data_5DYI # _model_server_result.job_id cnVRBuTtK5HGkB5V8H3ITA _model_server_result.datetime_utc '2025-07-02 23:39:50' _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 5dyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":800}' # _entry.id 5DYI # _exptl.entry_id 5DYI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 12 _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 5DYI _cell.length_a 146.44 _cell.length_b 176.21 _cell.length_c 256.87 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DYI _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,M,N,O,P,Q,R 1 1 G,H,I,J,K,L,S,T,U,V,W,X 2 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 x,y,z _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 ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N ? 2 U N N ? 2 V N N ? 2 W N N ? 2 X 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 5DYI _atom_sites.fract_transf_matrix[1][1] 0.006829 _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] 0.005675 _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] 0.003893 _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 M 2 ADP A 1 800 800 ADP ADP . N 2 ADP B 1 800 800 ADP ADP . O 2 ADP C 1 800 800 ADP ADP . P 2 ADP D 1 800 800 ADP ADP . Q 2 ADP E 1 800 800 ADP ADP . R 2 ADP F 1 800 800 ADP ADP . S 2 ADP G 1 800 800 ADP ADP . T 2 ADP H 1 800 800 ADP ADP . U 2 ADP I 1 800 800 ADP ADP . V 2 ADP J 1 800 800 ADP ADP . W 2 ADP K 1 800 800 ADP ADP . X 2 ADP L 1 800 800 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 . . . X 2 -58.236 -24.045 32.99 1 64.48 ? PB ADP 800 L 1 HETATM 2 O O1B ADP . . . X 2 -57.88 -22.703 32.472 1 64.47 ? O1B ADP 800 L 1 HETATM 3 O O2B ADP . . . X 2 -57.005 -24.848 33.13 1 63.56 ? O2B ADP 800 L 1 HETATM 4 O O3B ADP . . . X 2 -59.139 -24.134 34.184 1 64.52 ? O3B ADP 800 L 1 HETATM 5 P PA ADP . . . X 2 -59.861 -24.566 30.555 1 64.09 ? PA ADP 800 L 1 HETATM 6 O O1A ADP . . . X 2 -59.433 -25.592 29.602 1 63.53 ? O1A ADP 800 L 1 HETATM 7 O O2A ADP . . . X 2 -59.459 -23.203 30.261 1 64.97 ? O2A ADP 800 L 1 HETATM 8 O O3A ADP . . . X 2 -59.165 -24.847 31.959 1 64.25 ? O3A ADP 800 L 1 HETATM 9 O O5' ADP . . . X 2 -61.466 -24.687 30.625 1 64.62 ? O5' ADP 800 L 1 HETATM 10 C C5' ADP . . . X 2 -62.203 -23.886 29.704 1 65.6 ? C5' ADP 800 L 1 HETATM 11 C C4' ADP . . . X 2 -63.587 -24.426 29.479 1 66.98 ? C4' ADP 800 L 1 HETATM 12 O O4' ADP . . . X 2 -64.484 -23.347 29.173 1 67.78 ? O4' ADP 800 L 1 HETATM 13 C C3' ADP . . . X 2 -63.558 -25.396 28.315 1 67.38 ? C3' ADP 800 L 1 HETATM 14 O O3' ADP . . . X 2 -64.07 -26.663 28.743 1 69.14 ? O3' ADP 800 L 1 HETATM 15 C C2' ADP . . . X 2 -64.361 -24.699 27.226 1 68.07 ? C2' ADP 800 L 1 HETATM 16 O O2' ADP . . . X 2 -65.542 -25.428 26.877 1 68.76 ? O2' ADP 800 L 1 HETATM 17 C C1' ADP . . . X 2 -64.728 -23.319 27.765 1 68.63 ? C1' ADP 800 L 1 HETATM 18 N N9 ADP . . . X 2 -63.955 -22.2 27.136 1 69.34 ? N9 ADP 800 L 1 HETATM 19 C C8 ADP . . . X 2 -63.147 -21.347 27.795 1 69.86 ? C8 ADP 800 L 1 HETATM 20 N N7 ADP . . . X 2 -62.601 -20.422 26.969 1 70.12 ? N7 ADP 800 L 1 HETATM 21 C C5 ADP . . . X 2 -63.064 -20.663 25.731 1 70.06 ? C5 ADP 800 L 1 HETATM 22 C C6 ADP . . . X 2 -62.885 -20.069 24.382 1 71.01 ? C6 ADP 800 L 1 HETATM 23 N N6 ADP . . . X 2 -62.089 -18.999 24.203 1 72.28 ? N6 ADP 800 L 1 HETATM 24 N N1 ADP . . . X 2 -63.529 -20.628 23.34 1 71.78 ? N1 ADP 800 L 1 HETATM 25 C C2 ADP . . . X 2 -64.33 -21.695 23.503 1 71.64 ? C2 ADP 800 L 1 HETATM 26 N N3 ADP . . . X 2 -64.541 -22.274 24.703 1 70.43 ? N3 ADP 800 L 1 HETATM 27 C C4 ADP . . . X 2 -63.957 -21.827 25.843 1 69.8 ? C4 ADP 800 L 1 # _model_server_stats.io_time_ms 316 _model_server_stats.parse_time_ms 54 _model_server_stats.create_model_time_ms 64 _model_server_stats.query_time_ms 599 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #