data_7KYD
#
_model_server_result.job_id            EN-V-fXE-7XInMkko6qGKA 
_model_server_result.datetime_utc      '2025-09-04 01:33:21' 
_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          7kyd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":601}' 
#
_entry.id    7KYD 
#
_exptl.entry_id    7KYD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              473.417 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-O-[(S)-hydroxy(octanoyloxy)phosphoryl]adenosine" 
_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            7KYD 
_cell.length_a            55.851 
_cell.length_b            77.778 
_cell.length_c            113.315 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7KYD 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_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                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C18 H28 N5 O8 P' 
_chem_comp.formula_weight    473.417 
_chem_comp.id                C5Y 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-O-[(S)-hydroxy(octanoyloxy)phosphoryl]adenosine" 
_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
N32 C31 C5Y doub 70 n y 
N32 C02 C5Y sing 71 n y 
C31 N30 C5Y sing 72 n y 
N01 C02 C5Y sing 73 n n 
C02 C03 C5Y doub 74 n y 
N30 C04 C5Y doub 75 n y 
C03 C04 C5Y sing 76 n y 
C03 N29 C5Y sing 77 n y 
C04 N05 C5Y sing 78 n y 
O27 C26 C5Y sing 79 n n 
C26 C24 C5Y sing 80 n n 
C26 C06 C5Y sing 81 n n 
O25 C24 C5Y sing 82 n n 
N29 C28 C5Y doub 83 n y 
C24 C08 C5Y sing 84 n n 
N05 C06 C5Y sing 85 n n 
N05 C28 C5Y sing 86 n y 
C06 O07 C5Y sing 87 n n 
C08 O07 C5Y sing 88 n n 
C08 C09 C5Y sing 89 n n 
C20 C21 C5Y sing 90 n n 
C20 C19 C5Y sing 91 n n 
C09 O10 C5Y sing 92 n n 
C18 C19 C5Y sing 93 n n 
C18 C17 C5Y sing 94 n n 
C17 C16 C5Y sing 95 n n 
O10 P11 C5Y sing 96 n n 
C15 C16 C5Y sing 97 n n 
C15 C14 C5Y sing 98 n n 
O22 C14 C5Y doub 99 n n 
C14 O13 C5Y sing 100 n n 
O12 P11 C5Y doub 101 n n 
P11 O13 C5Y sing 102 n n 
P11 O23 C5Y sing 103 n n 
C15 H151 C5Y sing 104 n n 
C15 H152 C5Y sing 105 n n 
C17 H172 C5Y sing 106 n n 
C17 H171 C5Y sing 107 n n 
C20 H201 C5Y sing 108 n n 
C20 H202 C5Y sing 109 n n 
C21 H212 C5Y sing 110 n n 
C21 H213 C5Y sing 111 n n 
C21 H211 C5Y sing 112 n n 
C24 H241 C5Y sing 113 n n 
C26 H261 C5Y sing 114 n n 
C28 H281 C5Y sing 115 n n 
C06 H061 C5Y sing 116 n n 
C08 H081 C5Y sing 117 n n 
C09 H091 C5Y sing 118 n n 
C09 H092 C5Y sing 119 n n 
C16 H162 C5Y sing 120 n n 
C16 H161 C5Y sing 121 n n 
C18 H182 C5Y sing 122 n n 
C18 H181 C5Y sing 123 n n 
C19 H192 C5Y sing 124 n n 
C19 H191 C5Y sing 125 n n 
C31 H311 C5Y sing 126 n n 
N01 H012 C5Y sing 127 n n 
N01 H011 C5Y sing 128 n n 
O23 H1 C5Y sing 129 n n 
O25 H251 C5Y sing 130 n n 
O27 H271 C5Y sing 131 n n 
#
_atom_sites.entry_id                     7KYD 
_atom_sites.fract_transf_matrix[1][1]    0.017905 
_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]    0.012857 
_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]    0.008825 
_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 C5Y A 1 601 601 C5Y LIG . 
C 3 EDO A 1 602 701 EDO EDO . 
D 4 HOH A 1 701 58 HOH HOH . 
D 4 HOH A 2 702 62 HOH HOH . 
D 4 HOH A 3 703 52 HOH HOH . 
D 4 HOH A 4 704 23 HOH HOH . 
D 4 HOH A 5 705 94 HOH HOH . 
D 4 HOH A 6 706 65 HOH HOH . 
D 4 HOH A 7 707 3 HOH HOH . 
D 4 HOH A 8 708 19 HOH HOH . 
D 4 HOH A 9 709 54 HOH HOH . 
D 4 HOH A 10 710 81 HOH HOH . 
D 4 HOH A 11 711 30 HOH HOH . 
