data_9EZ1 # _model_server_result.job_id CyKZ0dMRjRCPRiv3WyhVJw _model_server_result.datetime_utc '2025-01-25 10:25:06' _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 9ez1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 9EZ1 # _exptl.entry_id 9EZ1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 430.62 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '1,4a,25-trihydroxyvitamin D3' _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 120 _cell.entry_id 9EZ1 _cell.length_a 65.98 _cell.length_b 65.98 _cell.length_c 263.47 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9EZ1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall 'P 65 2 (x,y,z+1/12)' _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 12_564 x,x-y+1,-z-1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -32.99 57.140356 -43.911667 # _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 'C27 H42 O4' _chem_comp.formula_weight 430.62 _chem_comp.id A1H9P _chem_comp.mon_nstd_flag . _chem_comp.name '1,4a,25-trihydroxyvitamin D3' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms (1S,2S,4S,6E)-6-[(2E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(E,2R)-6-methyl-6-oxidanyl-hept-4-en-2-yl]-2,3,3a,5,6,7-hexahydro-1H-inden-4-ylidene]ethylidene]-5-methylidene-cyclohexane-1,2,4-triol # 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 C26 C25 A1H9P sing 1 n n C27 C25 A1H9P sing 2 n n C25 O3 A1H9P sing 3 n n C25 C24 A1H9P sing 4 n n C24 C23 A1H9P doub 5 e n C23 C22 A1H9P sing 6 n n C22 C20 A1H9P sing 7 n n O4 C4 A1H9P sing 8 n n C18 C13 A1H9P sing 9 n n C19 C10 A1H9P doub 10 n n C11 C12 A1H9P sing 11 n n C11 C9 A1H9P sing 12 n n C12 C13 A1H9P sing 13 n n C20 C21 A1H9P sing 14 n n C20 C17 A1H9P sing 15 n n C13 C17 A1H9P sing 16 n n C13 C14 A1H9P sing 17 n n C2 C1 A1H9P sing 18 n n C2 C3 A1H9P sing 19 n n O1 C1 A1H9P sing 20 n n C10 C5 A1H9P sing 21 n n C10 C1 A1H9P sing 22 n n C4 C5 A1H9P sing 23 n n C4 C3 A1H9P sing 24 n n C5 C28 A1H9P doub 25 e n C17 C16 A1H9P sing 26 n n C9 C6 A1H9P sing 27 n n C3 O2 A1H9P sing 28 n n C28 C7 A1H9P sing 29 n n C7 C6 A1H9P doub 30 e n C6 C14 A1H9P sing 31 n n C14 C15 A1H9P sing 32 n n C16 C15 A1H9P sing 33 n n C14 H1 A1H9P sing 34 n n C9 H2 A1H9P sing 35 n n C9 H3 A1H9P sing 36 n n C11 H4 A1H9P sing 37 n n C11 H5 A1H9P sing 38 n n C12 H6 A1H9P sing 39 n n C12 H7 A1H9P sing 40 n n C18 H8 A1H9P sing 41 n n C18 H9 A1H9P sing 42 n n C18 H10 A1H9P sing 43 n n C19 H11 A1H9P sing 44 n n C19 H12 A1H9P sing 45 n n C21 H13 A1H9P sing 46 n n C21 H14 A1H9P sing 47 n n C21 H15 A1H9P sing 48 n n C23 H16 A1H9P sing 49 n n C17 H17 A1H9P sing 50 n n C7 H18 A1H9P sing 51 n n C28 H19 A1H9P sing 52 n n C4 H20 A1H9P sing 53 n n C3 H21 A1H9P sing 54 n n C2 H22 A1H9P sing 55 n n C2 H23 A1H9P sing 56 n n C1 H24 A1H9P sing 57 n n C16 H25 A1H9P sing 58 n n C16 H26 A1H9P sing 59 n n C20 H27 A1H9P sing 60 n n C22 H28 A1H9P sing 61 n n C22 H29 A1H9P sing 62 n n C24 H30 A1H9P sing 63 n n C26 H31 A1H9P sing 64 n n C26 H32 A1H9P sing 65 n n C26 H33 A1H9P sing 66 n n C15 H34 A1H9P sing 67 n n C15 H35 A1H9P sing 68 n n C27 H36 A1H9P sing 69 n n C27 H37 A1H9P sing 70 n n C27 H38 A1H9P sing 71 n n O4 H39 A1H9P sing 72 n n O2 H40 A1H9P sing 73 n n O1 H41 A1H9P sing 74 n n O3 H42 A1H9P sing 75 n n # _atom_sites.entry_id 9EZ1 _atom_sites.fract_transf_matrix[1][1] 0.015156 _atom_sites.fract_transf_matrix[1][2] 0.00875 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017501 _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] 0.003795 _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 A1H9P A 1 501 1 A1H9P LIG . D 4 ACT A 1 502 502 ACT ACT . E 5 HOH A 1 601 60 HOH HOH . E 5 HOH A 2 602 82 HOH HOH . E 5 HOH A 3 603 48 HOH HOH . E 5 HOH A 4 604 59 HOH HOH . E 5 HOH A 5 605 34 HOH HOH . E 5 HOH A 6 606 69 HOH HOH . E 5 HOH A 7 607 71 HOH HOH . E 5 HOH A 8 608 45 HOH HOH . E 5 HOH A 9 609 78 HOH HOH . E 5 HOH A 10 610 23 HOH HOH . E 5 HOH A 11 611 51 HOH HOH . E 5 HOH A 12 612 35 HOH HOH . E 5 HOH A 13 613 18 HOH HOH . E 5 HOH A 14 614 24 HOH HOH . E 5 HOH A 15 615 5 HOH HOH . E 5 HOH A 16 616 21 HOH HOH . E 5 HOH A 17 617 32 HOH HOH . E 5 HOH A 18 618 49 HOH HOH . E 5 HOH A 19 619 22 HOH HOH . E 5 HOH A 20 620 64 HOH HOH . E 5 HOH A 21 621 37 HOH HOH . E 5 HOH A 22 622 43 HOH HOH . E 5 HOH A 23 623 36 HOH HOH . E 5 HOH A 24 624 1 HOH HOH . E 5 HOH A 25 625 7 HOH HOH . E 5 HOH A 26 626 68 HOH HOH . E 5 HOH A 27 627 2 HOH HOH . E 5 HOH A 28 628 55 HOH HOH . E 5 HOH A 29 629 74 HOH HOH . E 5 HOH A 30 630 62 HOH HOH . E 5 HOH A 31 631 38 HOH HOH . E 5 HOH A 32 632 54 HOH HOH . E 5 HOH A 33 633 6 HOH HOH . E 5 HOH A 34 634 4 HOH HOH . E 5 HOH A 35 635 19 HOH HOH . E 5 HOH A 36 636 13 HOH HOH . E 5 HOH A 37 637 12 HOH HOH . E 5 HOH A 38 638 63 HOH HOH . E 5 HOH A 39 639 44 HOH HOH . E 5 HOH A 40 640 15 HOH HOH . E 5 HOH A 41 641 61 HOH HOH . E 5 HOH A 42 642 58 HOH HOH . E 5 HOH A 43 643 75 HOH HOH . E 5 HOH A 44 644 25 HOH HOH . E 5 HOH A 45 645 56 HOH HOH . E 5 HOH A 46 646 27 HOH HOH . E 5 HOH A 47 647 31 HOH HOH . E 5 HOH A 48 648 8 HOH HOH . E 5 HOH A 49 649 67 HOH HOH . E 5 HOH A 50 650 52 HOH HOH . E 5 HOH A 51 651 3 HOH HOH . E 5 HOH A 52 652 33 HOH HOH . E 5 HOH A 53 653 50 HOH HOH . E 5 HOH A 54 654 47 HOH HOH . E 5 HOH A 55 655 77 HOH HOH . E 5 HOH A 56 656 11 HOH HOH . E 5 HOH A 57 657 9 HOH HOH . E 5 HOH A 58 658 70 HOH HOH . E 5 HOH A 59 659 16 HOH HOH . E 5 HOH A 60 660 20 HOH HOH . E 5 HOH A 61 661 10 HOH HOH . E 5 HOH A 62 662 42 HOH HOH . E 5 HOH A 63 663 46 HOH HOH . E 5 HOH A 64 664 41 HOH HOH . E 5 HOH A 65 665 39 HOH HOH . E 5 HOH A 66 666 73 HOH HOH . E 5 HOH A 67 667 26 HOH HOH . E 5 HOH A 68 668 17 HOH HOH . E 5 HOH A 69 669 80 HOH HOH . E 5 HOH A 70 670 53 HOH HOH . E 5 HOH A 71 671 57 HOH HOH . E 5 HOH A 72 672 29 HOH HOH . E 5 HOH A 73 673 40 HOH HOH . E 5 HOH A 74 674 65 HOH HOH . E 5 HOH A 75 675 66 HOH HOH . E 5 HOH A 76 676 72 HOH HOH . F 5 HOH B 1 701 14 HOH HOH . F 5 HOH B 2 702 76 HOH HOH . F 5 HOH B 3 703 79 HOH HOH . F 5 HOH B 4 704 81 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 C14 A1H9P . . . C 3 -30.554 17.348 -4.532 1 43.83 ? C14 A1H9P 501 A 1 HETATM 2 C C6 A1H9P . . . C 3 -32.046 17.39 -4.774 1 42.26 ? C6 A1H9P 501 A 1 HETATM 3 C C9 A1H9P . . . C 3 -32.559 16.02 -5.127 1 46.27 ? C9 A1H9P 501 A 1 HETATM 4 C C11 A1H9P . . . C 3 -31.82 15.488 -6.363 1 44.51 ? C11 A1H9P 501 A 1 HETATM 5 C C12 A1H9P . . . C 3 -30.309 15.487 -6.148 1 43.07 ? C12 A1H9P 501 A 1 HETATM 6 C C18 A1H9P . . . C 3 -29.988 17.867 -6.932 1 42.07 ? C18 A1H9P 501 A 1 HETATM 7 C C5 A1H9P . . . C 3 -34.863 19.726 -5.358 1 37.24 ? C5 A1H9P 501 A 1 HETATM 8 C C10 A1H9P . . . C 3 -34.249 21.026 -5.712 1 40.09 ? C10 A1H9P 501 A 1 HETATM 9 C C19 A1H9P . . . C 3 -33.181 21.132 -6.491 1 43.93 ? C19 A1H9P 501 A 1 HETATM 10 C C21 A1H9P . . . C 3 -25.87 16.366 -5.212 1 41.75 ? C21 A1H9P 501 A 1 HETATM 11 C C23 A1H9P . . . C 3 -25.865 17.321 -8.254 1 43.34 ? C23 A1H9P 501 A 1 HETATM 12 C C25 A1H9P . . . C 3 -24.458 18.027 -10.335 1 42.83 ? C25 A1H9P 501 A 1 HETATM 13 C C17 A1H9P . . . C 3 -28.339 16.955 -5.194 1 40.29 ? C17 A1H9P 501 A 1 HETATM 14 C C7 A1H9P . . . C 3 -32.768 18.517 -4.792 1 39.71 ? C7 A1H9P 501 A 1 HETATM 15 C C28 A1H9P . . . C 3 -34.178 18.619 -5.031 1 37.26 ? C28 A1H9P 501 A 1 HETATM 16 C C4 A1H9P . . . C 3 -36.355 19.733 -5.598 1 43.11 ? C4 A1H9P 501 A 1 HETATM 17 C C3 A1H9P . . . C 3 -37.06 20.995 -5.104 1 41.69 ? C3 A1H9P 501 A 1 HETATM 18 C C2 A1H9P . . . C 3 -36.443 22.228 -5.752 1 36.91 ? C2 A1H9P 501 A 1 HETATM 19 C C1 A1H9P . . . C 3 -35.001 22.253 -5.264 1 39.55 ? C1 A1H9P 501 A 1 HETATM 20 C C16 A1H9P . . . C 3 -28.304 18.34 -4.523 1 41.76 ? C16 A1H9P 501 A 1 HETATM 21 C C20 A1H9P . . . C 3 -27.098 16.67 -6.067 1 40.8 ? C20 A1H9P 501 A 1 HETATM 22 C C22 A1H9P . . . C 3 -26.77 17.785 -7.09 1 40.23 ? C22 A1H9P 501 A 1 HETATM 23 C C24 A1H9P . . . C 3 -25.534 18.404 -9.3 1 37.96 ? C24 A1H9P 501 A 1 HETATM 24 C C26 A1H9P . . . C 3 -24.223 19.141 -11.34 1 45.97 ? C26 A1H9P 501 A 1 HETATM 25 C C15 A1H9P . . . C 3 -29.777 18.595 -4.061 1 42.74 ? C15 A1H9P 501 A 1 HETATM 26 C C27 A1H9P . . . C 3 -24.811 16.734 -11.051 1 42.62 ? C27 A1H9P 501 A 1 HETATM 27 C C13 A1H9P . . . C 3 -29.764 16.874 -5.779 1 41.89 ? C13 A1H9P 501 A 1 HETATM 28 O O4 A1H9P . . . C 3 -36.628 19.53 -6.983 1 45.01 ? O4 A1H9P 501 A 1 HETATM 29 O O2 A1H9P . . . C 3 -36.981 21.09 -3.672 1 44.03 ? O2 A1H9P 501 A 1 HETATM 30 O O1 A1H9P . . . C 3 -34.368 23.422 -5.724 1 37.64 ? O1 A1H9P 501 A 1 HETATM 31 O O3 A1H9P . . . C 3 -23.215 17.78 -9.65 1 43.18 ? O3 A1H9P 501 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #