data_8YHX
#
_model_server_result.job_id            YlSBnj4I3IF2SuBqGlQmdQ 
_model_server_result.datetime_utc      '2024-12-01 03:32:13' 
_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          8yhx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":501}' 
#
_entry.id    8YHX 
#
_exptl.entry_id    8YHX 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              559.316 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ADENOSINE-5-DIPHOSPHORIBOSE 
_entity.pdbx_number_of_molecules    6 
_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            8YHX 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YHX 
_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    octadecameric 
_pdbx_struct_assembly.oligomeric_count      18 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 S N N 
? 3 T N N 
? 3 U N N 
? 3 V N N 
? 3 W N N 
? 3 X N N 
#
_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                     8YHX 
_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
S 3 APR H 1 501 501 APR APR . 
T 3 APR J 1 501 502 APR APR . 
U 3 APR L 1 501 501 APR APR . 
V 3 APR N 1 501 501 APR APR . 
W 3 APR P 1 501 501 APR APR . 
X 3 APR R 1 501 501 APR APR . 
#
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 . . . X 3 179.617 231.012 216.914 1 106.14 ? N1 APR 501 R 1 
HETATM 2 C C2 APR . . . X 3 179.038 229.814 217.212 1 103.06 ? C2 APR 501 R 1 
HETATM 3 N N3 APR . . . X 3 178.527 229.597 218.451 1 102.04 ? N3 APR 501 R 1 
HETATM 4 C C4 APR . . . X 3 178.591 230.574 219.391 1 104.88 ? C4 APR 501 R 1 
HETATM 5 C C5 APR . . . X 3 179.153 231.747 219.102 1 107.34 ? C5 APR 501 R 1 
HETATM 6 C C6 APR . . . X 3 179.683 231.966 217.832 1 108.87 ? C6 APR 501 R 1 
HETATM 7 N N6 APR . . . X 3 180.353 232.926 216.975 1 110.94 ? N6 APR 501 R 1 
HETATM 8 N N7 APR . . . X 3 179.082 232.528 220.209 1 109.33 ? N7 APR 501 R 1 
HETATM 9 C C8 APR . . . X 3 178.47 231.823 221.177 1 107.82 ? C8 APR 501 R 1 
HETATM 10 N N9 APR . . . X 3 178.165 230.618 220.68 1 108.34 ? N9 APR 501 R 1 
HETATM 11 C C1' APR . . . X 3 177.515 229.593 221.394 1 113.23 ? C1' APR 501 R 1 
HETATM 12 C C2' APR . . . X 3 177.476 229.856 222.688 1 113.67 ? C2' APR 501 R 1 
HETATM 13 O O2' APR . . . X 3 178.703 229.38 223.345 1 113.3 ? O2' APR 501 R 1 
HETATM 14 C C3' APR . . . X 3 176.247 229.022 223.166 1 110.66 ? C3' APR 501 R 1 
HETATM 15 O O3' APR . . . X 3 176.602 227.748 223.343 1 114.2 ? O3' APR 501 R 1 
HETATM 16 O O4' APR . . . X 3 175.936 229.478 220.913 1 108.39 ? O4' APR 501 R 1 
HETATM 17 C C4' APR . . . X 3 175.228 229.142 221.974 1 106.66 ? C4' APR 501 R 1 
HETATM 18 C C5' APR . . . X 3 174.19 230.241 222.285 1 104.82 ? C5' APR 501 R 1 
HETATM 19 O O5' APR . . . X 3 173.166 229.707 223.037 1 113.03 ? O5' APR 501 R 1 
HETATM 20 P PA APR . . . X 3 172.033 230.732 223.62 1 121.22 ? PA APR 501 R 1 
HETATM 21 O O1A APR . . . X 3 170.959 229.937 224.388 1 112.49 -1 O1A APR 501 R 1 
HETATM 22 O O2A APR . . . X 3 172.687 231.735 224.556 1 112.05 ? O2A APR 501 R 1 
HETATM 23 O O3A APR . . . X 3 171.31 231.543 222.308 1 107.02 ? O3A APR 501 R 1 
HETATM 24 P PB APR . . . X 3 170.028 232.611 222.461 1 117.74 ? PB APR 501 R 1 
HETATM 25 O O1B APR . . . X 3 170.476 233.984 222.111 1 114.75 -1 O1B APR 501 R 1 
HETATM 26 O O2B APR . . . X 3 169.526 232.589 223.879 1 113.07 ? O2B APR 501 R 1 
HETATM 27 O O5D APR . . . X 3 168.832 232.135 221.454 1 113.81 ? O5D APR 501 R 1 
HETATM 28 C C5D APR . . . X 3 167.947 231.136 221.933 1 110.12 ? C5D APR 501 R 1 
HETATM 29 O O4D APR . . . X 3 168.287 230.13 219.847 1 114.5 ? O4D APR 501 R 1 
HETATM 30 O O1D APR . . . X 3 170.061 228.803 220.874 1 117.62 ? O1D APR 501 R 1 
HETATM 31 C C1D APR . . . X 3 168.942 228.677 220.127 1 117.64 ? C1D APR 501 R 1 
HETATM 32 O O2D APR . . . X 3 167.417 226.922 219.861 1 116.93 ? O2D APR 501 R 1 
HETATM 33 C C2D APR . . . X 3 168.022 227.934 220.785 1 118.88 ? C2D APR 501 R 1 
HETATM 34 O O3D APR . . . X 3 165.778 228.549 220.762 1 108.99 ? O3D APR 501 R 1 
HETATM 35 C C3D APR . . . X 3 166.949 228.887 221.271 1 110.69 ? C3D APR 501 R 1 
HETATM 36 C C4D APR . . . X 3 167.378 230.327 220.76 1 110.06 ? C4D APR 501 R 1 
#
_model_server_stats.io_time_ms              32 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    67 
_model_server_stats.query_time_ms           375 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           36 
#