data_7JRU
#
_model_server_result.job_id            FOYm2NSfYjj8CzFAehn2Lg 
_model_server_result.datetime_utc      '2025-07-16 17:40:29' 
_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          7jru 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":603}' 
#
_entry.id    7JRU 
#
_exptl.entry_id    7JRU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              312.253 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R)-3-(phosphonooxy)propane-1,2-diyl dibutanoate' 
_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            7JRU 
_cell.length_a            58.581 
_cell.length_b            84.434 
_cell.length_c            99.068 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7JRU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_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 
_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                      4 
_struct_asym.id                             D 
_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 59 A CYS 59 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf2 A SG CYS 53 A CYS 53 1_555 A SG CYS 59 A CYS 59 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 A SG CYS 225 A CYS 225 1_555 A SG CYS 244 A CYS 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf4 A SG CYS 297 A CYS 297 1_555 A SG CYS 343 A CYS 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf5 A SG CYS 417 A CYS 417 1_555 A SG CYS 503 A CYS 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
#
_chem_comp.formula           'C11 H21 O8 P' 
_chem_comp.formula_weight    312.253 
_chem_comp.id                VHY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R)-3-(phosphonooxy)propane-1,2-diyl dibutanoate' 
_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
C01 C02 VHY sing 414 n n 
C02 C03 VHY sing 415 n n 
C03 C04 VHY sing 416 n n 
C12 C11 VHY sing 417 n n 
C04 O05 VHY sing 418 n n 
C04 O20 VHY doub 419 n n 
O05 C06 VHY sing 420 n n 
C11 C10 VHY sing 421 n n 
C10 C09 VHY sing 422 n n 
C06 C07 VHY sing 423 n n 
C09 O13 VHY doub 424 n n 
C09 O08 VHY sing 425 n n 
C07 O08 VHY sing 426 n n 
C07 C14 VHY sing 427 n n 
C14 O15 VHY sing 428 n n 
O15 P16 VHY sing 429 n n 
P16 O17 VHY doub 430 n n 
P16 O19 VHY sing 431 n n 
P16 O18 VHY sing 432 n n 
C01 H1 VHY sing 433 n n 
C01 H2 VHY sing 434 n n 
C01 H3 VHY sing 435 n n 
C02 H4 VHY sing 436 n n 
C02 H5 VHY sing 437 n n 
C03 H6 VHY sing 438 n n 
C03 H7 VHY sing 439 n n 
C06 H8 VHY sing 440 n n 
C06 H9 VHY sing 441 n n 
C07 H10 VHY sing 442 n n 
C10 H11 VHY sing 443 n n 
C10 H12 VHY sing 444 n n 
C11 H13 VHY sing 445 n n 
C11 H14 VHY sing 446 n n 
C12 H15 VHY sing 447 n n 
C12 H16 VHY sing 448 n n 
C12 H17 VHY sing 449 n n 
C14 H18 VHY sing 450 n n 
C14 H19 VHY sing 451 n n 
O18 H20 VHY sing 452 n n 
O19 H21 VHY sing 453 n n 
#
_atom_sites.entry_id                     7JRU 
_atom_sites.fract_transf_matrix[1][1]    0.01707 
_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]    0.011844 
_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]    0.010094 
_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 MES A 1 601 1 MES MES . 
C 3 GOL A 1 602 1 GOL GOL . 
D 4 VHY A 1 603 1 VHY PA4 . 
E 5 HOH A 1 701 115 HOH HOH . 
E 5 HOH A 2 702 143 HOH HOH . 
E 5 HOH A 3 703 108 HOH HOH . 
E 5 HOH A 4 704 139 HOH HOH . 
E 5 HOH A 5 705 133 HOH HOH . 
E 5 HOH A 6 706 137 HOH HOH . 
E 5 HOH A 7 707 59 HOH HOH . 
E 5 HOH A 8 708 141 HOH HOH . 
E 5 HOH A 9 709 131 HOH HOH . 
E 5 HOH A 10 710 83 HOH HOH . 
E 5 HOH A 11 711 89 HOH HOH . 
E 5 HOH A 12 712 15 HOH HOH . 
E 5 HOH A 13 713 112 HOH HOH . 
E 5 HOH A 14 714 66 HOH HOH . 
E 5 HOH A 15 715 140 HOH HOH . 
E 5 HOH A 16 716 12 HOH HOH . 
E 5 HOH A 17 717 44 HOH HOH . 
E 5 HOH A 18 718 31 HOH HOH . 
E 5 HOH A 19 719 104 HOH HOH . 
E 5 HOH A 20 720 134 HOH HOH . 
E 5 HOH A 21 721 63 HOH HOH . 
E 5 HOH A 22 722 1 HOH HOH . 
E 5 HOH A 23 723 80 HOH HOH . 
E 5 HOH A 24 724 9 HOH HOH . 
E 5 HOH A 25 725 13 HOH HOH . 
E 5 HOH A 26 726 2 HOH HOH . 
