data_8YN1
#
_model_server_result.job_id            tQ_TYB2P0HJy8McdVJiyUQ 
_model_server_result.datetime_utc      '2025-03-04 19:02:45' 
_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          8yn1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":701}' 
#
_entry.id    8YN1 
#
_exptl.entry_id    8YN1 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ADENOSINE-5-DIPHOSPHORIBOSE 
_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            8YN1 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YN1 
_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,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    ? 
_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 
#
_struct_conn.conn_type_id                   covale 
_struct_conn.details                        ? 
_struct_conn.id                             covale1 
_struct_conn.ptnr1_label_asym_id            D 
_struct_conn.ptnr1_label_atom_id            C1D 
_struct_conn.ptnr1_label_comp_id            APR 
_struct_conn.ptnr1_label_seq_id             . 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             APR 
_struct_conn.ptnr1_auth_seq_id              701 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            E 
_struct_conn.ptnr2_label_atom_id            O2' 
_struct_conn.ptnr2_label_comp_id            ATP 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             B 
_struct_conn.ptnr2_auth_comp_id             ATP 
_struct_conn.ptnr2_auth_seq_id              601 
_struct_conn.ptnr2_symmetry                 1_555 
_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                1.373 
_struct_conn.pdbx_value_order               ? 
#
_chem_comp.formula           'C15 H23 N5 O14 P2' 
_chem_comp.formula_weight    559.316 
_chem_comp.id                APR 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              ADENOSINE-5-DIPHOSPHORIBOSE 
_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
N1 C2 APR sing 13 n y 
N1 C6 APR doub 14 n y 
C2 N3 APR doub 15 n y 
C2 H2 APR sing 16 n n 
N3 C4 APR sing 17 n y 
C4 C5 APR doub 18 n y 
C4 N9 APR sing 19 n y 
C5 C6 APR sing 20 n y 
C5 N7 APR sing 21 n y 
C6 N6 APR sing 22 n n 
N6 H61 APR sing 23 n n 
N6 H62 APR sing 24 n n 
N7 C8 APR doub 25 n y 
C8 N9 APR sing 26 n y 
C8 H8 APR sing 27 n n 
N9 C1' APR sing 28 n n 
C1' C2' APR sing 29 n n 
C1' O4' APR sing 30 n n 
C1' "H'1" APR sing 31 n n 
C2' O2' APR sing 32 n n 
C2' C3' APR sing 33 n n 
C2' "H'2" APR sing 34 n n 
O2' "HO'2" APR sing 35 n n 
C3' O3' APR sing 36 n n 
C3' C4' APR sing 37 n n 
C3' "H'3" APR sing 38 n n 
O3' "HO'3" APR sing 39 n n 
O4' C4' APR sing 40 n n 
C4' C5' APR sing 41 n n 
C4' "H'4" APR sing 42 n n 
C5' O5' APR sing 43 n n 
C5' "H5'1" APR sing 44 n n 
C5' "H5'2" APR sing 45 n n 
O5' PA APR sing 46 n n 
PA O1A APR doub 47 n n 
PA O2A APR sing 48 n n 
PA O3A APR sing 49 n n 
O2A HOA2 APR sing 50 n n 
O3A PB APR sing 51 n n 
PB O1B APR doub 52 n n 
PB O2B APR sing 53 n n 
PB O5D APR sing 54 n n 
O2B HOB2 APR sing 55 n n 
O5D C5D APR sing 56 n n 
C5D C4D APR sing 57 n n 
C5D H5R1 APR sing 58 n n 
C5D H5R2 APR sing 59 n n 
O4D C1D APR sing 60 n n 
O4D C4D APR sing 61 n n 
O1D C1D APR sing 62 n n 
O1D HOR1 APR sing 63 n n 
C1D C2D APR sing 64 n n 
C1D "HR'1" APR sing 65 n n 
O2D C2D APR sing 66 n n 
O2D HOR2 APR sing 67 n n 
C2D C3D APR sing 68 n n 
C2D "HR'2" APR sing 69 n n 
O3D C3D APR sing 70 n n 
O3D HOR3 APR sing 71 n n 
C3D C4D APR sing 72 n n 
C3D "HR'3" APR sing 73 n n 
C4D "HR'4" APR sing 74 n n 
#
_atom_sites.entry_id                     8YN1 
_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 
#
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
D 4 APR A 1 701 702 APR APR . 
E 5 ATP B 1 601 601 ATP ATP . 