D 4 HOH A 12 712 15 HOH HOH . 
D 4 HOH A 13 713 51 HOH HOH . 
D 4 HOH A 14 714 67 HOH HOH . 
D 4 HOH A 15 715 7 HOH HOH . 
D 4 HOH A 16 716 13 HOH HOH . 
D 4 HOH A 17 717 34 HOH HOH . 
D 4 HOH A 18 718 57 HOH HOH . 
D 4 HOH A 19 719 61 HOH HOH . 
D 4 HOH A 20 720 35 HOH HOH . 
D 4 HOH A 21 721 80 HOH HOH . 
D 4 HOH A 22 722 4 HOH HOH . 
D 4 HOH A 23 723 36 HOH HOH . 
D 4 HOH A 24 724 10 HOH HOH . 
D 4 HOH A 25 725 50 HOH HOH . 
D 4 HOH A 26 726 6 HOH HOH . 
D 4 HOH A 27 727 39 HOH HOH . 
D 4 HOH A 28 728 49 HOH HOH . 
D 4 HOH A 29 729 18 HOH HOH . 
D 4 HOH A 30 730 1 HOH HOH . 
D 4 HOH A 31 731 97 HOH HOH . 
D 4 HOH A 32 732 25 HOH HOH . 
D 4 HOH A 33 733 69 HOH HOH . 
D 4 HOH A 34 734 40 HOH HOH . 
D 4 HOH A 35 735 45 HOH HOH . 
D 4 HOH A 36 736 96 HOH HOH . 
D 4 HOH A 37 737 37 HOH HOH . 
D 4 HOH A 38 738 5 HOH HOH . 
D 4 HOH A 39 739 12 HOH HOH . 
D 4 HOH A 40 740 68 HOH HOH . 
D 4 HOH A 41 741 27 HOH HOH . 
D 4 HOH A 42 742 8 HOH HOH . 
D 4 HOH A 43 743 64 HOH HOH . 
D 4 HOH A 44 744 48 HOH HOH . 
D 4 HOH A 45 745 26 HOH HOH . 
D 4 HOH A 46 746 41 HOH HOH . 
D 4 HOH A 47 747 46 HOH HOH . 
D 4 HOH A 48 748 2 HOH HOH . 
D 4 HOH A 49 749 76 HOH HOH . 
D 4 HOH A 50 750 21 HOH HOH . 
D 4 HOH A 51 751 11 HOH HOH . 
D 4 HOH A 52 752 29 HOH HOH . 
D 4 HOH A 53 753 16 HOH HOH . 
D 4 HOH A 54 754 31 HOH HOH . 
D 4 HOH A 55 755 56 HOH HOH . 
D 4 HOH A 56 756 9 HOH HOH . 
D 4 HOH A 57 757 60 HOH HOH . 
D 4 HOH A 58 758 20 HOH HOH . 
D 4 HOH A 59 759 17 HOH HOH . 
D 4 HOH A 60 760 42 HOH HOH . 
D 4 HOH A 61 761 75 HOH HOH . 
D 4 HOH A 62 762 38 HOH HOH . 
D 4 HOH A 63 763 44 HOH HOH . 
D 4 HOH A 64 764 86 HOH HOH . 
D 4 HOH A 65 765 28 HOH HOH . 
D 4 HOH A 66 766 55 HOH HOH . 
D 4 HOH A 67 767 102 HOH HOH . 
D 4 HOH A 68 768 73 HOH HOH . 
D 4 HOH A 69 769 14 HOH HOH . 
D 4 HOH A 70 770 47 HOH HOH . 
D 4 HOH A 71 771 74 HOH HOH . 
D 4 HOH A 72 772 53 HOH HOH . 
D 4 HOH A 73 773 79 HOH HOH . 
D 4 HOH A 74 774 22 HOH HOH . 
D 4 HOH A 75 775 72 HOH HOH . 
D 4 HOH A 76 776 103 HOH HOH . 
D 4 HOH A 77 777 90 HOH HOH . 
D 4 HOH A 78 778 70 HOH HOH . 
D 4 HOH A 79 779 82 HOH HOH . 
D 4 HOH A 80 780 100 HOH HOH . 
D 4 HOH A 81 781 77 HOH HOH . 
D 4 HOH A 82 782 101 HOH HOH . 
D 4 HOH A 83 783 88 HOH HOH . 
D 4 HOH A 84 784 92 HOH HOH . 
D 4 HOH A 85 785 89 HOH HOH . 
D 4 HOH A 86 786 95 HOH HOH . 
D 4 HOH A 87 787 87 HOH HOH . 
D 4 HOH A 88 788 71 HOH HOH . 
