data_1YYF # _model_server_result.job_id dAnlhGIBw0pGJAMOJ94Phw _model_server_result.datetime_utc '2025-08-31 13:37:13' _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 1yyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":906}' # _entry.id 1YYF # _exptl.entry_id 1YYF _exptl.method 'X-RAY DIFFRACTION' # _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 2 _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 120 _cell.entry_id 1YYF _cell.length_a 181.196 _cell.length_b 181.196 _cell.length_c 529.924 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YYF _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 24-meric _pdbx_struct_assembly.oligomeric_count 24 _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 1,2,3,4,5,6 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 181.196 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 90.598 156.920339 0 4 'crystal symmetry operation' 16_545 y+1/3,x-1/3,-z+2/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 90.598 -52.30678 353.282667 5 'crystal symmetry operation' 17_555 x-y+1/3,-y+2/3,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 104.613559 353.282667 6 'crystal symmetry operation' 18_655 -x+4/3,-x+y+2/3,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 181.196 104.613559 353.282667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E 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 1YYF _atom_sites.fract_transf_matrix[1][1] 0.005519 _atom_sites.fract_transf_matrix[1][2] 0.003186 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006373 _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] 0.001887 _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 E 3 ADP A 1 905 905 ADP ADP . F 3 ADP B 1 906 906 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 3 110.391 25.008 124.584 1 82.94 ? PB ADP 906 B 1 HETATM 2 O O1B ADP . . . F 3 109.385 24.511 123.648 1 84.65 ? O1B ADP 906 B 1 HETATM 3 O O2B ADP . . . F 3 110.629 23.858 125.563 1 82.75 ? O2B ADP 906 B 1 HETATM 4 O O3B ADP . . . F 3 109.91 26.335 125.192 1 79.94 ? O3B ADP 906 B 1 HETATM 5 P PA ADP . . . F 3 112.129 25.067 122.254 1 97.15 ? PA ADP 906 B 1 HETATM 6 O O1A ADP . . . F 3 111.463 23.963 121.517 1 98.41 ? O1A ADP 906 B 1 HETATM 7 O O2A ADP . . . F 3 111.837 26.469 121.584 1 96.91 ? O2A ADP 906 B 1 HETATM 8 O O3A ADP . . . F 3 111.801 25.132 123.854 1 89.82 ? O3A ADP 906 B 1 HETATM 9 O O5' ADP . . . F 3 113.669 24.544 122.233 1 96.7 ? O5' ADP 906 B 1 HETATM 10 C C5' ADP . . . F 3 114.622 24.994 123.2 1 97.92 ? C5' ADP 906 B 1 HETATM 11 C C4' ADP . . . F 3 115.983 25.448 122.621 1 96.7 ? C4' ADP 906 B 1 HETATM 12 O O4' ADP . . . F 3 116.968 24.472 122.892 1 95.47 ? O4' ADP 906 B 1 HETATM 13 C C3' ADP . . . F 3 115.888 25.445 121.126 1 96.22 ? C3' ADP 906 B 1 HETATM 14 O O3' ADP . . . F 3 117.065 26.038 120.601 1 96.98 ? O3' ADP 906 B 1 HETATM 15 C C2' ADP . . . F 3 115.775 23.946 120.963 1 94.9 ? C2' ADP 906 B 1 HETATM 16 O O2' ADP . . . F 3 115.986 23.664 119.611 1 96.55 ? O2' ADP 906 B 1 HETATM 17 C C1' ADP . . . F 3 116.756 23.374 122.016 1 93.83 ? C1' ADP 906 B 1 HETATM 18 N N9 ADP . . . F 3 116.192 22.22 122.778 1 90.28 ? N9 ADP 906 B 1 HETATM 19 C C8 ADP . . . F 3 115.344 22.252 123.869 1 89.28 ? C8 ADP 906 B 1 HETATM 20 N N7 ADP . . . F 3 115.055 20.99 124.256 1 88.23 ? N7 ADP 906 B 1 HETATM 21 C C5 ADP . . . F 3 115.698 20.135 123.432 1 86.13 ? C5 ADP 906 B 1 HETATM 22 C C6 ADP . . . F 3 115.727 18.752 123.386 1 83.16 ? C6 ADP 906 B 1 HETATM 23 N N6 ADP . . . F 3 114.912 18.036 124.124 1 80.44 ? N6 ADP 906 B 1 HETATM 24 N N1 ADP . . . F 3 116.454 18.144 122.416 1 82.69 ? N1 ADP 906 B 1 HETATM 25 C C2 ADP . . . F 3 117.161 18.922 121.512 1 84.54 ? C2 ADP 906 B 1 HETATM 26 N N3 ADP . . . F 3 117.168 20.299 121.539 1 85.25 ? N3 ADP 906 B 1 HETATM 27 C C4 ADP . . . F 3 116.424 20.894 122.502 1 87.57 ? C4 ADP 906 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 360 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #