data_5ID9 # _model_server_result.job_id qboClCjVrOkk_v2j3NSfaw _model_server_result.datetime_utc '2024-10-12 19:24:43' _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 5id9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5ID9 # _exptl.entry_id 5ID9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 395.537 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-sulfanylidene-4-[(tetradecanoyloxy)methyl]-1,3,2lambda~5~-dioxaphospholane-2-thiolate _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 5ID9 _cell.length_a 93.86 _cell.length_b 93.86 _cell.length_c 141.79 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ID9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,G,H,I,J _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 2 _struct_asym.id B _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 A SG CYS 53 A CYS 53 1_555 A SG CYS 62 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf2 A SG CYS 75 A CYS 75 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf3 A SG CYS 90 A CYS 90 1_555 A SG CYS 101 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? disulf ? disulf4 A SG CYS 123 A CYS 123 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 167 A CYS 167 1_555 A SG CYS 176 A CYS 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf6 A SG CYS 199 A CYS 199 1_555 A SG CYS 245 A CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 244 A CYS 244 1_555 A SG CYS 252 A CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 A SG CYS 264 A CYS 264 1_555 A SG CYS 278 A CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf9 A SG CYS 277 A CYS 277 1_555 A SG CYS 288 A CYS 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? disulf ? disulf10 A SG CYS 315 A CYS 315 1_555 A SG CYS 360 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf11 A SG CYS 359 A CYS 359 1_555 A SG CYS 368 A CYS 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf12 A SG CYS 391 A CYS 391 1_555 A SG CYS 437 A CYS 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf13 A SG CYS 436 A CYS 436 1_555 A SG CYS 447 A CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf14 A SG CYS 460 A CYS 460 1_555 A SG CYS 476 A CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf15 A SG CYS 475 A CYS 475 1_555 A SG CYS 486 A CYS 486 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? disulf ? disulf16 A SG CYS 513 A CYS 513 1_555 A SG CYS 558 A CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf17 A SG CYS 557 A CYS 557 1_555 A SG CYS 566 A CYS 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? # _chem_comp.formula 'C17 H32 O4 P S2 -1' _chem_comp.formula_weight 395.537 _chem_comp.id 6A4 _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-sulfanylidene-4-[(tetradecanoyloxy)methyl]-1,3,2lambda~5~-dioxaphospholane-2-thiolate _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 S4 P1 6A4 doub 1 n n S5 P1 6A4 sing 2 n n P1 O2 6A4 sing 3 n n P1 O1 6A4 sing 4 n n O2 C2 6A4 sing 5 n n O1 C1 6A4 sing 6 n n C1 C2 6A4 sing 7 n n C1 C3 6A4 sing 8 n n C3 O3 6A4 sing 9 n n O18 C4 6A4 doub 10 n n O3 C4 6A4 sing 11 n n C4 C5 6A4 sing 12 n n C5 C6 6A4 sing 13 n n C6 C7 6A4 sing 14 n n C7 C8 6A4 sing 15 n n C8 C9 6A4 sing 16 n n C9 C10 6A4 sing 17 n n C10 C11 6A4 sing 18 n n C11 C12 6A4 sing 19 n n C12 C13 6A4 sing 20 n n C14 C13 6A4 sing 21 n n C14 C15 6A4 sing 22 n n C16 C15 6A4 sing 23 n n C16 C17 6A4 sing 24 n n C2 H3 6A4 sing 25 n n C2 H4 6A4 sing 26 n n C1 H5 6A4 sing 27 n n C3 H6 6A4 sing 28 n n C3 H7 6A4 sing 29 n n C5 H8 6A4 sing 30 n n C5 H9 6A4 sing 31 n n C6 H10 6A4 sing 32 n n C6 H11 6A4 sing 33 n n C7 H12 6A4 sing 34 n n C7 H13 6A4 sing 35 n n C8 H14 6A4 sing 36 n n C8 H15 6A4 sing 37 n n C9 H16 6A4 sing 38 n n C9 H17 6A4 sing 39 n n C10 H18 6A4 sing 40 n n C10 H19 6A4 sing 41 n n C11 H20 6A4 sing 42 n n C11 H21 6A4 sing 43 n n C12 H22 6A4 sing 44 n n C12 H23 6A4 sing 45 n n C13 H24 6A4 sing 46 n n C13 H25 6A4 sing 47 n n C14 H26 6A4 sing 48 n n C14 H27 6A4 sing 49 n n C15 H28 6A4 sing 50 n n C15 H29 6A4 sing 51 n n C16 H30 6A4 sing 52 n n C16 H31 6A4 sing 53 n n C17 H32 6A4 sing 54 n n C17 H33 6A4 sing 55 n n C17 H34 6A4 sing 56 n n # _atom_sites.entry_id 5ID9 _atom_sites.fract_transf_matrix[1][1] 0.010654 _atom_sites.fract_transf_matrix[1][2] 0.006151 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012302 _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] 0.007053 _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 6A4 A 1 601 1 6A4 m2c . C 3 MLI A 1 602 1 MLI MLI . D 3 MLI A 1 603 2 MLI MLI . E 3 MLI A 1 604 3 MLI MLI . F 4 FMT A 1 605 4 FMT FMT . G 4 FMT A 1 606 5 FMT FMT . H 4 FMT A 1 607 6 FMT FMT . I 4 FMT A 1 608 7 FMT FMT . J 5 HOH A 1 701 94 HOH HOH . J 5 HOH A 2 702 12 HOH HOH . J 5 HOH A 3 703 6 HOH HOH . J 5 HOH A 4 704 86 HOH HOH . J 5 HOH A 5 705 90 HOH HOH . J 5 HOH A 6 706 4 HOH HOH . J 5 HOH A 7 707 68 HOH HOH . J 5 HOH A 8 708 57 HOH HOH . J 5 HOH A 9 709 22 HOH HOH . J 5 HOH A 10 710 49 HOH HOH . J 5 HOH A 11 711 97 HOH HOH . J 5 HOH A 12 712 39 HOH HOH . J 5 HOH A 13 713 26 HOH HOH . J 5 HOH A 14 714 36 HOH HOH . J 5 HOH A 15 715 67 HOH HOH . J 5 HOH A 16 716 16 HOH HOH . J 5 HOH A 17 717 23 HOH HOH . J 5 HOH A 18 718 73 HOH HOH . J 5 HOH A 19 719 2 HOH HOH . J 5 HOH A 20 720 75 HOH HOH . J 5 HOH A 21 721 58 HOH HOH . J 5 HOH A 22 722 35 HOH HOH . J 5 HOH A 23 723 27 HOH HOH . J 5 HOH A 24 724 54 HOH HOH . J 5 HOH A 25 725 38 HOH HOH . J 5 HOH A 26 726 99 HOH HOH . J 5 HOH A 27 727 92 HOH HOH . J 5 HOH A 28 728 53 HOH HOH . J 5 HOH A 29 729 91 HOH HOH . J 5 HOH A 30 730 21 HOH HOH . J 5 HOH A 31 731 25 HOH HOH . J 5 HOH A 32 732 93 HOH HOH . J 5 HOH A 33 733 70 HOH HOH . J 5 HOH A 34 734 1 HOH HOH . J 5 HOH A 35 735 82 HOH HOH . J 5 HOH A 36 736 10 HOH HOH . J 5 HOH A 37 737 17 HOH HOH . J 5 HOH A 38 738 45 HOH HOH . J 5 HOH A 39 739 24 HOH HOH . J 5 HOH A 40 740 71 HOH HOH . J 5 HOH A 41 741 41 HOH HOH . J 5 HOH A 42 742 29 HOH HOH . J 5 HOH A 43 743 77 HOH HOH . J 5 HOH A 44 744 74 HOH HOH . J 5 HOH A 45 745 88 HOH HOH . J 5 HOH A 46 746 55 HOH HOH . J 5 HOH A 47 747 44 HOH HOH . J 5 HOH A 48 748 11 HOH HOH . J 5 HOH A 49 749 65 HOH HOH . J 5 HOH A 50 750 72 HOH HOH . J 5 HOH A 51 751 14 HOH HOH . J 5 HOH A 52 752 42 HOH HOH . J 5 HOH A 53 753 31 HOH HOH . J 5 HOH A 54 754 79 HOH HOH . J 5 HOH A 55 755 69 HOH HOH . J 5 HOH A 56 756 46 HOH HOH . J 5 HOH A 57 757 59 HOH HOH . J 5 HOH A 58 758 87 HOH HOH . J 5 HOH A 59 759 89 HOH HOH . J 5 HOH A 60 760 8 HOH HOH . J 5 HOH A 61 761 3 HOH HOH . J 5 HOH A 62 762 15 HOH HOH . J 5 HOH A 63 763 5 HOH HOH . J 5 HOH A 64 764 28 HOH HOH . J 5 HOH A 65 765 78 HOH HOH . J 5 HOH A 66 766 30 HOH HOH . J 5 HOH A 67 767 63 HOH HOH . J 5 HOH A 68 768 96 HOH HOH . J 5 HOH A 69 769 48 HOH HOH . J 5 HOH A 70 770 43 HOH HOH . J 5 HOH A 71 771 32 HOH HOH . J 5 HOH A 72 772 19 HOH HOH . J 5 HOH A 73 773 13 HOH HOH . J 5 HOH A 74 774 9 HOH HOH . J 5 HOH A 75 775 34 HOH HOH . J 5 HOH A 76 776 40 HOH HOH . J 5 HOH A 77 777 50 HOH HOH . J 5 HOH A 78 778 83 HOH HOH . J 5 HOH A 79 779 56 HOH HOH . J 5 HOH A 80 780 81 HOH HOH . J 5 HOH A 81 781 66 HOH HOH . J 5 HOH A 82 782 95 HOH HOH . J 5 HOH A 83 783 7 HOH HOH . J 5 HOH A 84 784 61 HOH HOH . J 5 HOH A 85 785 64 HOH HOH . J 5 HOH A 86 786 20 HOH HOH . J 5 HOH A 87 787 51 HOH HOH . J 5 HOH A 88 788 85 HOH HOH . J 5 HOH A 89 789 80 HOH HOH . J 5 HOH A 90 790 33 HOH HOH . J 5 HOH A 91 791 62 HOH HOH . J 5 HOH A 92 792 47 HOH HOH . J 5 HOH A 93 793 84 HOH HOH . J 5 HOH A 94 794 18 HOH HOH . J 5 HOH A 95 795 52 HOH HOH . J 5 HOH A 96 796 37 HOH HOH . J 5 HOH A 97 797 76 HOH HOH . J 5 HOH A 98 798 60 HOH HOH . J 5 HOH A 99 799 98 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 S S4 6A4 . . . B 2 28.781 14.14 80.606 1 54.04 ? S4 6A4 601 A 1 HETATM 2 P P1 6A4 . . . B 2 29.346 12.932 82.045 1 64.36 ? P1 6A4 601 A 1 HETATM 3 O O1 6A4 . . . B 2 30.394 13.419 83.156 1 63.06 ? O1 6A4 601 A 1 HETATM 4 S S5 6A4 . . . B 2 30.113 11.283 81.352 1 66.95 ? S5 6A4 601 A 1 HETATM 5 O O2 6A4 . . . B 2 28.095 12.66 83.019 1 73.56 ? O2 6A4 601 A 1 HETATM 6 C C2 6A4 . . . B 2 28.48 12.825 84.382 1 69.4 ? C2 6A4 601 A 1 HETATM 7 C C1 6A4 . . . B 2 30.004 12.658 84.308 1 67.41 ? C1 6A4 601 A 1 HETATM 8 C C3 6A4 . . . B 2 30.665 12.975 85.625 1 70.72 ? C3 6A4 601 A 1 HETATM 9 O O3 6A4 . . . B 2 30.303 11.908 86.516 1 71.92 ? O3 6A4 601 A 1 HETATM 10 C C4 6A4 . . . B 2 31.21 10.798 86.764 1 62.28 ? C4 6A4 601 A 1 HETATM 11 O O18 6A4 . . . B 2 31.793 10.282 85.825 1 70.59 ? O18 6A4 601 A 1 HETATM 12 C C5 6A4 . . . B 2 31.43 10.305 88.168 1 62.01 ? C5 6A4 601 A 1 HETATM 13 C C6 6A4 . . . B 2 31.538 11.485 89.129 1 63.2 ? C6 6A4 601 A 1 HETATM 14 C C7 6A4 . . . B 2 32.984 11.894 89.414 1 63.56 ? C7 6A4 601 A 1 HETATM 15 C C8 6A4 . . . B 2 32.998 13.28 90.07 1 64.37 ? C8 6A4 601 A 1 HETATM 16 C C9 6A4 . . . B 2 34.396 13.874 90.181 1 64.31 ? C9 6A4 601 A 1 HETATM 17 C C10 6A4 . . . B 2 34.356 15.4 90.233 1 62.05 ? C10 6A4 601 A 1 HETATM 18 C C11 6A4 . . . B 2 35.76 15.972 90.443 1 66.18 ? C11 6A4 601 A 1 HETATM 19 C C12 6A4 . . . B 2 35.969 16.48 91.873 1 71.95 ? C12 6A4 601 A 1 HETATM 20 C C13 6A4 . . . B 2 37.444 16.492 92.308 1 73.57 ? C13 6A4 601 A 1 HETATM 21 C C14 6A4 . . . B 2 38.116 17.849 92.081 1 82.78 ? C14 6A4 601 A 1 HETATM 22 C C15 6A4 . . . B 2 37.655 18.92 93.083 1 91.5 ? C15 6A4 601 A 1 HETATM 23 C C16 6A4 . . . B 2 38.373 20.254 92.835 1 91.36 ? C16 6A4 601 A 1 HETATM 24 C C17 6A4 . . . B 2 37.622 21.457 93.384 1 86.07 ? C17 6A4 601 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 24 #