data_8YL7
#
_model_server_result.job_id            q21fIXIhMGsF8oAk8L3hug 
_model_server_result.datetime_utc      '2025-02-22 05:50:25' 
_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          8yl7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":701}' 
#
_entry.id    8YL7 
#
_exptl.entry_id    8YL7 
_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            8YL7 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YL7 
_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                     8YL7 
_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 4 103.426 109.513 107.536 1 101.51 ? O5' A1L15 701 A 1 
HETATM 2 C C5' A1L15 . . . D 4 103.82 110.545 106.669 1 101.51 ? C5' A1L15 701 A 1 
HETATM 3 C C4' A1L15 . . . D 4 102.56 111.416 106.343 1 101.51 ? C4' A1L15 701 A 1 
HETATM 4 O O4' A1L15 . . . D 4 102.083 111.049 105.214 1 101.51 ? O4' A1L15 701 A 1 
HETATM 5 C C3' A1L15 . . . D 4 101.444 111.156 107.379 1 101.51 ? C3' A1L15 701 A 1 
HETATM 6 O O3' A1L15 . . . D 4 101.133 112.298 108.039 1 101.51 ? O3' A1L15 701 A 1 
HETATM 7 C C2' A1L15 . . . D 4 100.249 110.741 106.547 1 101.51 ? C2' A1L15 701 A 1 
HETATM 8 C C1' A1L15 . . . D 4 100.486 111.187 105.357 1 101.51 ? C1' A1L15 701 A 1 
HETATM 9 N N1 A1L15 . . . D 4 96.828 110.76 101.783 1 101.51 ? N1 A1L15 701 A 1 
HETATM 10 C C2 A1L15 . . . D 4 97.234 111.845 102.42 1 101.51 ? C2 A1L15 701 A 1 
HETATM 11 N N3 A1L15 . . . D 4 98.202 111.799 103.319 1 101.51 ? N3 A1L15 701 A 1 
HETATM 12 C C4 A1L15 . . . D 4 98.812 110.649 103.614 1 101.51 ? C4 A1L15 701 A 1 
HETATM 13 C C5 A1L15 . . . D 4 98.417 109.505 102.97 1 101.51 ? C5 A1L15 701 A 1 
HETATM 14 C C6 A1L15 . . . D 4 97.383 109.587 102.03 1 101.51 ? C6 A1L15 701 A 1 
HETATM 15 O O2' A1L15 . . . D 4 99.018 111.369 107.133 1 101.51 ? O2' A1L15 701 A 1 
HETATM 16 N N9 A1L15 . . . D 4 99.793 110.305 104.456 1 101.51 ? N9 A1L15 701 A 1 
HETATM 17 C C8 A1L15 . . . D 4 99.998 109.006 104.353 1 101.51 ? C8 A1L15 701 A 1 
HETATM 18 N N7 A1L15 . . . D 4 99.169 108.507 103.453 1 101.51 ? N7 A1L15 701 A 1 
HETATM 19 N N6 A1L15 . . . D 4 96.935 108.397 101.338 1 101.51 ? N6 A1L15 701 A 1 
HETATM 20 C C1D A1L15 . . . D 4 102.087 101.986 111.757 1 101.51 ? C1D A1L15 701 A 1 
HETATM 21 C C2D A1L15 . . . D 4 101.391 102.637 112.555 1 101.51 ? C2D A1L15 701 A 1 
HETATM 22 C C35 A1L15 . . . D 4 104.36 101.333 111.305 1 101.51 ? C35 A1L15 701 A 1 
HETATM 23 C C36 A1L15 . . . D 4 105.302 101.267 112.092 1 101.51 ? C36 A1L15 701 A 1 
HETATM 24 C C38 A1L15 . . . D 4 106.653 100.881 111.201 1 101.51 ? C38 A1L15 701 A 1 
HETATM 25 C C39 A1L15 . . . D 4 107.083 99.508 111.619 1 101.51 ? C39 A1L15 701 A 1 
HETATM 26 C C3D A1L15 . . . D 4 101.058 104.074 111.754 1 101.51 ? C3D A1L15 701 A 1 
HETATM 27 C C4D A1L15 . . . D 4 100.929 103.771 110.497 1 101.51 ? C4D A1L15 701 A 1 
HETATM 28 C C54 A1L15 . . . D 4 105.075 101.707 109.963 1 101.51 ? C54 A1L15 701 A 1 
HETATM 29 C C56 A1L15 . . . D 4 103.638 100.334 108.656 1 101.51 ? C56 A1L15 701 A 1 
HETATM 30 C C58 A1L15 . . . D 4 103.323 101.705 107.009 1 101.51 ? C58 A1L15 701 A 1 
