data_8VBY
#
_model_server_result.job_id            dG8hePoZzXNKuOQM2qJxOw 
_model_server_result.datetime_utc      '2024-11-22 06:40:25' 
_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          8vby 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":711}' 
#
_entry.id    8VBY 
#
_exptl.entry_id    8VBY 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              486.726 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CHOLESTEROL HEMISUCCINATE' 
_entity.pdbx_number_of_molecules    4 
_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            8VBY 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8VBY 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,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 
_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    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
? 5 E N N 
? 5 K N N 
? 5 L N N 
? 5 MA 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 130 A CYS 180 1_555 A SG CYS 139 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
covale ? covale1 A ND2 ASN 138 A ASN 188 1_555 D C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
metalc ? metalc1 A O VAL 28 A VAL 78 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc2 A OD1 ASP 141 A ASP 191 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? 
metalc ? metalc3 A OD2 ASP 141 A ASP 191 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? 
metalc ? metalc4 A NE2 HIS 143 A HIS 193 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc5 A NE2 HIS 325 A HIS 375 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc6 A OE2 GLU 346 A GLU 396 1_555 N ZN ZN . A ZN 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc7 A O LEU 368 A LEU 418 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc8 A OD1 ASP 371 A ASP 421 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? 
metalc ? metalc9 A OG SER 372 A SER 422 1_555 O NA NA . A NA 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
#
_chem_comp.formula           'C31 H50 O4' 
_chem_comp.formula_weight    486.726 
_chem_comp.id                Y01 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'CHOLESTEROL HEMISUCCINATE' 
_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
CAA CBA Y01 sing 678 n n 
CBA CAB Y01 sing 679 n n 
CBA CAN Y01 sing 680 n n 
CAN CAJ Y01 sing 681 n n 
CAJ CAO Y01 sing 682 n n 
CAO CBB Y01 sing 683 n n 
CBB CAC Y01 sing 684 n n 
CBB CBE Y01 sing 685 n n 
CBE CAP Y01 sing 686 n n 
CBE CBI Y01 sing 687 n n 
CAP CAQ Y01 sing 688 n n 
CAQ CBG Y01 sing 689 n n 
CBG CBI Y01 sing 690 n n 
CBG CBD Y01 sing 691 n n 
CBI CAE Y01 sing 692 n n 
CBI CAU Y01 sing 693 n n 
CAU CAS Y01 sing 694 n n 
CAS CBF Y01 sing 695 n n 
CBF CBD Y01 sing 696 n n 
CBF CBH Y01 sing 697 n n 
CBD CAK Y01 sing 698 n n 
CAK CAI Y01 sing 699 n n 
CAI CAZ Y01 doub 700 n n 
CAZ CAV Y01 sing 701 n n 
CAZ CBH Y01 sing 702 n n 
CAV CBC Y01 sing 703 n n 
CBH CAD Y01 sing 704 n n 
CBH CAT Y01 sing 705 n n 
CAT CAR Y01 sing 706 n n 
CAR CBC Y01 sing 707 n n 
CBC OAW Y01 sing 708 n n 
OAW CAY Y01 sing 709 n n 
CAY OAG Y01 doub 710 n n 
CAY CAM Y01 sing 711 n n 
CAM CAL Y01 sing 712 n n 
CAL CAX Y01 sing 713 n n 
CAX OAH Y01 sing 714 n n 
CAX OAF Y01 doub 715 n n 
CAA HAA1 Y01 sing 716 n n 
CAA HAA2 Y01 sing 717 n n 
CAA HAA3 Y01 sing 718 n n 
CBA HBA Y01 sing 719 n n 
CAB HAB1 Y01 sing 720 n n 
CAB HAB2 Y01 sing 721 n n 
CAB HAB3 Y01 sing 722 n n 
CAN HAN1 Y01 sing 723 n n 
CAN HAN2 Y01 sing 724 n n 
CAJ HAJ1 Y01 sing 725 n n 
CAJ HAJ2 Y01 sing 726 n n 
CAO HAO1 Y01 sing 727 n n 
CAO HAO2 Y01 sing 728 n n 
CBB HBB Y01 sing 729 n n 
CAC HAC1 Y01 sing 730 n n 
CAC HAC2 Y01 sing 731 n n 
CAC HAC3 Y01 sing 732 n n 
CBE HBE Y01 sing 733 n n 
CAP HAP1 Y01 sing 734 n n 
CAP HAP2 Y01 sing 735 n n 
CAQ HAQ1 Y01 sing 736 n n 
CAQ HAQ2 Y01 sing 737 n n 
CBG HBG Y01 sing 738 n n 
CBD HBD Y01 sing 739 n n 
CAE HAE1 Y01 sing 740 n n 
CAE HAE2 Y01 sing 741 n n 
CAE HAE3 Y01 sing 742 n n 
CAU HAU1 Y01 sing 743 n n 
CAU HAU2 Y01 sing 744 n n 
CAS HAS1 Y01 sing 745 n n 
CAS HAS2 Y01 sing 746 n n 
CBF HBF Y01 sing 747 n n 
CAK HAK1 Y01 sing 748 n n 
CAK HAK2 Y01 sing 749 n n 
CAI HAI Y01 sing 750 n n 
CAV HAV1 Y01 sing 751 n n 
CAV HAV2 Y01 sing 752 n n 
CBC HBC Y01 sing 753 n n 
CAD HAD1 Y01 sing 754 n n 
CAD HAD2 Y01 sing 755 n n 
CAD HAD3 Y01 sing 756 n n 
CAT HAT1 Y01 sing 757 n n 
CAT HAT2 Y01 sing 758 n n 
CAR HAR1 Y01 sing 759 n n 
CAR HAR2 Y01 sing 760 n n 
CAM HAM1 Y01 sing 761 n n 
CAM HAM2 Y01 sing 762 n n 
CAL HAL1 Y01 sing 763 n n 
CAL HAL2 Y01 sing 764 n n 
OAH HAH Y01 sing 765 n n 
#
_atom_sites.entry_id                     8VBY 
_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
B 2 42L A 1 701 701 42L 42L . 
C 3 A1AAF A 1 702 702 A1AAF MRS . 
D 4 NAG A 1 703 705 NAG NAG . 
E 5 Y01 A 1 704 709 Y01 Y01 . 
F 6 D10 A 1 705 713 D10 D10 . 
G 7 LNK A 1 706 714 LNK LNK . 
H 6 D10 A 1 707 715 D10 D10 . 
I 7 LNK A 1 708 717 LNK LNK . 
J 7 LNK A 1 709 718 LNK LNK . 
K 5 Y01 A 1 710 723 Y01 Y01 . 
L 5 Y01 A 1 711 727 Y01 Y01 . 
M 8 HP6 A 1 712 728 HP6 HP6 . 
N 9 ZN A 1 713 729 ZN ZN . 
O 10 NA A 1 714 730 NA NA . 
P 8 HP6 A 1 715 732 HP6 HP6 . 
Q 11 D12 A 1 716 734 D12 D12 . 
R 11 D12 A 1 717 736 D12 D12 . 
S 6 D10 A 1 718 738 D10 D10 . 
T 8 HP6 A 1 719 748 HP6 HP6 . 
U 8 HP6 A 1 720 749 HP6 HP6 . 
V 7 LNK A 1 721 750 LNK LNK . 
W 7 LNK A 1 722 751 LNK LNK . 
X 7 LNK A 1 723 752 LNK LNK . 
Y 6 D10 A 1 724 753 D10 D10 . 
Z 12 MYS A 1 725 754 MYS MYS . 
AA 11 D12 A 1 726 755 D12 D12 . 
BA 8 HP6 A 1 727 756 HP6 HP6 . 
CA 11 D12 A 1 728 758 D12 D12 . 
DA 13 OCT A 1 729 759 OCT OCT . 
EA 13 OCT A 1 730 762 OCT OCT . 
FA 8 HP6 A 1 731 763 HP6 HP6 . 
GA 7 LNK A 1 732 764 LNK LNK . 
HA 8 HP6 A 1 733 765 HP6 HP6 . 
IA 6 D10 A 1 734 766 D10 D10 . 
JA 6 D10 A 1 735 770 D10 D10 . 
KA 11 D12 A 1 736 772 D12 D12 . 
LA 8 HP6 A 1 737 774 HP6 HP6 . 
MA 5 Y01 A 1 738 776 Y01 Y01 . 
NA 11 D12 A 1 739 777 D12 D12 . 
OA 6 D10 A 1 740 778 D10 D10 . 
PA 6 D10 A 1 741 1 D10 D10 . 
QA 14 HOH A 1 801 12 HOH HOH . 
QA 14 HOH A 2 802 11 HOH HOH . 
QA 14 HOH A 3 803 7 HOH HOH . 
QA 14 HOH A 4 804 8 HOH HOH . 
QA 14 HOH A 5 805 3 HOH HOH . 
QA 14 HOH A 6 806 4 HOH HOH . 
QA 14 HOH A 7 807 10 HOH HOH . 
QA 14 HOH A 8 808 9 HOH HOH . 
QA 14 HOH A 9 809 6 HOH HOH . 