#
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 N N1 APR . . . D 4 114.143 115.617 107.016 1 14.8 ? N1 APR 701 A 1 
HETATM 2 C C2 APR . . . D 4 113.362 115.552 108.098 1 14.8 ? C2 APR 701 A 1 
HETATM 3 N N3 APR . . . D 4 112.295 114.793 108.318 1 14.8 ? N3 APR 701 A 1 
HETATM 4 C C4 APR . . . D 4 112.04 114.021 107.259 1 14.8 ? C4 APR 701 A 1 
HETATM 5 C C5 APR . . . D 4 112.746 113.967 106.079 1 14.8 ? C5 APR 701 A 1 
HETATM 6 C C6 APR . . . D 4 113.858 114.821 105.961 1 14.8 ? C6 APR 701 A 1 
HETATM 7 N N6 APR . . . D 4 114.633 114.892 104.886 1 14.8 ? N6 APR 701 A 1 
HETATM 8 N N7 APR . . . D 4 112.18 113.05 105.234 1 14.8 ? N7 APR 701 A 1 
HETATM 9 C C8 APR . . . D 4 111.156 112.56 105.906 1 14.8 ? C8 APR 701 A 1 
HETATM 10 N N9 APR . . . D 4 111.015 113.125 107.154 1 14.8 ? N9 APR 701 A 1 
HETATM 11 C C1' APR . . . D 4 110.015 112.886 108.204 1 14.8 ? C1' APR 701 A 1 
HETATM 12 C C2' APR . . . D 4 108.668 113.597 108.058 1 14.8 ? C2' APR 701 A 1 
HETATM 13 O O2' APR . . . D 4 107.97 113.627 109.29 1 14.8 ? O2' APR 701 A 1 
HETATM 14 C C3' APR . . . D 4 107.999 112.622 107.094 1 14.8 ? C3' APR 701 A 1 
HETATM 15 O O3' APR . . . D 4 106.596 112.798 106.976 1 14.8 ? O3' APR 701 A 1 
HETATM 16 O O4' APR . . . D 4 109.671 111.512 108.288 1 14.8 ? O4' APR 701 A 1 
HETATM 17 C C4' APR . . . D 4 108.356 111.29 107.752 1 14.8 ? C4' APR 701 A 1 
HETATM 18 C C5' APR . . . D 4 108.432 110.096 106.836 1 14.8 ? C5' APR 701 A 1 
HETATM 19 O O5' APR . . . D 4 107.399 110.142 105.851 1 14.8 ? O5' APR 701 A 1 
HETATM 20 P PA APR . . . D 4 107.78 109.645 104.381 1 14.8 ? PA APR 701 A 1 
HETATM 21 O O1A APR . . . D 4 108.689 110.589 103.697 1 14.8 ? O1A APR 701 A 1 
HETATM 22 O O2A APR . . . D 4 108.144 108.212 104.368 1 14.8 ? O2A APR 701 A 1 
HETATM 23 O O3A APR . . . D 4 106.309 109.691 103.825 1 14.8 ? O3A APR 701 A 1 
HETATM 24 P PB APR . . . D 4 105.141 110.733 103.557 1 14.8 ? PB APR 701 A 1 
HETATM 25 O O1B APR . . . D 4 103.914 109.913 103.447 1 14.8 ? O1B APR 701 A 1 
HETATM 26 O O2B APR . . . D 4 105.142 111.831 104.551 1 14.8 ? O2B APR 701 A 1 
HETATM 27 O O5D APR . . . D 4 105.449 111.352 102.121 1 14.8 ? O5D APR 701 A 1 
HETATM 28 C C5D APR . . . D 4 104.365 112.119 101.581 1 14.8 ? C5D APR 701 A 1 
HETATM 29 O O4D APR . . . D 4 105.346 111.713 99.444 1 14.8 ? O4D APR 701 A 1 
HETATM 30 C C1D APR . . . D 4 104.586 111.462 98.27 1 14.8 ? C1D APR 701 A 1 
HETATM 31 O O2D APR . . . D 4 102.563 112.443 97.352 1 14.8 ? O2D APR 701 A 1 
HETATM 32 C C2D APR . . . D 4 103.203 112.03 98.545 1 14.8 ? C2D APR 701 A 1 
HETATM 33 O O3D APR . . . D 4 103.746 114.359 98.676 1 14.8 ? O3D APR 701 A 1 
HETATM 34 C C3D APR . . . D 4 103.495 113.206 99.468 1 14.8 ? C3D APR 701 A 1 
HETATM 35 C C4D APR . . . D 4 104.716 112.722 100.249 1 14.8 ? C4D APR 701 A 1 
#
_model_server_stats.io_time_ms              84 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           572 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           35 
#