data_8DYU
#
_model_server_result.job_id            PqMgCmECsxQSgt0x1aSrog 
_model_server_result.datetime_utc      '2024-11-09 23:23:38' 
_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":"G","auth_seq_id":4704}' 
#
_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 . . . G 3 204.91 203.586 218.788 1 49.18 ? PB ADP 4704 A 1 
HETATM 2 O O1B ADP . . . G 3 206.228 203.157 218.193 1 49.18 ? O1B ADP 4704 A 1 
HETATM 3 O O2B ADP . . . G 3 204.528 205.015 218.488 1 49.18 ? O2B ADP 4704 A 1 
HETATM 4 O O3B ADP . . . G 3 203.789 202.589 218.621 1 49.18 ? O3B ADP 4704 A 1 
HETATM 5 P PA ADP . . . G 3 204.049 204.2 221.313 1 49.18 ? PA ADP 4704 A 1 
HETATM 6 O O1A ADP . . . G 3 202.775 204.292 220.508 1 49.18 ? O1A ADP 4704 A 1 
HETATM 7 O O2A ADP . . . G 3 204.601 205.413 222.021 1 49.18 ? O2A ADP 4704 A 1 
HETATM 8 O O3A ADP . . . G 3 205.188 203.592 220.365 1 49.18 ? O3A ADP 4704 A 1 
HETATM 9 O O5' ADP . . . G 3 203.869 203.007 222.368 1 49.18 ? O5' ADP 4704 A 1 
HETATM 10 C C5' ADP . . . G 3 202.855 203.069 223.362 1 49.18 ? C5' ADP 4704 A 1 
HETATM 11 C C4' ADP . . . G 3 202.816 201.717 224.062 1 49.18 ? C4' ADP 4704 A 1 
HETATM 12 O O4' ADP . . . G 3 204.102 201.109 223.929 1 49.18 ? O4' ADP 4704 A 1 
HETATM 13 C C3' ADP . . . G 3 202.476 201.785 225.545 1 49.18 ? C3' ADP 4704 A 1 
HETATM 14 O O3' ADP . . . G 3 201.266 201.07 225.805 1 49.18 ? O3' ADP 4704 A 1 
HETATM 15 C C2' ADP . . . G 3 203.65 201.152 226.263 1 49.18 ? C2' ADP 4704 A 1 
HETATM 16 O O2' ADP . . . G 3 203.231 200.066 227.094 1 49.18 ? O2' ADP 4704 A 1 
HETATM 17 C C1' ADP . . . G 3 204.588 200.632 225.182 1 49.18 ? C1' ADP 4704 A 1 
HETATM 18 N N9 ADP . . . G 3 205.977 201.114 225.376 1 49.18 ? N9 ADP 4704 A 1 
HETATM 19 C C8 ADP . . . G 3 206.716 201.761 224.453 1 49.18 ? C8 ADP 4704 A 1 
HETATM 20 N N7 ADP . . . G 3 207.947 202.052 224.944 1 49.18 ? N7 ADP 4704 A 1 
HETATM 21 C C5 ADP . . . G 3 208.006 201.581 226.199 1 49.18 ? C5 ADP 4704 A 1 
HETATM 22 C C6 ADP . . . G 3 209.013 201.545 227.278 1 49.18 ? C6 ADP 4704 A 1 
HETATM 23 N N6 ADP . . . G 3 210.236 202.098 227.113 1 49.18 ? N6 ADP 4704 A 1 
HETATM 24 N N1 ADP . . . G 3 208.664 200.952 228.439 1 49.18 ? N1 ADP 4704 A 1 
HETATM 25 C C2 ADP . . . G 3 207.449 200.408 228.634 1 49.18 ? C2 ADP 4704 A 1 
HETATM 26 N N3 ADP . . . G 3 206.495 200.399 227.688 1 49.18 ? N3 ADP 4704 A 1 
HETATM 27 C C4 ADP . . . G 3 206.711 200.955 226.475 1 49.18 ? C4 ADP 4704 A 1 
HETATM 28 H "H5'1" ADP . . . G 3 201.997 203.257 222.951 1 49.18 ? "H5'1" ADP 4704 A 1 
HETATM 29 H "H5'2" ADP . . . G 3 203.066 203.788 223.978 1 49.18 ? "H5'2" ADP 4704 A 1 
HETATM 30 H H4' ADP . . . G 3 202.151 201.165 223.621 1 49.18 ? H4' ADP 4704 A 1 
HETATM 31 H H3' ADP . . . G 3 202.385 202.704 225.841 1 49.18 ? H3' ADP 4704 A 1 
HETATM 32 H HO3' ADP . . . G 3 201.276 200.34 225.389 1 49.18 ? HO3' ADP 4704 A 1 
HETATM 33 H H2' ADP . . . G 3 204.088 201.835 226.795 1 49.18 ? H2' ADP 4704 A 1 
HETATM 34 H HO2' ADP . . . G 3 202.457 199.822 226.877 1 49.18 ? HO2' ADP 4704 A 1 
HETATM 35 H H1' ADP . . . G 3 204.571 199.662 225.193 1 49.18 ? H1' ADP 4704 A 1 
HETATM 36 H H8 ADP . . . G 3 206.413 201.993 223.561 1 49.18 ? H8 ADP 4704 A 1 
HETATM 37 H HN61 ADP . . . G 3 210.441 202.475 226.368 1 49.18 ? HN61 ADP 4704 A 1 
HETATM 38 H HN62 ADP . . . G 3 210.81 202.072 227.753 1 49.18 ? HN62 ADP 4704 A 1 
HETATM 39 H H2 ADP . . . G 3 207.258 199.99 229.488 1 49.18 ? H2 ADP 4704 A 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    41 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           39 
#