data_5XPP
#
_model_server_result.job_id            gkcDjiMbikKJGk0cK0YH6A 
_model_server_result.datetime_utc      '2025-07-30 23:05:39' 
_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          5xpp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":501}' 
#
_entry.id    5XPP 
#
_exptl.entry_id    5XPP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              480.679 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-oxidanyl-hexan-2-yl]-7~{ a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol' 
_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          95.65 
_cell.angle_gamma         90 
_cell.entry_id            5XPP 
_cell.length_a            154.38 
_cell.length_b            42.86 
_cell.length_c            41.74 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XPP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C31 H44 O4' 
_chem_comp.formula_weight    480.679 
_chem_comp.id                8BF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{a}~{S},7~{a}~{R})-1-[(2~{R},6~{R})-6-(4-hydroxyphenyl)-6-oxidanyl-hexan-2-yl]-7~{ a}-methyl-2,3,3~{a},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-1,3-diol' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '25RS-(Hydroxyphenyl)-2-methylidene-19,26,27-trinor-1,25-dihydroxyvitamin D3' 
#
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
C31 C3 8BF doub 1 n n 
O29 C2 8BF sing 2 n n 
C3 C2 8BF sing 3 n n 
C3 C4 8BF sing 4 n n 
C2 C1 8BF sing 5 n n 
C4 O30 8BF sing 6 n n 
C4 C5 8BF sing 7 n n 
C1 C6 8BF sing 8 n n 
C5 C6 8BF sing 9 n n 
C6 C7 8BF doub 10 n n 
C7 C8 8BF sing 11 n n 
C8 C9 8BF doub 12 e n 
C9 C14 8BF sing 13 n n 
C9 C10 8BF sing 14 n n 
C15 C14 8BF sing 15 n n 
C15 C16 8BF sing 16 n n 
C32 C13 8BF sing 17 n n 
C14 C13 8BF sing 18 n n 
C16 C17 8BF sing 19 n n 
C10 C11 8BF sing 20 n n 
C21 C22 8BF sing 21 n n 
C21 C20 8BF sing 22 n n 
C13 C17 8BF sing 23 n n 
C13 C12 8BF sing 24 n n 
C19 C20 8BF sing 25 n n 
C19 C18 8BF sing 26 n n 
C11 C12 8BF sing 27 n n 
C17 C18 8BF sing 28 n n 
C22 C23 8BF sing 29 n n 
C22 O34 8BF sing 30 n n 
C24 C23 8BF doub 31 n y 
C24 C25 8BF sing 32 n y 
C18 C33 8BF sing 33 n n 
C23 C28 8BF sing 34 n y 
C25 C26 8BF doub 35 n y 
C28 C27 8BF doub 36 n y 
C26 C27 8BF sing 37 n y 
C26 O35 8BF sing 38 n n 
O35 H1 8BF sing 39 n n 
C25 H2 8BF sing 40 n n 
C24 H3 8BF sing 41 n n 
C27 H4 8BF sing 42 n n 
C28 H5 8BF sing 43 n n 
C22 H6 8BF sing 44 n n 
O34 H7 8BF sing 45 n n 
C21 H8 8BF sing 46 n n 
C21 H9 8BF sing 47 n n 
C20 H10 8BF sing 48 n n 
C20 H11 8BF sing 49 n n 
C19 H12 8BF sing 50 n n 
C19 H13 8BF sing 51 n n 
C18 H14 8BF sing 52 n n 
C33 H15 8BF sing 53 n n 
C33 H16 8BF sing 54 n n 
C33 H17 8BF sing 55 n n 
C17 H18 8BF sing 56 n n 
C32 H19 8BF sing 57 n n 
C32 H20 8BF sing 58 n n 
C32 H21 8BF sing 59 n n 
C12 H22 8BF sing 60 n n 
C12 H23 8BF sing 61 n n 
C11 H24 8BF sing 62 n n 
C11 H25 8BF sing 63 n n 
C10 H26 8BF sing 64 n n 
C10 H27 8BF sing 65 n n 
C16 H28 8BF sing 66 n n 
C16 H29 8BF sing 67 n n 
C15 H30 8BF sing 68 n n 
C15 H31 8BF sing 69 n n 
C14 H32 8BF sing 70 n n 
C8 H33 8BF sing 71 n n 
C7 H34 8BF sing 72 n n 
C1 H35 8BF sing 73 n n 
C1 H36 8BF sing 74 n n 
C5 H37 8BF sing 75 n n 
C5 H38 8BF sing 76 n n 
C4 H39 8BF sing 77 n n 
O30 H40 8BF sing 78 n n 
C31 H41 8BF sing 79 n n 
C31 H42 8BF sing 80 n n 
C2 H43 8BF sing 81 n n 
O29 H44 8BF sing 82 n n 
#
_atom_sites.entry_id                     5XPP 
_atom_sites.fract_transf_matrix[1][1]    0.006478 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000641 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.023332 
_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]    0.024075 
_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
C 3 8BF A 1 501 1 8BF ak4 . 
D 4 HOH A 1 601 5 HOH HOH . 
D 4 HOH A 2 602 10 HOH HOH . 
D 4 HOH A 3 603 2 HOH HOH . 
D 4 HOH A 4 604 1 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 O O35 8BF . . . C 3 6.11 2.273 29.031 1 45.15 ? O35 8BF 501 A 1 
HETATM 2 C C26 8BF . . . C 3 7.03 1.461 28.463 1 41.81 ? C26 8BF 501 A 1 
HETATM 3 C C25 8BF . . . C 3 8.102 1.976 27.75 1 41.66 ? C25 8BF 501 A 1 
HETATM 4 C C24 8BF . . . C 3 9.009 1.105 27.177 1 42.21 ? C24 8BF 501 A 1 
HETATM 5 C C27 8BF . . . C 3 6.851 0.105 28.61 1 41.32 ? C27 8BF 501 A 1 
HETATM 6 C C28 8BF . . . C 3 7.751 -0.779 28.04 1 41.19 ? C28 8BF 501 A 1 
HETATM 7 C C23 8BF . . . C 3 8.84 -0.287 27.317 1 41.19 ? C23 8BF 501 A 1 
HETATM 8 C C22 8BF . . . C 3 9.773 -1.297 26.729 1 38.07 ? C22 8BF 501 A 1 
HETATM 9 O O34 8BF . . . C 3 10.106 -2.252 27.767 1 38.27 ? O34 8BF 501 A 1 
HETATM 10 C C21 8BF . . . C 3 11.007 -0.646 26.066 1 35.36 ? C21 8BF 501 A 1 
HETATM 11 C C20 8BF . . . C 3 11.966 0.011 27.083 1 34.34 ? C20 8BF 501 A 1 
HETATM 12 C C19 8BF . . . C 3 12.96 0.974 26.414 1 32.22 ? C19 8BF 501 A 1 
HETATM 13 C C18 8BF . . . C 3 13.309 2.166 27.302 1 29.09 ? C18 8BF 501 A 1 
HETATM 14 C C33 8BF . . . C 3 13.763 1.639 28.67 1 29.95 ? C33 8BF 501 A 1 
HETATM 15 C C17 8BF . . . C 3 14.386 3.093 26.72 1 26.51 ? C17 8BF 501 A 1 
HETATM 16 C C13 8BF . . . C 3 13.929 4.432 26.158 1 25.36 ? C13 8BF 501 A 1 
HETATM 17 C C32 8BF . . . C 3 12.839 4.289 25.091 1 26.33 ? C32 8BF 501 A 1 
HETATM 18 C C12 8BF . . . C 3 13.493 5.481 27.166 1 24.78 ? C12 8BF 501 A 1 
HETATM 19 C C11 8BF . . . C 3 13.445 6.872 26.529 1 24.4 ? C11 8BF 501 A 1 
HETATM 20 C C10 8BF . . . C 3 14.732 7.268 25.777 1 24.62 ? C10 8BF 501 A 1 
HETATM 21 C C16 8BF . . . C 3 15.267 2.511 25.61 1 26.29 ? C16 8BF 501 A 1 
HETATM 22 C C15 8BF . . . C 3 15.867 3.689 24.857 1 24.86 ? C15 8BF 501 A 1 
HETATM 23 C C14 8BF . . . C 3 15.253 4.872 25.575 1 25.11 ? C14 8BF 501 A 1 
HETATM 24 C C9 8BF . . . C 3 15.067 6.142 24.832 1 24.73 ? C9 8BF 501 A 1 
HETATM 25 C C8 8BF . . . C 3 15.214 6.209 23.507 1 25.24 ? C8 8BF 501 A 1 
HETATM 26 C C7 8BF . . . C 3 14.99 7.439 22.753 1 26.65 ? C7 8BF 501 A 1 
HETATM 27 C C6 8BF . . . C 3 14.854 7.468 21.409 1 27.17 ? C6 8BF 501 A 1 
HETATM 28 C C1 8BF . . . C 3 14.975 6.201 20.578 1 27.24 ? C1 8BF 501 A 1 
HETATM 29 C C5 8BF . . . C 3 14.572 8.816 20.761 1 27.01 ? C5 8BF 501 A 1 
HETATM 30 C C4 8BF . . . C 3 15.223 8.89 19.374 1 26.79 ? C4 8BF 501 A 1 
HETATM 31 O O30 8BF . . . C 3 16.661 8.89 19.427 1 25.12 ? O30 8BF 501 A 1 
HETATM 32 C C3 8BF . . . C 3 14.805 7.679 18.594 1 26.68 ? C3 8BF 501 A 1 
HETATM 33 C C31 8BF . . . C 3 14.025 7.804 17.53 1 25.95 ? C31 8BF 501 A 1 
HETATM 34 C C2 8BF . . . C 3 15.324 6.372 19.109 1 27.12 ? C2 8BF 501 A 1 
HETATM 35 O O29 8BF . . . C 3 14.754 5.232 18.465 1 29.02 ? O29 8BF 501 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           35 
#