data_8YL6
#
_model_server_result.job_id            daoqrDekkTa6fehcue8Qqg 
_model_server_result.datetime_utc      '2025-02-26 07:48:27' 
_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          8yl6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":701}' 
#
_entry.id    8YL6 
#
_exptl.entry_id    8YL6 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              1048.481 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate' 
_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            8YL6 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YL6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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    ? 
_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 
#
_chem_comp.formula           'C25 H37 N10 O26 P5' 
_chem_comp.formula_weight    1048.481 
_chem_comp.id                A1L15 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ADPr-ATP 
#
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
N64 C63 A1L15 sing 1 n n 
N57 C56 A1L15 doub 2 n y 
N57 C58 A1L15 sing 3 n y 
O2D C2D A1L15 sing 4 n n 
N6 C6 A1L15 sing 5 n n 
C56 N55 A1L15 sing 6 n y 
C63 C58 A1L15 doub 7 n y 
C63 N62 A1L15 sing 8 n y 
C58 C59 A1L15 sing 9 n y 
O4D C1D A1L15 sing 10 n n 
O4D C4D A1L15 sing 11 n n 
C6 N1 A1L15 doub 12 n y 
C6 C5 A1L15 sing 13 n y 
C1D C2D A1L15 sing 14 n n 
C1D O34 A1L15 sing 15 n n 
N1 C2 A1L15 sing 16 n y 
C2D C3D A1L15 sing 17 n n 
C4D C3D A1L15 sing 18 n n 
C4D C5D A1L15 sing 19 n n 
N55 C59 A1L15 sing 20 n y 
N55 C54 A1L15 sing 21 n n 
N62 C61 A1L15 doub 22 n y 
C59 N60 A1L15 doub 23 n y 
O3D C3D A1L15 sing 24 n n 
C35 O34 A1L15 sing 25 n n 
C35 C54 A1L15 sing 26 n n 
C35 C36 A1L15 sing 27 n n 
C2 N3 A1L15 doub 28 n y 
C5 N7 A1L15 sing 29 n y 
C5 C4 A1L15 doub 30 n y 
C5D O5D A1L15 sing 31 n n 
C54 O53 A1L15 sing 32 n n 
N7 C8 A1L15 doub 33 n y 
O49 P47 A1L15 doub 34 n n 
O53 C38 A1L15 sing 35 n n 
C61 N60 A1L15 sing 36 n y 
C36 C38 A1L15 sing 37 n n 
C36 O37 A1L15 sing 38 n n 
C39 C38 A1L15 sing 39 n n 
C39 O40 A1L15 sing 40 n n 
N3 C4 A1L15 sing 41 n y 
O52 P41 A1L15 doub 42 n n 
C4 N9 A1L15 sing 43 n y 
O5D PB A1L15 sing 44 n n 
O40 P41 A1L15 sing 45 n n 
C8 N9 A1L15 sing 46 n y 
O46 P47 A1L15 sing 47 n n 
O46 P44 A1L15 sing 48 n n 
P47 O50 A1L15 sing 49 n n 
P47 O48 A1L15 sing 50 n n 
N9 C1' A1L15 sing 51 n n 
P41 O43 A1L15 sing 52 n n 
P41 O42 A1L15 sing 53 n n 
O3A PB A1L15 sing 54 n n 
O3A PA A1L15 sing 55 n n 
O2A PA A1L15 doub 56 n n 
PB O1B A1L15 doub 57 n n 
