data_8DYV
#
_model_server_result.job_id            dhB0ozJmHjSMYusSyaes4A 
_model_server_result.datetime_utc      '2025-07-08 04:24:05' 
_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          8dyv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":4704}' 
#
_entry.id    8DYV 
#
_exptl.entry_id    8DYV 
_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            8DYV 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DYV 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 C N N 
? 3 D N N 
? 3 F 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                     8DYV 
_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
C 3 ADP A 1 4701 4701 ADP ADP . 
D 3 ADP A 1 4702 4801 ADP ADP . 
E 4 ATP A 1 4703 4802 ATP ATP . 
F 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 . . . F 3 204.958 207.102 176.945 1 90.96 ? PB ADP 4704 A 1 
HETATM 2 O O1B ADP . . . F 3 204.318 205.75 176.772 1 90.96 ? O1B ADP 4704 A 1 
HETATM 3 O O2B ADP . . . F 3 206.458 207.107 176.78 1 90.96 -1 O2B ADP 4704 A 1 
HETATM 4 O O3B ADP . . . F 3 204.446 207.881 178.131 1 90.96 ? O3B ADP 4704 A 1 
HETATM 5 P PA ADP . . . F 3 202.973 207.658 175.087 1 90.96 ? PA ADP 4704 A 1 
HETATM 6 O O1A ADP . . . F 3 203.091 206.553 174.067 1 90.96 -1 O1A ADP 4704 A 1 
HETATM 7 O O2A ADP . . . F 3 202 207.535 176.235 1 90.96 ? O2A ADP 4704 A 1 
HETATM 8 O O3A ADP . . . F 3 204.439 207.94 175.679 1 90.96 ? O3A ADP 4704 A 1 
HETATM 9 O O5' ADP . . . F 3 202.66 209.028 174.312 1 90.96 ? O5' ADP 4704 A 1 
HETATM 10 C C5' ADP . . . F 3 201.625 209.101 173.337 1 90.96 ? C5' ADP 4704 A 1 
HETATM 11 C C4' ADP . . . F 3 201.716 210.476 172.685 1 90.96 ? C4' ADP 4704 A 1 
HETATM 12 O O4' ADP . . . F 3 203.042 210.969 172.889 1 90.96 ? O4' ADP 4704 A 1 
HETATM 13 C C3' ADP . . . F 3 201.432 210.494 171.188 1 90.96 ? C3' ADP 4704 A 1 
HETATM 14 O O3' ADP . . . F 3 200.387 211.425 170.896 1 90.96 ? O3' ADP 4704 A 1 
HETATM 15 C C2' ADP . . . F 3 202.733 210.916 170.534 1 90.96 ? C2' ADP 4704 A 1 
HETATM 16 O O2' ADP . . . F 3 202.54 212.001 169.621 1 90.96 ? O2' ADP 4704 A 1 
HETATM 17 C C1' ADP . . . F 3 203.664 211.336 171.658 1 90.96 ? C1' ADP 4704 A 1 
HETATM 18 N N9 ADP . . . F 3 204.963 210.634 171.525 1 90.96 ? N9 ADP 4704 A 1 
HETATM 19 C C8 ADP . . . F 3 205.452 209.714 172.377 1 90.96 ? C8 ADP 4704 A 1 
HETATM 20 N N7 ADP . . . F 3 206.667 209.273 171.96 1 90.96 ? N7 ADP 4704 A 1 
HETATM 21 C C5 ADP . . . F 3 206.968 209.917 170.822 1 90.96 ? C5 ADP 4704 A 1 
HETATM 22 C C6 ADP . . . F 3 208.095 209.922 169.866 1 90.96 ? C6 ADP 4704 A 1 
HETATM 23 N N6 ADP . . . F 3 209.174 209.125 170.048 1 90.96 ? N6 ADP 4704 A 1 
HETATM 24 N N1 ADP . . . F 3 208.006 210.75 168.805 1 90.96 ? N1 ADP 4704 A 1 
HETATM 25 C C2 ADP . . . F 3 206.94 211.55 168.61 1 90.96 ? C2 ADP 4704 A 1 
HETATM 26 N N3 ADP . . . F 3 205.885 211.59 169.439 1 90.96 ? N3 ADP 4704 A 1 
HETATM 27 C C4 ADP . . . F 3 205.843 210.816 170.543 1 90.96 ? C4 ADP 4704 A 1 
HETATM 28 H "H5'1" ADP . . . F 3 200.651 208.975 173.814 1 90.96 ? "H5'1" ADP 4704 A 1 
HETATM 29 H "H5'2" ADP . . . F 3 201.762 208.299 172.61 1 90.96 ? "H5'2" ADP 4704 A 1 
HETATM 30 H H4' ADP . . . F 3 200.995 211.14 173.181 1 90.96 ? H4' ADP 4704 A 1 
HETATM 31 H H3' ADP . . . F 3 201.153 209.495 170.826 1 90.96 ? H3' ADP 4704 A 1 
HETATM 32 H HO3' ADP . . . F 3 200.111 211.326 169.975 1 90.96 ? HO3' ADP 4704 A 1 
HETATM 33 H H2' ADP . . . F 3 203.162 210.05 170.014 1 90.96 ? H2' ADP 4704 A 1 
HETATM 34 H HO2' ADP . . . F 3 202.094 211.68 168.825 1 90.96 ? HO2' ADP 4704 A 1 
HETATM 35 H H1' ADP . . . F 3 203.813 212.424 171.616 1 90.96 ? H1' ADP 4704 A 1 
HETATM 36 H H8 ADP . . . F 3 204.949 209.37 173.272 1 90.96 ? H8 ADP 4704 A 1 
HETATM 37 H HN61 ADP . . . F 3 209.221 208.512 170.849 1 90.96 ? HN61 ADP 4704 A 1 
HETATM 38 H HN62 ADP . . . F 3 209.933 209.145 169.382 1 90.96 ? HN62 ADP 4704 A 1 
HETATM 39 H H2 ADP . . . F 3 206.932 212.19 167.736 1 90.96 ? H2 ADP 4704 A 1 
#
_model_server_stats.io_time_ms              83 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    49 
_model_server_stats.query_time_ms           337 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           39 
#