D 4 HOH A 89 789 32 HOH HOH . 
D 4 HOH A 90 790 85 HOH HOH . 
D 4 HOH A 91 791 66 HOH HOH . 
D 4 HOH A 92 792 91 HOH HOH . 
D 4 HOH A 93 793 83 HOH HOH . 
D 4 HOH A 94 794 99 HOH HOH . 
D 4 HOH A 95 795 84 HOH HOH . 
D 4 HOH A 96 796 93 HOH HOH . 
D 4 HOH A 97 797 98 HOH HOH . 
D 4 HOH A 98 798 78 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 C15 C5Y . . . B 2 -15.952 -6.348 12.61 1 37.96 ? C15 C5Y 601 A 1 
HETATM 2 C C17 C5Y . . . B 2 -14.3 -8.135 12.157 1 43.9 ? C17 C5Y 601 A 1 
HETATM 3 C C20 C5Y . . . B 2 -11.904 -9.988 9.864 1 43.33 ? C20 C5Y 601 A 1 
HETATM 4 C C21 C5Y . . . B 2 -11.37 -11.418 9.928 1 47.02 ? C21 C5Y 601 A 1 
HETATM 5 C C24 C5Y . . . B 2 -17.114 -1.46 8.481 1 39.86 ? C24 C5Y 601 A 1 
HETATM 6 C C26 C5Y . . . B 2 -15.888 -0.795 7.946 1 39.66 ? C26 C5Y 601 A 1 
HETATM 7 C C28 C5Y . . . B 2 -14.043 -3.366 9.185 1 39.54 ? C28 C5Y 601 A 1 
HETATM 8 C C02 C5Y . . . B 2 -11.161 -3.588 6.9 1 34.16 ? C02 C5Y 601 A 1 
HETATM 9 C C03 C5Y . . . B 2 -12.373 -3.319 7.8 1 40.76 ? C03 C5Y 601 A 1 
HETATM 10 C C04 C5Y . . . B 2 -12.941 -2.075 7.836 1 44.21 ? C04 C5Y 601 A 1 
HETATM 11 C C06 C5Y . . . B 2 -14.875 -0.969 9.042 1 39.85 ? C06 C5Y 601 A 1 
HETATM 12 C C08 C5Y . . . B 2 -16.992 -1.208 9.953 1 44.6 ? C08 C5Y 601 A 1 
HETATM 13 C C09 C5Y . . . B 2 -17.643 -2.246 10.858 1 42.48 ? C09 C5Y 601 A 1 
HETATM 14 C C14 C5Y . . . B 2 -16.137 -4.879 12.976 1 45.17 ? C14 C5Y 601 A 1 
HETATM 15 C C16 C5Y . . . B 2 -14.467 -6.695 12.63 1 39.77 ? C16 C5Y 601 A 1 
HETATM 16 C C18 C5Y . . . B 2 -13.158 -8.237 11.15 1 42.05 ? C18 C5Y 601 A 1 
HETATM 17 C C19 C5Y . . . B 2 -12.655 -9.677 11.156 1 40.82 ? C19 C5Y 601 A 1 
HETATM 18 C C31 C5Y . . . B 2 -11.284 -1.246 6.187 1 38.28 ? C31 C5Y 601 A 1 
HETATM 19 N N01 C5Y . . . B 2 -10.544 -4.898 6.848 1 38.76 ? N01 C5Y 601 A 1 
HETATM 20 N N05 C5Y . . . B 2 -13.968 -2.114 8.694 1 42.63 ? N05 C5Y 601 A 1 
HETATM 21 N N29 C5Y . . . B 2 -13.058 -4.098 8.632 1 35.04 ? N29 C5Y 601 A 1 
HETATM 22 N N30 C5Y . . . B 2 -12.442 -1.067 7.075 1 38.34 ? N30 C5Y 601 A 1 
HETATM 23 N N32 C5Y . . . B 2 -10.639 -2.532 6.104 1 39.71 ? N32 C5Y 601 A 1 
HETATM 24 O O07 C5Y . . . B 2 -15.607 -1.191 10.227 1 45.39 ? O07 C5Y 601 A 1 
HETATM 25 O O10 C5Y . . . B 2 -16.942 -2.24 12.074 1 39.95 ? O10 C5Y 601 A 1 
HETATM 26 O O12 C5Y . . . B 2 -19.154 -2.614 13.367 1 39.57 -1 O12 C5Y 601 A 1 
HETATM 27 O O13 C5Y . . . B 2 -17.35 -4.441 13.516 1 46.14 ? O13 C5Y 601 A 1 
HETATM 28 O O22 C5Y . . . B 2 -15.252 -4.106 12.805 1 43.45 ? O22 C5Y 601 A 1 
HETATM 29 O O23 C5Y . . . B 2 -17.108 -2.147 14.663 1 37.92 ? O23 C5Y 601 A 1 
HETATM 30 O O25 C5Y . . . B 2 -18.373 -0.763 8.029 1 43.79 ? O25 C5Y 601 A 1 
HETATM 31 O O27 C5Y . . . B 2 -16.153 0.516 7.713 1 38.77 ? O27 C5Y 601 A 1 
HETATM 32 P P11 C5Y . . . B 2 -17.662 -2.829 13.434 1 38 ? P11 C5Y 601 A 1 
HETATM 33 H H151 C5Y . . . B 2 -16.478 -6.968 13.329 1 45.55 ? H151 C5Y 601 A 1 
HETATM 34 H H152 C5Y . . . B 2 -16.352 -6.526 11.618 1 45.55 ? H152 C5Y 601 A 1 
HETATM 35 H H172 C5Y . . . B 2 -14.08 -8.768 13.011 1 52.68 ? H172 C5Y 601 A 1 
HETATM 36 H H171 C5Y . . . B 2 -15.22 -8.466 11.688 1 52.68 ? H171 C5Y 601 A 1 
HETATM 37 H H201 C5Y . . . B 2 -12.577 -9.889 9.019 1 52 ? H201 C5Y 601 A 1 
HETATM 38 H H202 C5Y . . . B 2 -11.076 -9.295 9.749 1 52 ? H202 C5Y 601 A 1 
HETATM 39 H H212 C5Y . . . B 2 -12.153 -12.111 9.634 1 56.43 ? H212 C5Y 601 A 1 
HETATM 40 H H213 C5Y . . . B 2 -11.052 -11.641 10.943 1 56.43 ? H213 C5Y 601 A 1 
HETATM 41 H H211 C5Y . . . B 2 -10.524 -11.52 9.254 1 56.43 ? H211 C5Y 601 A 1 
HETATM 42 H H241 C5Y . . . B 2 -17.129 -2.506 8.192 1 47.84 ? H241 C5Y 601 A 1 
HETATM 43 H H261 C5Y . . . B 2 -15.533 -1.262 7.035 1 47.59 ? H261 C5Y 601 A 1 
HETATM 44 H H281 C5Y . . . B 2 -14.772 -3.723 9.902 1 47.44 ? H281 C5Y 601 A 1 
HETATM 45 H H061 C5Y . . . B 2 -14.29 -0.067 9.185 1 47.82 ? H061 C5Y 601 A 1 
HETATM 46 H H081 C5Y . . . B 2 -17.477 -0.253 10.126 1 53.52 ? H081 C5Y 601 A 1 
HETATM 47 H H091 C5Y . . . B 2 -17.583 -3.228 10.4 1 50.98 ? H091 C5Y 601 A 1 
HETATM 48 H H092 C5Y . . . B 2 -18.683 -1.989 11.029 1 50.98 ? H092 C5Y 601 A 1 
HETATM 49 H H162 C5Y . . . B 2 -13.927 -6.027 11.967 1 47.72 ? H162 C5Y 601 A 1 
HETATM 50 H H161 C5Y . . . B 2 -14.081 -6.594 13.639 1 47.72 ? H161 C5Y 601 A 1 
HETATM 51 H H182 C5Y . . . B 2 -13.516 -7.975 10.159 1 50.46 ? H182 C5Y 601 A 1 
HETATM 52 H H181 C5Y . . . B 2 -12.355 -7.564 11.433 1 50.46 ? H181 C5Y 601 A 1 
HETATM 53 H H192 C5Y . . . B 2 -11.987 -9.819 12 1 48.99 ? H192 C5Y 601 A 1 
HETATM 54 H H191 C5Y . . . B 2 -13.501 -10.35 11.247 1 48.99 ? H191 C5Y 601 A 1 
HETATM 55 H H311 C5Y . . . B 2 -10.917 -0.415 5.597 1 45.94 ? H311 C5Y 601 A 1 
HETATM 56 H H012 C5Y . . . B 2 -10.434 -5.362 5.967 1 46.51 ? H012 C5Y 601 A 1 
HETATM 57 H H011 C5Y . . . B 2 -10.226 -5.336 7.693 1 46.51 ? H011 C5Y 601 A 1 
HETATM 58 H H251 C5Y . . . B 2 -19.021 -1.404 7.793 1 52.55 ? H251 C5Y 601 A 1 
HETATM 59 H H271 C5Y . . . B 2 -15.592 1.036 8.263 1 46.53 ? H271 C5Y 601 A 1 
#
_model_server_stats.io_time_ms              74 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           252 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           59 
#