data_8C88
#
_model_server_result.job_id            lBMHprIBipdySgw3Iyrdlg 
_model_server_result.datetime_utc      '2024-11-28 00:55:15' 
_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          8c88 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Z","auth_seq_id":407}' 
#
_entry.id    8C88 
#
_exptl.entry_id    8C88 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              594.993 
_entity.id                          14 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            SPEROIDENONE 
_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            8C88 
_cell.length_a            100.91 
_cell.length_b            100.91 
_cell.length_c            237.02 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8C88 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        94 
_symmetry.space_group_name_Hall    'P 4n 2n' 
_symmetry.space_group_name_H-M     'P 42 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      14 
_struct_asym.id                             Z 
_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
disulf ? disulf1 B SG CYS 214 L CYS 214 1_555 C SG CYS 19 M CYS 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
metalc ? metalc1 B NE2 HIS 190 L HIS 190 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc2 B NE2 HIS 230 L HIS 230 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? 
metalc ? metalc3 C NE2 HIS 219 M HIS 219 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc4 C OE1 GLU 234 M GLU 234 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? 
metalc ? metalc5 C OE2 GLU 234 M GLU 234 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? 
metalc ? metalc6 C NE2 HIS 266 M HIS 266 1_555 X FE FE . M FE 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
#
_chem_comp.formula           'C41 H70 O2' 
_chem_comp.formula_weight    594.993 
_chem_comp.id                SPN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              SPEROIDENONE 
_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
CMA O1 SPN sing 790 n n 
CMA HMA1 SPN sing 791 n n 
CMA HMA2 SPN sing 792 n n 
CMA HMA3 SPN sing 793 n n 
O1 C1 SPN sing 794 n n 
CM1 C1 SPN sing 795 n n 
CM1 HM11 SPN sing 796 n n 
CM1 HM12 SPN sing 797 n n 
CM1 HM13 SPN sing 798 n n 
CM2 C1 SPN sing 799 n n 
CM2 HM21 SPN sing 800 n n 
CM2 HM22 SPN sing 801 n n 
CM2 HM23 SPN sing 802 n n 
C1 C2 SPN sing 803 n n 
C2 O2 SPN doub 804 n n 
C2 C3 SPN sing 805 n n 
C3 C4 SPN sing 806 n n 
C3 H31 SPN sing 807 n n 
C3 H32 SPN sing 808 n n 
C4 C5 SPN doub 809 e n 
C4 H4 SPN sing 810 n n 
C5 CM3 SPN sing 811 n n 
C5 C6 SPN sing 812 n n 
CM3 HM31 SPN sing 813 n n 
CM3 HM32 SPN sing 814 n n 
CM3 HM33 SPN sing 815 n n 
C6 C7 SPN sing 816 n n 
C6 H61 SPN sing 817 n n 
C6 H62 SPN sing 818 n n 
C7 C8 SPN sing 819 n n 
C7 H71 SPN sing 820 n n 
C7 H72 SPN sing 821 n n 
C8 C9 SPN doub 822 e n 
C8 H8 SPN sing 823 n n 
C9 CM4 SPN sing 824 n n 
C9 C10 SPN sing 825 n n 
CM4 HM41 SPN sing 826 n n 
CM4 HM42 SPN sing 827 n n 
