 XAT sing 1010 n n 
C10 C11 XAT sing 1011 n n 
C10 H10 XAT sing 1012 n n 
C11 C12 XAT doub 1013 e n 
C11 H11 XAT sing 1014 n n 
C12 C13 XAT sing 1015 n n 
C12 H12 XAT sing 1016 n n 
C13 C14 XAT doub 1017 e n 
C13 C20 XAT sing 1018 n n 
C14 C15 XAT sing 1019 n n 
C14 H14 XAT sing 1020 n n 
C15 C35 XAT doub 1021 e n 
C15 H15 XAT sing 1022 n n 
C16 H161 XAT sing 1023 n n 
C16 H162 XAT sing 1024 n n 
C16 H163 XAT sing 1025 n n 
C17 H171 XAT sing 1026 n n 
C17 H172 XAT sing 1027 n n 
C17 H173 XAT sing 1028 n n 
C18 H181 XAT sing 1029 n n 
C18 H182 XAT sing 1030 n n 
C18 H183 XAT sing 1031 n n 
C19 H191 XAT sing 1032 n n 
C19 H192 XAT sing 1033 n n 
C19 H193 XAT sing 1034 n n 
C20 H201 XAT sing 1035 n n 
C20 H202 XAT sing 1036 n n 
C20 H203 XAT sing 1037 n n 
O3 HO3 XAT sing 1038 n n 
C21 C22 XAT sing 1039 n n 
C21 C26 XAT sing 1040 n n 
C21 C36 XAT sing 1041 n n 
C21 C37 XAT sing 1042 n n 
C22 C23 XAT sing 1043 n n 
C22 H221 XAT sing 1044 n n 
C22 H222 XAT sing 1045 n n 
C23 C24 XAT sing 1046 n n 
C23 O23 XAT sing 1047 n n 
C23 H23 XAT sing 1048 n n 
C24 C25 XAT sing 1049 n n 
C24 H241 XAT sing 1050 n n 
C24 H242 XAT sing 1051 n n 
C25 C26 XAT sing 1052 n n 
C25 C38 XAT sing 1053 n n 
C25 O24 XAT sing 1054 n n 
C26 C27 XAT sing 1055 n n 
C26 O24 XAT sing 1056 n n 
C27 C28 XAT doub 1057 e n 
C27 H27 XAT sing 1058 n n 
C28 C29 XAT sing 1059 n n 
C28 H28 XAT sing 1060 n n 
C29 C30 XAT doub 1061 e n 
C29 C39 XAT sing 1062 n n 
C30 C31 XAT sing 1063 n n 
C30 H30 XAT sing 1064 n n 
C31 C32 XAT doub 1065 e n 
C31 H31 XAT sing 1066 n n 
C32 C33 XAT sing 1067 n n 
C32 H32 XAT sing 1068 n n 
C33 C34 XAT doub 1069 e n 
C33 C40 XAT sing 1070 n n 
C34 C35 XAT sing 1071 n n 
C34 H34 XAT sing 1072 n n 
C35 H35 XAT sing 1073 n n 
C36 H361 XAT sing 1074 n n 
C36 H362 XAT sing 1075 n n 
C36 H363 XAT sing 1076 n n 
C37 H371 XAT sing 1077 n n 
C37 H372 XAT sing 1078 n n 
C37 H373 XAT sing 1079 n n 
C38 H381 XAT sing 1080 n n 
C38 H382 XAT sing 1081 n n 
C38 H383 XAT sing 1082 n n 
C39 H391 XAT sing 1083 n n 
C39 H392 XAT sing 1084 n n 
C39 H393 XAT sing 1085 n n 
C40 H401 XAT sing 1086 n n 
C40 H402 XAT sing 1087 n n 
C40 H403 XAT sing 1088 n n 
O23 H1 XAT sing 1089 n n 
#
_atom_sites.entry_id                     8IX1 
_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 2 CHL G 1 601 601 CHL CHL . 
E 3 CLA G 1 602 602 CLA CLA . 
F 3 CLA G 1 603 603 CLA CLA . 
G 3 CLA G 1 604 604 CLA CLA . 
H 2 CHL G 1 605 605 CHL CHL . 
I 2 CHL G 1 606 606 CHL CHL . 
J 2 CHL G 1 607 608 CHL CHL . 
K 2 CHL G 1 608 609 CHL CHL . 
L 3 CLA G 1 609 610 CLA CLA . 
M 3 CLA G 1 610 611 CLA CLA . 
N 3 CLA G 1 611 612 CLA CLA . 
