data_8DYU
#
_model_server_result.job_id            UlV-imK3l95joexDAqW_cg 
_model_server_result.datetime_utc      '2024-11-09 23:19:59' 
_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          8dyu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":4701}' 
#
_entry.id    8DYU 
#
_exptl.entry_id    8DYU 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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            8DYU 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DYU 
_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,F,G 
_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 D N N 
? 3 F N N 
? 3 G N N 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_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
PB O1B ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     8DYU 
_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 3 ADP A 1 4701 4701 ADP ADP . 
E 4 ATP A 1 4702 4802 ATP ATP . 
F 3 ADP A 1 4703 4804 ADP ADP . 
G 3 ADP A 1 4704 4805 ADP ADP . 
#
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 P PB ADP . . . D 3 195.173 205.182 160.682 1 48.82 ? PB ADP 4701 A 1 
HETATM 2 O O1B ADP . . . D 3 194.371 203.926 160.455 1 48.82 ? O1B ADP 4701 A 1 
HETATM 3 O O2B ADP . . . D 3 196.583 204.946 161.165 1 48.82 ? O2B ADP 4701 A 1 
HETATM 4 O O3B ADP . . . D 3 194.428 206.256 161.436 1 48.82 ? O3B ADP 4701 A 1 
HETATM 5 P PA ADP . . . D 3 194.086 206.023 158.253 1 48.82 ? PA ADP 4701 A 1 
HETATM 6 O O1A ADP . . . D 3 193.743 204.725 157.564 1 48.82 ? O1A ADP 4701 A 1 
HETATM 7 O O2A ADP . . . D 3 193.024 206.714 159.074 1 48.82 ? O2A ADP 4701 A 1 
HETATM 8 O O3A ADP . . . D 3 195.364 205.792 159.205 1 48.82 ? O3A ADP 4701 A 1 
HETATM 9 O O5' ADP . . . D 3 194.619 207.07 157.15 1 48.82 ? O5' ADP 4701 A 1 
HETATM 10 C C5' ADP . . . D 3 195.352 206.63 156.007 1 48.82 ? C5' ADP 4701 A 1 
HETATM 11 C C4' ADP . . . D 3 195.548 207.765 155.004 1 48.82 ? C4' ADP 4701 A 1 
HETATM 12 O O4' ADP . . . D 3 196.109 207.247 153.796 1 48.82 ? O4' ADP 4701 A 1 
HETATM 13 C C3' ADP . . . D 3 194.245 208.461 154.645 1 48.82 ? C3' ADP 4701 A 1 
HETATM 14 O O3' ADP . . . D 3 194.401 209.88 154.754 1 48.82 ? O3' ADP 4701 A 1 
HETATM 15 C C2' ADP . . . D 3 193.947 208.056 153.218 1 48.82 ? C2' ADP 4701 A 1 
HETATM 16 O O2' ADP . . . D 3 193.507 209.172 152.439 1 48.82 ? O2' ADP 4701 A 1 
HETATM 17 C C1' ADP . . . D 3 195.245 207.477 152.684 1 48.82 ? C1' ADP 4701 A 1 
HETATM 18 N N9 ADP . . . D 3 194.967 206.184 152.027 1 48.82 ? N9 ADP 4701 A 1 
HETATM 19 C C8 ADP . . . D 3 195.3 204.979 152.526 1 48.82 ? C8 ADP 4701 A 1 
HETATM 20 N N7 ADP . . . D 3 194.907 203.991 151.687 1 48.82 ? N7 ADP 4701 A 1 
HETATM 21 C C5 ADP . . . D 3 194.309 204.568 150.634 1 48.82 ? C5 ADP 4701 A 1 
HETATM 22 C C6 ADP . . . D 3 193.669 204.093 149.395 1 48.82 ? C6 ADP 4701 A 1 
HETATM 23 N N6 ADP . . . D 3 193.604 202.77 149.137 1 48.82 ? N6 ADP 4701 A 1 
HETATM 24 N N1 ADP . . . D 3 193.162 205.016 148.549 1 48.82 ? N1 ADP 4701 A 1 
HETATM 25 C C2 ADP . . . D 3 193.231 206.334 148.815 1 48.82 ? C2 ADP 4701 A 1 
HETATM 26 N N3 ADP . . . D 3 193.802 206.83 149.928 1 48.82 ? N3 ADP 4701 A 1 
HETATM 27 C C4 ADP . . . D 3 194.35 206.014 150.859 1 48.82 ? C4 ADP 4701 A 1 
HETATM 28 H "H5'1" ADP . . . D 3 194.871 205.906 155.575 1 48.82 ? "H5'1" ADP 4701 A 1 
HETATM 29 H "H5'2" ADP . . . D 3 196.216 206.29 156.286 1 48.82 ? "H5'2" ADP 4701 A 1 
HETATM 30 H H4' ADP . . . D 3 196.161 208.417 155.379 1 48.82 ? H4' ADP 4701 A 1 
HETATM 31 H H3' ADP . . . D 3 193.527 208.154 155.221 1 48.82 ? H3' ADP 4701 A 1 
HETATM 32 H HO3' ADP . . . D 3 194.073 210.257 154.079 1 48.82 ? HO3' ADP 4701 A 1 
HETATM 33 H H2' ADP . . . D 3 193.27 207.362 153.222 1 48.82 ? H2' ADP 4701 A 1 
HETATM 34 H HO2' ADP . . . D 3 192.74 209.401 152.694 1 48.82 ? HO2' ADP 4701 A 1 
HETATM 35 H H1' ADP . . . D 3 195.647 208.101 152.059 1 48.82 ? H1' ADP 4701 A 1 
HETATM 36 H H8 ADP . . . D 3 195.761 204.83 153.366 1 48.82 ? H8 ADP 4701 A 1 
HETATM 37 H HN61 ADP . . . D 3 193.936 202.206 149.695 1 48.82 ? HN61 ADP 4701 A 1 
HETATM 38 H HN62 ADP . . . D 3 193.231 202.49 148.414 1 48.82 ? HN62 ADP 4701 A 1 
HETATM 39 H H2 ADP . . . D 3 192.853 206.957 148.175 1 48.82 ? H2 ADP 4701 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    65 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           39 
#