CM4 HM43 SPN sing 828 n n 
C10 C11 SPN sing 829 n n 
C10 H101 SPN sing 830 n n 
C10 H102 SPN sing 831 n n 
C11 C12 SPN sing 832 n n 
C11 H111 SPN sing 833 n n 
C11 H112 SPN sing 834 n n 
C12 C13 SPN doub 835 e n 
C12 H12 SPN sing 836 n n 
C13 CM5 SPN sing 837 n n 
C13 C14 SPN sing 838 n n 
CM5 HM51 SPN sing 839 n n 
CM5 HM52 SPN sing 840 n n 
CM5 HM53 SPN sing 841 n n 
C14 C15 SPN sing 842 n n 
C14 H141 SPN sing 843 n n 
C14 H142 SPN sing 844 n n 
C15 C16 SPN sing 845 n n 
C15 H151 SPN sing 846 n n 
C15 H152 SPN sing 847 n n 
C16 C17 SPN sing 848 n n 
C16 H161 SPN sing 849 n n 
C16 H162 SPN sing 850 n n 
C17 C18 SPN sing 851 n n 
C17 H171 SPN sing 852 n n 
C17 H172 SPN sing 853 n n 
C18 CM6 SPN sing 854 n n 
C18 C19 SPN doub 855 e n 
CM6 HM61 SPN sing 856 n n 
CM6 HM62 SPN sing 857 n n 
CM6 HM63 SPN sing 858 n n 
C19 C20 SPN sing 859 n n 
C19 H19 SPN sing 860 n n 
C20 C21 SPN sing 861 n n 
C20 H201 SPN sing 862 n n 
C20 H202 SPN sing 863 n n 
C21 C22 SPN sing 864 n n 
C21 H211 SPN sing 865 n n 
C21 H212 SPN sing 866 n n 
C22 CM7 SPN sing 867 n n 
C22 C23 SPN sing 868 n n 
C22 H22 SPN sing 869 n n 
CM7 HM71 SPN sing 870 n n 
CM7 HM72 SPN sing 871 n n 
CM7 HM73 SPN sing 872 n n 
C23 C24 SPN sing 873 n n 
C23 H231 SPN sing 874 n n 
C23 H232 SPN sing 875 n n 
C24 C25 SPN sing 876 n n 
C24 H241 SPN sing 877 n n 
C24 H242 SPN sing 878 n n 
C25 C26 SPN doub 879 e n 
C25 H25 SPN sing 880 n n 
C26 CM8 SPN sing 881 n n 
C26 C27 SPN sing 882 n n 
CM8 HM81 SPN sing 883 n n 
CM8 HM82 SPN sing 884 n n 
CM8 HM83 SPN sing 885 n n 
C27 C28 SPN sing 886 n n 
C27 H271 SPN sing 887 n n 
C27 H272 SPN sing 888 n n 
C28 C29 SPN sing 889 n n 
C28 H281 SPN sing 890 n n 
C28 H282 SPN sing 891 n n 
C29 C30 SPN doub 892 n n 
C29 H29 SPN sing 893 n n 
C30 CM9 SPN sing 894 n n 
C30 CMB SPN sing 895 n n 
CM9 HM91 SPN sing 896 n n 
CM9 HM92 SPN sing 897 n n 
CM9 HM93 SPN sing 898 n n 
CMB HMB1 SPN sing 899 n n 
CMB HMB2 SPN sing 900 n n 
CMB HMB3 SPN sing 901 n n 
#
_atom_sites.entry_id                     8C88 
_atom_sites.fract_transf_matrix[1][1]    0.00991 
_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]    0.00991 
_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]    0.004219 
_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 NKP H 1 301 301 NKP NKP . 
E 5 LDA H 1 302 702 LDA LDA . 
F 6 UNL H 1 303 802 UNL UNL . 
G 6 UNL H 1 304 803 UNL UNL . 
H 6 UNL H 1 305 804 UNL UNL . 
I 7 OLC L 1 501 501 OLC OLC . 
J 8 BCL L 1 502 302 BCL BCL . 
K 8 BCL L 1 503 304 BCL BCL . 
L 9 BPH L 1 504 402 BPH BPH . 
M 6 UNL L 1 505 805 UNL UNL . 
N 6 UNL L 1 506 807 UNL UNL . 
O 6 UNL L 1 507 808 UNL UNL . 
P 10 DIO L 1 508 40 DIO DIO . 
Q 11 EDO L 1 509 46 EDO EDO . 
R 11 EDO L 1 510 48 EDO EDO . 
S 11 EDO L 1 511 50 EDO EDO . 
T 4 NKP M 1 401 401 NKP NKP . 
U 8 BCL M 1 402 301 BCL BCL . 
V 8 BCL M 1 403 303 BCL BCL . 
W 9 BPH M 1 404 401 BPH BPH . 
X 12 FE M 1 405 500 FE FE . 
Y 13 U10 M 1 406 501 U10 U10 . 
Z 14 SPN M 1 407 600 SPN SPN . 
AA 5 LDA M 1 408 701 LDA LDA . 
BA 5 LDA M 1 409 705 LDA LDA . 
CA 5 LDA M 1 410 709 LDA LDA . 
DA 5 LDA M 1 411 710 LDA LDA . 
EA 6 UNL M 1 412 810 UNL UNL . 
FA 15 PO4 M 1 413 2 PO4 PO4 . 
GA 15 PO4 M 1 414 3 PO4 PO4 . 
HA 5 LDA M 1 415 1 LDA LDA . 
IA 16 HOH H 1 401 21 HOH HOH . 
IA 16 HOH H 2 402 18 HOH HOH . 
IA 16 HOH H 3 403 17 HOH HOH . 
JA 16 HOH L 1 601 9 HOH HOH . 
JA 16 HOH L 2 602 11 HOH HOH . 
JA 16 HOH L 3 603 10 HOH HOH . 
JA 16 HOH L 4 604 4 HOH HOH . 
JA 16 HOH L 5 605 14 HOH HOH . 
JA 16 HOH L 6 606 25 HOH HOH . 
JA 16 HOH L 7 607 5 HOH HOH . 
JA 16 HOH L 8 608 13 HOH HOH . 
KA 16 HOH M 1 501 12 HOH HOH . 
KA 16 HOH M 2 502 8 HOH HOH . 
KA 16 HOH M 3 503 2 HOH HOH . 
KA 16 HOH M 4 504 3 HOH HOH . 
KA 16 HOH M 5 505 6 HOH HOH . 
KA 16 HOH M 6 506 16 HOH HOH . 
KA 16 HOH M 7 507 1 HOH HOH . 
KA 16 HOH M 8 508 24 HOH HOH . 
KA 16 HOH M 9 509 15 HOH HOH . 
KA 16 HOH M 10 510 22 HOH HOH . 
KA 16 HOH M 11 511 7 HOH HOH . 
KA 16 HOH M 12 512 19 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 CMA SPN . . . Z 14 -17.189 -13.588 -20.93 1 85.63 ? CMA SPN 407 M 1 
HETATM 2 O O1 SPN . . . Z 14 -17.351 -14.552 -19.909 1 85.97 ? O1 SPN 407 M 1 
HETATM 3 C CM1 SPN . . . Z 14 -18.801 -16.373 -19.098 1 79.62 ? CM1 SPN 407 M 1 
HETATM 4 C CM2 SPN . . . Z 14 -18.772 -15.755 -21.548 1 80.36 ? CM2 SPN 407 M 1 
HETATM 5 C C1 SPN . . . Z 14 -17.951 -15.805 -20.246 1 88 ? C1 SPN 407 M 1 
HETATM 6 C C2 SPN . . . Z 14 -16.785 -16.763 -20.551 1 88.96 ? C2 SPN 407 M 1 
HETATM 7 O O2 SPN . . . Z 14 -16.946 -17.693 -21.314 1 88.9 ? O2 SPN 407 M 1 
HETATM 8 C C3 SPN . . . Z 14 -15.451 -16.501 -19.875 1 84.45 ? C3 SPN 407 M 1 
HETATM 9 C C4 SPN . . . Z 14 -14.564 -17.699 -19.837 1 79.92 ? C4 SPN 407 M 1 
HETATM 10 C C5 SPN . . . Z 14 -13.428 -17.805 -19.146 1 81.62 ? C5 SPN 407 M 1 
HETATM 11 C CM3 SPN . . . Z 14 -12.877 -16.711 -18.281 1 78.66 ? CM3 SPN 407 M 1 
HETATM 12 C C6 SPN . . . Z 14 -12.642 -19.093 -19.205 1 80.74 ? C6 SPN 407 M 1 
HETATM 13 C C7 SPN . . . Z 14 -11.409 -19.198 -18.292 1 79.2 ? C7 SPN 407 M 1 
HETATM 14 C C8 SPN . . . Z 14 -10.8 -20.573 -18.306 1 73.72 ? C8 SPN 407 M 1 
HETATM 15 C C9 SPN . . . Z 14 -9.711 -21.006 -17.648 1 75.1 ? C9 SPN 407 M 1 
HETATM 16 C CM4 SPN . . . Z 14 -8.871 -20.149 -16.741 1 71.98 ? CM4 SPN 407 M 1 
HETATM 17 C C10 SPN . . . Z 14 -9.234 -22.435 -17.775 1 71.65 ? C10 SPN 407 M 1 
HETATM 18 C C11 SPN . . . Z 14 -7.73 -22.658 -17.475 1 68.02 ? C11 SPN 407 M 1 
HETATM 19 C C12 SPN . . . Z 14 -7.437 -24.136 -17.457 1 72.66 ? C12 SPN 407 M 1 
HETATM 20 C C13 SPN . . . Z 14 -6.386 -24.837 -17.002 1 62 ? C13 SPN 407 M 1 
HETATM 21 C CM5 SPN . . . Z 14 -5.183 -24.195 -16.372 1 61.35 ? CM5 SPN 407 M 1 
HETATM 22 C C14 SPN . . . Z 14 -6.393 -26.355 -17.118 1 59.05 ? C14 SPN 407 M 1 
HETATM 23 C C15 SPN . . . Z 14 -5.37 -27.112 -16.251 1 58.74 ? C15 SPN 407 M 1 
HETATM 24 C C16 SPN . . . Z 14 -5.48 -28.641 -16.242 1 53.37 ? C16 SPN 407 M 1 
HETATM 25 C C17 SPN . . . Z 14 -6.879 -29.17 -15.934 1 58.37 ? C17 SPN 407 M 1 
HETATM 26 C C18 SPN . . . Z 14 -7.048 -30.673 -15.996 1 66.59 ? C18 SPN 407 M 1 
HETATM 27 C CM6 SPN . . . Z 14 -5.756 -31.457 -15.925 1 59.72 ? CM6 SPN 407 M 1 
HETATM 28 C C19 SPN . . . Z 14 -8.271 -31.248 -16.11 1 59.46 ? C19 SPN 407 M 1 
HETATM 29 C C20 SPN . . . Z 14 -8.516 -32.73 -16.166 1 55.19 ? C20 SPN 407 M 1 
HETATM 30 C C21 SPN . . . Z 14 -9.866 -33.195 -16.727 1 55.18 ? C21 SPN 407 M 1 
HETATM 31 C C22 SPN . . . Z 14 -10.177 -34.685 -16.437 1 58.98 ? C22 SPN 407 M 1 
HETATM 32 C CM7 SPN . . . Z 14 -9.166 -35.693 -17 1 54.2 ? CM7 SPN 407 M 1 
HETATM 33 C C23 SPN . . . Z 14 -11.606 -35.07 -16.805 1 54.38 ? C23 SPN 407 M 1 
HETATM 34 C C24 SPN . . . Z 14 -12.112 -36.071 -15.773 1 67.35 ? C24 SPN 407 M 1 
HETATM 35 C C25 SPN . . . Z 14 -13.611 -36.144 -15.674 1 78.71 ? C25 SPN 407 M 1 
HETATM 36 C C26 SPN . . . Z 14 -14.358 -36.109 -14.556 1 77.17 ? C26 SPN 407 M 1 
HETATM 37 C CM8 SPN . . . Z 14 -13.787 -35.992 -13.18 1 69.55 ? CM8 SPN 407 M 1 
HETATM 38 C C27 SPN . . . Z 14 -15.865 -36.19 -14.589 1 77.52 ? C27 SPN 407 M 1 
HETATM 39 C C28 SPN . . . Z 14 -16.405 -37.617 -14.382 1 80.46 ? C28 SPN 407 M 1 
HETATM 40 C C29 SPN . . . Z 14 -17.324 -38.052 -15.49 1 92.07 ? C29 SPN 407 M 1 
HETATM 41 C C30 SPN . . . Z 14 -17.079 -38.907 -16.5 1 96.37 ? C30 SPN 407 M 1 
HETATM 42 C CM9 SPN . . . Z 14 -15.743 -39.58 -16.652 1 85.86 ? CM9 SPN 407 M 1 
HETATM 43 C CMB SPN . . . Z 14 -18.058 -39.289 -17.575 1 90.91 ? CMB SPN 407 M 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           40 
_model_server_stats.create_model_time_ms    42 
_model_server_stats.query_time_ms           967 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#