PB O2B A1L15 sing 58 n n 
C2' C1' A1L15 sing 59 n n 
C2' O2' A1L15 sing 60 n n 
C2' C3' A1L15 sing 61 n n 
O43 P44 A1L15 sing 62 n n 
P44 O51 A1L15 doub 63 n n 
P44 O45 A1L15 sing 64 n n 
C1' O4' A1L15 sing 65 n n 
C3' O3' A1L15 sing 66 n n 
C3' C4' A1L15 sing 67 n n 
PA O5' A1L15 sing 68 n n 
PA O1A A1L15 sing 69 n n 
O4' C4' A1L15 sing 70 n n 
O5' C5' A1L15 sing 71 n n 
C4' C5' A1L15 sing 72 n n 
C5' H1 A1L15 sing 73 n n 
C5' H2 A1L15 sing 74 n n 
C4' H3 A1L15 sing 75 n n 
C3' H4 A1L15 sing 76 n n 
O3' H5 A1L15 sing 77 n n 
C2' H6 A1L15 sing 78 n n 
C1' H7 A1L15 sing 79 n n 
C2 H8 A1L15 sing 80 n n 
O2' H9 A1L15 sing 81 n n 
C8 H10 A1L15 sing 82 n n 
N6 H11 A1L15 sing 83 n n 
N6 H12 A1L15 sing 84 n n 
C1D H13 A1L15 sing 85 n n 
C2D H14 A1L15 sing 86 n n 
C35 H15 A1L15 sing 87 n n 
C36 H16 A1L15 sing 88 n n 
C38 H17 A1L15 sing 89 n n 
C39 H18 A1L15 sing 90 n n 
C39 H19 A1L15 sing 91 n n 
C3D H20 A1L15 sing 92 n n 
C4D H21 A1L15 sing 93 n n 
C54 H22 A1L15 sing 94 n n 
C56 H23 A1L15 sing 95 n n 
C5D H24 A1L15 sing 96 n n 
C5D H25 A1L15 sing 97 n n 
C61 H26 A1L15 sing 98 n n 
N64 H27 A1L15 sing 99 n n 
N64 H28 A1L15 sing 100 n n 
O1A H29 A1L15 sing 101 n n 
O2B H30 A1L15 sing 102 n n 
O2D H31 A1L15 sing 103 n n 
O37 H32 A1L15 sing 104 n n 
O3D H33 A1L15 sing 105 n n 
O42 H34 A1L15 sing 106 n n 
O45 H35 A1L15 sing 107 n n 
O48 H36 A1L15 sing 108 n n 
O50 H37 A1L15 sing 109 n n 
#
_atom_sites.entry_id                     8YL6 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          D 
_pdbx_nonpoly_scheme.entity_id        4 
_pdbx_nonpoly_scheme.mon_id           A1L15 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      701 
_pdbx_nonpoly_scheme.auth_seq_num     701 
_pdbx_nonpoly_scheme.pdb_mon_id       A1L15 
_pdbx_nonpoly_scheme.auth_mon_id      DRT 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 O5' A1L15 . . . D 4 127.752 99.902 113.893 1 91.73 ? O5' A1L15 701 A 1 
HETATM 2 C C5' A1L15 . . . D 4 128.909 100.556 114.351 1 91.73 ? C5' A1L15 701 A 1 
HETATM 3 C C4' A1L15 . . . D 4 130.099 99.571 114.132 1 91.73 ? C4' A1L15 701 A 1 
HETATM 4 O O4' A1L15 . . . D 4 129.633 98.453 113.731 1 91.73 ? O4' A1L15 701 A 1 
HETATM 5 C C3' A1L15 . . . D 4 130.96 100.073 112.963 1 91.73 ? C3' A1L15 701 A 1 
HETATM 6 O O3' A1L15 . . . D 4 131.992 100.812 113.434 1 91.73 ? O3' A1L15 701 A 1 
HETATM 7 C C2' A1L15 . . . D 4 131.496 98.797 112.345 1 91.73 ? C2' A1L15 701 A 1 
HETATM 8 C C1' A1L15 . . . D 4 130.709 97.826 112.7 1 91.73 ? C1' A1L15 701 A 1 
HETATM 9 N N1 A1L15 . . . D 4 130.962 94.713 108.612 1 91.73 ? N1 A1L15 701 A 1 
HETATM 10 C C2 A1L15 . . . D 4 131.835 94.845 109.594 1 91.73 ? C2 A1L15 701 A 1 
HETATM 11 N N3 A1L15 . . . D 4 131.631 95.69 110.588 1 91.73 ? N3 A1L15 701 A 1 
HETATM 12 C C4 A1L15 . . . D 4 130.527 96.443 110.646 1 91.73 ? C4 A1L15 701 A 1 
HETATM 13 C C5 A1L15 . . . D 4 129.604 96.325 109.642 1 91.73 ? C5 A1L15 701 A 1 
HETATM 14 C C6 A1L15 . . . D 4 129.85 95.426 108.601 1 91.73 ? C6 A1L15 701 A 1 
HETATM 15 O O2' A1L15 . . . D 4 132.885 98.564 112.864 1 91.73 ? O2' A1L15 701 A 1 
HETATM 16 N N9 A1L15 . . . D 4 130.055 97.361 111.502 1 91.73 ? N9 A1L15 701 A 1 
HETATM 17 C C8 A1L15 . . . D 4 128.895 97.795 111.047 1 91.73 ? C8 A1L15 701 A 1 
HETATM 18 N N7 A1L15 . . . D 4 128.61 97.175 109.919 1 91.73 ? N7 A1L15 701 A 1 
HETATM 19 N N6 A1L15 . . . D 4 128.889 95.295 107.525 1 91.73 ? N6 A1L15 701 A 1 
HETATM 20 C C1D A1L15 . . . D 4 125.544 107.278 108.608 1 91.73 ? C1D A1L15 701 A 1 
HETATM 21 C C2D A1L15 . . . D 4 126.728 107.595 108.768 1 91.73 ? C2D A1L15 701 A 1 
HETATM 22 C C35 A1L15 . . . D 4 123.338 107.715 109.485 1 91.73 ? C35 A1L15 701 A 1 
HETATM 23 C C36 A1L15 . . . D 4 122.886 108.598 110.215 1 91.73 ? C36 A1L15 701 A 1 
HETATM 24 C C38 A1L15 . . . D 4 121.383 108.091 110.708 1 91.73 ? C38 A1L15 701 A 1 
HETATM 25 C C39 A1L15 . . . D 4 120.406 109.189 110.416 1 91.73 ? C39 A1L15 701 A 1 
HETATM 26 C C3D A1L15 . . . D 4 127.472 106.257 109.449 1 91.73 ? C3D A1L15 701 A 1 
HETATM 27 C C4D A1L15 . . . D 4 126.999 105.248 108.809 1 91.73 ? C4D A1L15 701 A 1 
HETATM 28 C C54 A1L15 . . . D 4 122.479 106.465 109.884 1 91.73 ? C54 A1L15 701 A 1 
HETATM 29 C C56 A1L15 . . . D 4 122.283 105.743 107.644 1 91.73 ? C56 A1L15 701 A 1 
HETATM 30 C C58 A1L15 . . . D 4 122.868 103.685 107.918 1 91.73 ? C58 A1L15 701 A 1 
HETATM 31 C C59 A1L15 . . . D 4 122.9 104.305 109.134 1 91.73 ? C59 A1L15 701 A 1 
HETATM 32 C C5D A1L15 . . . D 4 126.889 104.041 109.784 1 91.73 ? C5D A1L15 701 A 1 
HETATM 33 C C61 A1L15 . . . D 4 123.577 102.356 110.124 1 91.73 ? C61 A1L15 701 A 1 
HETATM 34 C C63 A1L15 . . . D 4 123.209 102.337 107.852 1 91.73 ? C63 A1L15 701 A 1 
HETATM 35 N N55 A1L15 . . . D 4 122.532 105.563 108.926 1 91.73 ? N55 A1L15 701 A 1 
HETATM 36 N N57 A1L15 . . . D 4 122.48 104.598 107.019 1 91.73 ? N57 A1L15 701 A 1 
HETATM 37 N N60 A1L15 . . . D 4 123.26 103.628 110.224 1 91.73 ? N60 A1L15 701 A 1 
HETATM 38 N N62 A1L15 . . . D 4 123.552 101.72 108.965 1 91.73 ? N62 A1L15 701 A 1 