O 3 CLA G 1 612 613 CLA CLA . 
P 3 CLA G 1 613 614 CLA CLA . 
Q 4 LUT G 1 614 1620 LUT LUT . 
R 4 LUT G 1 615 1621 LUT LUT . 
S 5 XAT G 1 616 1622 XAT XAT . 
T 6 NEX G 1 617 1623 NEX NEX . 
U 7 LHG G 1 618 2630 LHG LHG . 
V 2 CHL G 1 619 607 CHL CHL . 
W 2 CHL N 1 301 607 CHL CHL . 
X 2 CHL N 1 302 601 CHL CHL . 
Y 3 CLA N 1 303 602 CLA CLA . 
Z 3 CLA N 1 304 603 CLA CLA . 
AA 3 CLA N 1 305 604 CLA CLA . 
BA 2 CHL N 1 306 605 CHL CHL . 
CA 2 CHL N 1 307 606 CHL CHL . 
DA 2 CHL N 1 308 607 CHL CHL . 
EA 2 CHL N 1 309 608 CHL CHL . 
FA 2 CHL N 1 310 609 CHL CHL . 
GA 3 CLA N 1 311 610 CLA CLA . 
HA 3 CLA N 1 312 611 CLA CLA . 
IA 3 CLA N 1 313 612 CLA CLA . 
JA 3 CLA N 1 314 613 CLA CLA . 
KA 3 CLA N 1 315 614 CLA CLA . 
LA 4 LUT N 1 316 1620 LUT LUT . 
MA 4 LUT N 1 317 1621 LUT LUT . 
NA 5 XAT N 1 318 1622 XAT XAT . 
OA 6 NEX N 1 319 1623 NEX NEX . 
PA 7 LHG N 1 320 2630 LHG LHG . 
QA 5 XAT N 1 321 1622 XAT XAT . 
RA 2 CHL Y 1 601 601 CHL CHL . 
SA 3 CLA Y 1 602 602 CLA CLA . 
TA 3 CLA Y 1 603 603 CLA CLA . 
UA 3 CLA Y 1 604 604 CLA CLA . 
VA 2 CHL Y 1 605 605 CHL CHL . 
WA 2 CHL Y 1 606 606 CHL CHL . 
XA 2 CHL Y 1 607 608 CHL CHL . 
YA 2 CHL Y 1 608 609 CHL CHL . 
ZA 3 CLA Y 1 609 610 CLA CLA . 
AB 3 CLA Y 1 610 611 CLA CLA . 
BB 3 CLA Y 1 611 612 CLA CLA . 
CB 3 CLA Y 1 612 613 CLA CLA . 
DB 3 CLA Y 1 613 614 CLA CLA . 
EB 4 LUT Y 1 614 1620 LUT LUT . 
FB 4 LUT Y 1 615 1621 LUT LUT . 
GB 6 NEX Y 1 616 1623 NEX NEX . 
HB 7 LHG Y 1 617 2630 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 XAT . . . S 5 99.97 101.386 124.732 1 24.93 ? C1 XAT 616 G 1 
HETATM 2 C C2 XAT . . . S 5 98.576 101.301 124.137 1 17.81 ? C2 XAT 616 G 1 
HETATM 3 C C3 XAT . . . S 5 98.625 100.389 122.931 1 28.36 ? C3 XAT 616 G 1 
HETATM 4 C C4 XAT . . . S 5 98.75 98.978 123.473 1 22.95 ? C4 XAT 616 G 1 
HETATM 5 C C5 XAT . . . S 5 99.936 98.754 124.425 1 23.36 ? C5 XAT 616 G 1 
HETATM 6 C C6 XAT . . . S 5 100.563 100.007 125.098 1 27.08 ? C6 XAT 616 G 1 
HETATM 7 C C7 XAT . . . S 5 100.915 99.76 126.56 1 21.08 ? C7 XAT 616 G 1 
HETATM 8 C C8 XAT . . . S 5 102.209 99.717 126.87 1 21.89 ? C8 XAT 616 G 1 
HETATM 9 C C9 XAT . . . S 5 102.704 99.497 128.239 1 22.91 ? C9 XAT 616 G 1 
HETATM 10 C C10 XAT . . . S 5 104.028 99.501 128.425 1 23.45 ? C10 XAT 616 G 1 
HETATM 11 C C11 XAT . . . S 5 104.647 99.313 129.73 1 23.21 ? C11 XAT 616 G 1 
HETATM 12 C C12 XAT . . . S 5 105.966 99.163 129.773 1 24.27 ? C12 XAT 616 G 1 
HETATM 13 C C13 XAT . . . S 5 106.673 99.001 131.052 1 21.33 ? C13 XAT 616 G 1 
HETATM 14 C C14 XAT . . . S 5 107.914 98.495 131.086 1 22.18 ? C14 XAT 616 G 1 
HETATM 15 C C15 XAT . . . S 5 108.591 98.393 132.372 1 25.46 ? C15 XAT 616 G 1 
HETATM 16 C C16 XAT . . . S 5 99.919 102.319 125.937 1 19.69 ? C16 XAT 616 G 1 
HETATM 17 C C17 XAT . . . S 5 100.905 102.039 123.72 1 20.98 ? C17 XAT 616 G 1 
HETATM 18 C C18 XAT . . . S 5 99.812 97.534 125.348 1 22.85 ? C18 XAT 616 G 1 
HETATM 19 C C19 XAT . . . S 5 101.757 99.284 129.381 1 20.49 ? C19 XAT 616 G 1 
HETATM 20 C C20 XAT . . . S 5 105.989 99.421 132.32 1 26.04 ? C20 XAT 616 G 1 
HETATM 21 O O3 XAT . . . S 5 97.438 100.534 122.147 1 33.5 ? O3 XAT 616 G 1 
HETATM 22 O O4 XAT . . . S 5 101.229 99.251 124.078 1 26.47 ? O4 XAT 616 G 1 
HETATM 23 C C21 XAT . . . S 5 117.295 100.018 141.366 1 24.74 ? C21 XAT 616 G 1 
HETATM 24 C C22 XAT . . . S 5 118.729 100.114 141.852 1 23.78 ? C22 XAT 616 G 1 
HETATM 25 C C23 XAT . . . S 5 118.934 99.106 142.963 1 23.42 ? C23 XAT 616 G 1 
HETATM 26 C C24 XAT . . . S 5 118.953 97.726 142.331 1 22.81 ? C24 XAT 616 G 1 
HETATM 27 C C25 XAT . . . S 5 117.814 97.426 141.339 1 22.58 ? C25 XAT 616 G 1 
HETATM 28 C C26 XAT . . . S 5 116.97 98.618 140.809 1 22.29 ? C26 XAT 616 G 1 
HETATM 29 C C27 XAT . . . S 5 116.645 98.514 139.323 1 24.24 ? C27 XAT 616 G 1 
HETATM 30 C C28 XAT . . . S 5 115.412 98.18 138.939 1 21.11 ? C28 XAT 616 G 1 
HETATM 31 C C29 XAT . . . S 5 115.053 98.083 137.514 1 22.4 ? C29 XAT 616 G 1 
HETATM 32 C C30 XAT . . . S 5 113.811 97.712 137.178 1 21.01 ? C30 XAT 616 G 1 
HETATM 33 C C31 XAT . . . S 5 113.394 97.613 135.784 1 21.19 ? C31 XAT 616 G 1 
HETATM 34 C C32 XAT . . . S 5 112.094 97.591 135.511 1 22.4 ? C32 XAT 616 G 1 
HETATM 35 C C33 XAT . . . S 5 111.616 97.509 134.122 1 22.05 ? C33 XAT 616 G 1 
HETATM 36 C C34 XAT . . . S 5 110.383 97.944 133.849 1 21.84 ? C34 XAT 616 G 1 
HETATM 37 C C35 XAT . . . S 5 109.83 97.938 132.501 1 20.57 ? C35 XAT 616 G 1 
HETATM 38 C C36 XAT . . . S 5 117.081 101.102 140.316 1 22.89 ? C36 XAT 616 G 1 
HETATM 39 C C37 XAT . . . S 5 116.331 100.303 142.512 1 26.74 ? C37 XAT 616 G 1 
HETATM 40 C C38 XAT . . . S 5 118.153 96.373 140.274 1 21.51 ? C38 XAT 616 G 1 
HETATM 41 C C39 XAT . . . S 5 116.068 98.413 136.463 1 22.29 ? C39 XAT 616 G 1 
HETATM 42 C C40 XAT . . . S 5 112.488 96.946 133.043 1 21.71 ? C40 XAT 616 G 1 
HETATM 43 O O23 XAT . . . S 5 120.167 99.354 143.646 1 27.96 ? O23 XAT 616 G 1 
HETATM 44 O O24 XAT . . . S 5 116.451 97.635 141.711 1 26.34 ? O24 XAT 616 G 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           330 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           44 
#