QA 14 HOH A 10 810 5 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 CAA Y01 . . . L 5 146.564 158.437 133.28 1 68.82 ? CAA Y01 711 A 1 
HETATM 2 C CBA Y01 . . . L 5 145.712 159.3 134.205 1 71.61 ? CBA Y01 711 A 1 
HETATM 3 C CAB Y01 . . . L 5 146.327 160.689 134.343 1 70.11 ? CAB Y01 711 A 1 
HETATM 4 C CAN Y01 . . . L 5 144.265 159.42 133.723 1 67.95 ? CAN Y01 711 A 1 
HETATM 5 C CAJ Y01 . . . L 5 143.664 158.16 133.113 1 67.26 ? CAJ Y01 711 A 1 
HETATM 6 C CAO Y01 . . . L 5 142.159 158.294 132.897 1 64.42 ? CAO Y01 711 A 1 
HETATM 7 C CBB Y01 . . . L 5 141.587 157.46 131.741 1 68.78 ? CBB Y01 711 A 1 
HETATM 8 C CAC Y01 . . . L 5 141.929 155.985 131.936 1 66.54 ? CAC Y01 711 A 1 
HETATM 9 C CBE Y01 . . . L 5 140.081 157.716 131.578 1 71.59 ? CBE Y01 711 A 1 
HETATM 10 C CAP Y01 . . . L 5 139.66 159.109 132.121 1 68.2 ? CAP Y01 711 A 1 
HETATM 11 C CAQ Y01 . . . L 5 138.488 159.609 131.257 1 66.09 ? CAQ Y01 711 A 1 
HETATM 12 C CBG Y01 . . . L 5 138.13 158.404 130.399 1 71.63 ? CBG Y01 711 A 1 
HETATM 13 C CBI Y01 . . . L 5 139.467 157.686 130.155 1 73 ? CBI Y01 711 A 1 
HETATM 14 C CAE Y01 . . . L 5 140.373 158.454 129.188 1 67.66 ? CAE Y01 711 A 1 
HETATM 15 C CAU Y01 . . . L 5 139.094 156.313 129.595 1 67.44 ? CAU Y01 711 A 1 
HETATM 16 C CAS Y01 . . . L 5 138.272 156.435 128.309 1 68.81 ? CAS Y01 711 A 1 
HETATM 17 C CBF Y01 . . . L 5 137.021 157.313 128.427 1 64.26 ? CBF Y01 711 A 1 
HETATM 18 C CBD Y01 . . . L 5 137.303 158.639 129.146 1 68.72 ? CBD Y01 711 A 1 
HETATM 19 C CAK Y01 . . . L 5 135.978 159.314 129.482 1 66.64 ? CAK Y01 711 A 1 
HETATM 20 C CAI Y01 . . . L 5 135.024 159.29 128.334 1 67.05 ? CAI Y01 711 A 1 
HETATM 21 C CAZ Y01 . . . L 5 135.2 158.57 127.228 1 64.73 ? CAZ Y01 711 A 1 
HETATM 22 C CAV Y01 . . . L 5 134.336 158.814 126.017 1 61.87 ? CAV Y01 711 A 1 
HETATM 23 C CBH Y01 . . . L 5 136.332 157.575 127.067 1 63.63 ? CBH Y01 711 A 1 
HETATM 24 C CAD Y01 . . . L 5 137.331 158.118 126.033 1 65.18 ? CAD Y01 711 A 1 
HETATM 25 C CAT Y01 . . . L 5 135.689 156.278 126.544 1 63.6 ? CAT Y01 711 A 1 
HETATM 26 C CAR Y01 . . . L 5 134.93 156.477 125.239 1 65.29 ? CAR Y01 711 A 1 
HETATM 27 C CBC Y01 . . . L 5 133.841 157.529 125.359 1 67.65 ? CBC Y01 711 A 1 
HETATM 28 O OAW Y01 . . . L 5 133.429 157.807 124.011 1 76.35 ? OAW Y01 711 A 1 
HETATM 29 C CAY Y01 . . . L 5 132.189 158.211 123.744 1 75 ? CAY Y01 711 A 1 
HETATM 30 O OAG Y01 . . . L 5 131.322 158.312 124.576 1 74.42 ? OAG Y01 711 A 1 
HETATM 31 C CAM Y01 . . . L 5 132.039 158.514 122.277 1 71.35 ? CAM Y01 711 A 1 
HETATM 32 C CAL Y01 . . . L 5 133.02 159.558 121.78 1 68.38 ? CAL Y01 711 A 1 
HETATM 33 C CAX Y01 . . . L 5 133.351 159.483 120.278 1 68.5 ? CAX Y01 711 A 1 
HETATM 34 O OAH Y01 . . . L 5 132.38 159.603 119.504 1 70.59 ? OAH Y01 711 A 1 
HETATM 35 O OAF Y01 . . . L 5 134.542 159.312 119.951 1 65.11 ? OAF Y01 711 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           35 
#