HETATM 39 N N64 A1L15 . . . D 4 123.186 101.634 106.595 1 91.73 ? N64 A1L15 701 A 1 
HETATM 40 O O1A A1L15 . . . D 4 125.73 101.449 114.087 1 91.73 ? O1A A1L15 701 A 1 
HETATM 41 O O1B A1L15 . . . D 4 125.951 104.026 112.653 1 91.73 ? O1B A1L15 701 A 1 
HETATM 42 O O2A A1L15 . . . D 4 125.776 99.893 112.225 1 91.73 ? O2A A1L15 701 A 1 
HETATM 43 O O2B A1L15 . . . D 4 128.305 103.983 113.365 1 91.73 ? O2B A1L15 701 A 1 
HETATM 44 O O2D A1L15 . . . D 4 127.347 107.837 107.477 1 91.73 ? O2D A1L15 701 A 1 
HETATM 45 O O34 A1L15 . . . D 4 124.811 107.492 109.803 1 91.73 ? O34 A1L15 701 A 1 
HETATM 46 O O37 A1L15 . . . D 4 123.741 108.749 111.407 1 91.73 ? O37 A1L15 701 A 1 
HETATM 47 O O3A A1L15 . . . D 4 127.381 101.909 112.121 1 91.73 ? O3A A1L15 701 A 1 
HETATM 48 O O3D A1L15 . . . D 4 128.858 106.28 109.161 1 91.73 ? O3D A1L15 701 A 1 
HETATM 49 O O40 A1L15 . . . D 4 120.962 110.323 110.988 1 91.73 ? O40 A1L15 701 A 1 
HETATM 50 O O42 A1L15 . . . D 4 120.616 112.234 112.682 1 91.73 ? O42 A1L15 701 A 1 
HETATM 51 O O43 A1L15 . . . D 4 118.766 110.458 112.464 1 91.73 ? O43 A1L15 701 A 1 
HETATM 52 O O45 A1L15 . . . D 4 116.581 110.261 113.781 1 91.73 ? O45 A1L15 701 A 1 
HETATM 53 O O46 A1L15 . . . D 4 116.388 110.927 111.307 1 91.73 ? O46 A1L15 701 A 1 
HETATM 54 O O48 A1L15 . . . D 4 114.282 112.003 112.309 1 91.73 ? O48 A1L15 701 A 1 
HETATM 55 O O49 A1L15 . . . D 4 114.245 111.343 109.944 1 91.73 ? O49 A1L15 701 A 1 
HETATM 56 O O4D A1L15 . . . D 4 125.624 105.703 108.312 1 91.73 ? O4D A1L15 701 A 1 
HETATM 57 O O50 A1L15 . . . D 4 114.204 109.624 111.704 1 91.73 ? O50 A1L15 701 A 1 
HETATM 58 O O51 A1L15 . . . D 4 117.357 112.492 113.093 1 91.73 ? O51 A1L15 701 A 1 
HETATM 59 O O52 A1L15 . . . D 4 119.251 112.16 110.629 1 91.73 ? O52 A1L15 701 A 1 
HETATM 60 O O53 A1L15 . . . D 4 121.102 107.061 110.039 1 91.73 ? O53 A1L15 701 A 1 
HETATM 61 O O5D A1L15 . . . D 4 127.754 104.254 110.873 1 91.73 ? O5D A1L15 701 A 1 
HETATM 62 P P41 A1L15 . . . D 4 119.906 111.341 111.701 1 91.73 ? P41 A1L15 701 A 1 
HETATM 63 P P44 A1L15 . . . D 4 117.259 111.046 112.69 1 91.73 ? P44 A1L15 701 A 1 
HETATM 64 P P47 A1L15 . . . D 4 114.748 110.974 111.314 1 91.73 ? P47 A1L15 701 A 1 
HETATM 65 P PA A1L15 . . . D 4 126.621 100.796 113.081 1 91.73 ? PA A1L15 701 A 1 
HETATM 66 P PB A1L15 . . . D 4 127.334 103.553 112.303 1 91.73 ? PB A1L15 701 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           208 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           66 
#