HETATM 31 C C59 A1L15 . . . D 4 104.156 102.299 107.916 1 101.51 ? C59 A1L15 701 A 1 
HETATM 32 C C5D A1L15 . . . D 4 101.827 104.726 109.671 1 101.51 ? C5D A1L15 701 A 1 
HETATM 33 C C61 A1L15 . . . D 4 104.285 104.172 106.597 1 101.51 ? C61 A1L15 701 A 1 
HETATM 34 C C63 A1L15 . . . D 4 102.987 102.424 105.859 1 101.51 ? C63 A1L15 701 A 1 
HETATM 35 N N55 A1L15 . . . D 4 104.326 101.434 108.91 1 101.51 ? N55 A1L15 701 A 1 
HETATM 36 N N57 A1L15 . . . D 4 103.021 100.491 107.495 1 101.51 ? N57 A1L15 701 A 1 
HETATM 37 N N60 A1L15 . . . D 4 104.625 103.529 107.693 1 101.51 ? N60 A1L15 701 A 1 
HETATM 38 N N62 A1L15 . . . D 4 103.484 103.634 105.699 1 101.51 ? N62 A1L15 701 A 1 
HETATM 39 N N64 A1L15 . . . D 4 102.118 101.876 104.853 1 101.51 ? N64 A1L15 701 A 1 
HETATM 40 O O1A A1L15 . . . D 4 105.057 107.578 107.033 1 101.51 ? O1A A1L15 701 A 1 
HETATM 41 O O1B A1L15 . . . D 4 104.117 107.154 110.234 1 101.51 ? O1B A1L15 701 A 1 
HETATM 42 O O2A A1L15 . . . D 4 103.057 107.795 105.63 1 101.51 ? O2A A1L15 701 A 1 
HETATM 43 O O2B A1L15 . . . D 4 102.046 108.471 110.036 1 101.51 ? O2B A1L15 701 A 1 
HETATM 44 O O2D A1L15 . . . D 4 100.134 101.942 112.781 1 101.51 ? O2D A1L15 701 A 1 
HETATM 45 O O34 A1L15 . . . D 4 103.428 102.447 111.76 1 101.51 ? O34 A1L15 701 A 1 
HETATM 46 O O37 A1L15 . . . D 4 105.508 102.587 112.722 1 101.51 ? O37 A1L15 701 A 1 
HETATM 47 O O3A A1L15 . . . D 4 102.757 106.959 108.048 1 101.51 ? O3A A1L15 701 A 1 
HETATM 48 O O3D A1L15 . . . D 4 99.831 104.611 112.23 1 101.51 ? O3D A1L15 701 A 1 
HETATM 49 O O40 A1L15 . . . D 4 108.454 99.525 111.838 1 101.51 ? O40 A1L15 701 A 1 
HETATM 50 O O42 A1L15 . . . D 4 108.283 100.582 114.171 1 101.51 ? O42 A1L15 701 A 1 
HETATM 51 O O43 A1L15 . . . D 4 110.536 99.537 113.53 1 101.51 ? O43 A1L15 701 A 1 
HETATM 52 O O45 A1L15 . . . D 4 111.802 99.215 111.315 1 101.51 ? O45 A1L15 701 A 1 
HETATM 53 O O46 A1L15 . . . D 4 111.021 97.087 112.467 1 101.51 ? O46 A1L15 701 A 1 
HETATM 54 O O48 A1L15 . . . D 4 113.306 96.01 111.911 1 101.51 ? O48 A1L15 701 A 1 
HETATM 55 O O49 A1L15 . . . D 4 111.297 94.607 111.825 1 101.51 ? O49 A1L15 701 A 1 
HETATM 56 O O4D A1L15 . . . D 4 101.426 102.33 110.339 1 101.51 ? O4D A1L15 701 A 1 
HETATM 57 O O50 A1L15 . . . D 4 111.693 96.311 110.099 1 101.51 ? O50 A1L15 701 A 1 
HETATM 58 O O51 A1L15 . . . D 4 112.894 98.592 113.414 1 101.51 ? O51 A1L15 701 A 1 
HETATM 59 O O52 A1L15 . . . D 4 108.425 98.142 113.975 1 101.51 ? O52 A1L15 701 A 1 
HETATM 60 O O53 A1L15 . . . D 4 106.319 100.848 109.985 1 101.51 ? O53 A1L15 701 A 1 
HETATM 61 O O5D A1L15 . . . D 4 101.877 105.935 110.375 1 101.51 ? O5D A1L15 701 A 1 
HETATM 62 P P41 A1L15 . . . D 4 108.907 99.443 113.406 1 101.51 ? P41 A1L15 701 A 1 
HETATM 63 P P44 A1L15 . . . D 4 111.584 98.614 112.672 1 101.51 ? P44 A1L15 701 A 1 
HETATM 64 P P47 A1L15 . . . D 4 111.84 95.986 111.561 1 101.51 ? P47 A1L15 701 A 1 
HETATM 65 P PA A1L15 . . . D 4 103.6 107.948 107.026 1 101.51 ? PA A1L15 701 A 1 
HETATM 66 P PB A1L15 . . . D 4 102.719 107.169 109.688 1 101.51 ? PB A1L15 701 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           66 
#