E 5 HOH A 27 727 38 HOH HOH . 
E 5 HOH A 28 728 135 HOH HOH . 
E 5 HOH A 29 729 82 HOH HOH . 
E 5 HOH A 30 730 117 HOH HOH . 
E 5 HOH A 31 731 70 HOH HOH . 
E 5 HOH A 32 732 41 HOH HOH . 
E 5 HOH A 33 733 22 HOH HOH . 
E 5 HOH A 34 734 18 HOH HOH . 
E 5 HOH A 35 735 17 HOH HOH . 
E 5 HOH A 36 736 29 HOH HOH . 
E 5 HOH A 37 737 65 HOH HOH . 
E 5 HOH A 38 738 73 HOH HOH . 
E 5 HOH A 39 739 35 HOH HOH . 
E 5 HOH A 40 740 5 HOH HOH . 
E 5 HOH A 41 741 3 HOH HOH . 
E 5 HOH A 42 742 10 HOH HOH . 
E 5 HOH A 43 743 51 HOH HOH . 
E 5 HOH A 44 744 120 HOH HOH . 
E 5 HOH A 45 745 124 HOH HOH . 
E 5 HOH A 46 746 20 HOH HOH . 
E 5 HOH A 47 747 96 HOH HOH . 
E 5 HOH A 48 748 138 HOH HOH . 
E 5 HOH A 49 749 57 HOH HOH . 
E 5 HOH A 50 750 8 HOH HOH . 
E 5 HOH A 51 751 99 HOH HOH . 
E 5 HOH A 52 752 119 HOH HOH . 
E 5 HOH A 53 753 24 HOH HOH . 
E 5 HOH A 54 754 95 HOH HOH . 
E 5 HOH A 55 755 61 HOH HOH . 
E 5 HOH A 56 756 142 HOH HOH . 
E 5 HOH A 57 757 76 HOH HOH . 
E 5 HOH A 58 758 46 HOH HOH . 
E 5 HOH A 59 759 114 HOH HOH . 
E 5 HOH A 60 760 25 HOH HOH . 
E 5 HOH A 61 761 130 HOH HOH . 
E 5 HOH A 62 762 6 HOH HOH . 
E 5 HOH A 63 763 98 HOH HOH . 
E 5 HOH A 64 764 86 HOH HOH . 
E 5 HOH A 65 765 88 HOH HOH . 
E 5 HOH A 66 766 42 HOH HOH . 
E 5 HOH A 67 767 21 HOH HOH . 
E 5 HOH A 68 768 40 HOH HOH . 
E 5 HOH A 69 769 50 HOH HOH . 
E 5 HOH A 70 770 105 HOH HOH . 
E 5 HOH A 71 771 77 HOH HOH . 
E 5 HOH A 72 772 87 HOH HOH . 
E 5 HOH A 73 773 49 HOH HOH . 
E 5 HOH A 74 774 92 HOH HOH . 
E 5 HOH A 75 775 75 HOH HOH . 
E 5 HOH A 76 776 106 HOH HOH . 
E 5 HOH A 77 777 52 HOH HOH . 
E 5 HOH A 78 778 19 HOH HOH . 
E 5 HOH A 79 779 32 HOH HOH . 
E 5 HOH A 80 780 36 HOH HOH . 
E 5 HOH A 81 781 43 HOH HOH . 
E 5 HOH A 82 782 60 HOH HOH . 
E 5 HOH A 83 783 101 HOH HOH . 
E 5 HOH A 84 784 26 HOH HOH . 
E 5 HOH A 85 785 33 HOH HOH . 
E 5 HOH A 86 786 7 HOH HOH . 
E 5 HOH A 87 787 45 HOH HOH . 
E 5 HOH A 88 788 23 HOH HOH . 
E 5 HOH A 89 789 69 HOH HOH . 
E 5 HOH A 90 790 14 HOH HOH . 
E 5 HOH A 91 791 48 HOH HOH . 
E 5 HOH A 92 792 58 HOH HOH . 
E 5 HOH A 93 793 84 HOH HOH . 
E 5 HOH A 94 794 11 HOH HOH . 
E 5 HOH A 95 795 127 HOH HOH . 
E 5 HOH A 96 796 78 HOH HOH . 
E 5 HOH A 97 797 34 HOH HOH . 
E 5 HOH A 98 798 97 HOH HOH . 
E 5 HOH A 99 799 102 HOH HOH . 
E 5 HOH A 100 800 53 HOH HOH . 
E 5 HOH A 101 801 74 HOH HOH . 
E 5 HOH A 102 802 28 HOH HOH . 
E 5 HOH A 103 803 111 HOH HOH . 
E 5 HOH A 104 804 93 HOH HOH . 
E 5 HOH A 105 805 81 HOH HOH . 
E 5 HOH A 106 806 39 HOH HOH . 
E 5 HOH A 107 807 110 HOH HOH . 
E 5 HOH A 108 808 16 HOH HOH . 
E 5 HOH A 109 809 68 HOH HOH . 
E 5 HOH A 110 810 126 HOH HOH . 
E 5 HOH A 111 811 113 HOH HOH . 
E 5 HOH A 112 812 94 HOH HOH . 
E 5 HOH A 113 813 121 HOH HOH . 
E 5 HOH A 114 814 136 HOH HOH . 
E 5 HOH A 115 815 72 HOH HOH . 
E 5 HOH A 116 816 55 HOH HOH . 
E 5 HOH A 117 817 118 HOH HOH . 
E 5 HOH A 118 818 30 HOH HOH . 
E 5 HOH A 119 819 4 HOH HOH . 
E 5 HOH A 120 820 122 HOH HOH . 
E 5 HOH A 121 821 64 HOH HOH . 
E 5 HOH A 122 822 109 HOH HOH . 
E 5 HOH A 123 823 116 HOH HOH . 
E 5 HOH A 124 824 37 HOH HOH . 
E 5 HOH A 125 825 54 HOH HOH . 
E 5 HOH A 126 826 103 HOH HOH . 
E 5 HOH A 127 827 128 HOH HOH . 
E 5 HOH A 128 828 47 HOH HOH . 
E 5 HOH A 129 829 71 HOH HOH . 
E 5 HOH A 130 830 123 HOH HOH . 
E 5 HOH A 131 831 27 HOH HOH . 
E 5 HOH A 132 832 129 HOH HOH . 
E 5 HOH A 133 833 91 HOH HOH . 
E 5 HOH A 134 834 107 HOH HOH . 
E 5 HOH A 135 835 100 HOH HOH . 
E 5 HOH A 136 836 90 HOH HOH . 
E 5 HOH A 137 837 79 HOH HOH . 
E 5 HOH A 138 838 62 HOH HOH . 
E 5 HOH A 139 839 85 HOH HOH . 
E 5 HOH A 140 840 125 HOH HOH . 
E 5 HOH A 141 841 67 HOH HOH . 
E 5 HOH A 142 842 132 HOH HOH . 
E 5 HOH A 143 843 56 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 C01 VHY . . . D 4 2.014 10.518 -26.995 0.86 41.68 ? C01 VHY 603 A 1 
HETATM 2 C C02 VHY . . . D 4 0.941 9.776 -26.192 0.86 52.79 ? C02 VHY 603 A 1 
HETATM 3 C C03 VHY . . . D 4 1.132 8.259 -26.136 0.86 45 ? C03 VHY 603 A 1 
HETATM 4 C C04 VHY . . . D 4 2.223 7.83 -25.156 0.86 38.68 ? C04 VHY 603 A 1 
HETATM 5 C C06 VHY . . . D 4 2.715 6.225 -23.499 0.86 33.03 ? C06 VHY 603 A 1 
HETATM 6 C C07 VHY . . . D 4 1.582 6.768 -22.618 0.86 38.27 ? C07 VHY 603 A 1 
HETATM 7 C C09 VHY . . . D 4 -0.436 5.55 -22.949 0.86 38.38 ? C09 VHY 603 A 1 
HETATM 8 C C10 VHY . . . D 4 -0.509 4.514 -24.064 0.86 28.88 ? C10 VHY 603 A 1 
HETATM 9 C C11 VHY . . . D 4 -1.917 3.982 -24.322 0.86 28.91 ? C11 VHY 603 A 1 
HETATM 10 C C12 VHY . . . D 4 -2.645 4.79 -25.395 0.86 22.98 ? C12 VHY 603 A 1 
HETATM 11 C C14 VHY . . . D 4 2.219 7.414 -21.393 0.86 37.93 ? C14 VHY 603 A 1 
HETATM 12 O O05 VHY . . . D 4 2.441 6.471 -24.846 0.86 30.31 ? O05 VHY 603 A 1 
HETATM 13 O O08 VHY . . . D 4 0.736 5.731 -22.203 0.86 41.22 ? O08 VHY 603 A 1 
HETATM 14 O O13 VHY . . . D 4 -1.39 6.198 -22.696 0.86 52.65 ? O13 VHY 603 A 1 
HETATM 15 O O15 VHY . . . D 4 2.613 6.402 -20.5 0.86 36.39 ? O15 VHY 603 A 1 
HETATM 16 O O17 VHY . . . D 4 3.975 7.818 -18.806 0.86 32.08 ? O17 VHY 603 A 1 
HETATM 17 O O18 VHY . . . D 4 3.27 5.604 -18.076 0.86 27.64 ? O18 VHY 603 A 1 
HETATM 18 O O19 VHY . . . D 4 1.569 7.409 -18.358 0.86 38.94 ? O19 VHY 603 A 1 
HETATM 19 O O20 VHY . . . D 4 2.895 8.67 -24.669 0.86 45.21 ? O20 VHY 603 A 1 
HETATM 20 P P16 VHY . . . D 4 2.853 6.808 -18.9 0.86 47.25 ? P16 VHY 603 A 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           330 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           20 
#