data_4XYK # _model_server_result.job_id LjDTOITdnmMtmurisI4Iog _model_server_result.datetime_utc '2025-08-31 12:26:40' _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 4xyk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":801}' # _entry.id 4XYK # _exptl.entry_id 4XYK _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.78 _cell.angle_gamma 90 _cell.entry_id 4XYK _cell.length_a 79.345 _cell.length_b 168.373 _cell.length_c 133.272 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XYK _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T _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 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 E N N ? 2 I N N ? 2 L N N ? 2 R 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 4XYK _atom_sites.fract_transf_matrix[1][1] 0.012603 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003092 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005939 _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] 0.007726 _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 2 ADP A 1 801 801 ADP ADP . F 3 PO4 A 1 802 802 PO4 PO4 . G 3 PO4 A 1 803 803 PO4 PO4 . H 3 PO4 A 1 804 804 PO4 PO4 . I 2 ADP B 1 801 801 ADP ADP . J 3 PO4 B 1 802 802 PO4 PO4 . K 3 PO4 B 1 803 803 PO4 PO4 . L 2 ADP C 1 801 801 ADP ADP . M 3 PO4 C 1 802 802 PO4 PO4 . N 3 PO4 C 1 803 803 PO4 PO4 . O 3 PO4 C 1 804 804 PO4 PO4 . P 3 PO4 C 1 805 805 PO4 PO4 . Q 3 PO4 D 1 801 804 PO4 PO4 . R 2 ADP D 1 802 801 ADP ADP . S 3 PO4 D 1 803 802 PO4 PO4 . T 3 PO4 D 1 804 803 PO4 PO4 . # 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 . . . I 2 -21.847 42.108 144.42 1 160.21 ? PB ADP 801 B 1 HETATM 2 O O1B ADP . . . I 2 -21.609 41.259 142.975 1 154.1 ? O1B ADP 801 B 1 HETATM 3 O O2B ADP . . . I 2 -22.827 43.178 144.066 1 21.46 ? O2B ADP 801 B 1 HETATM 4 O O3B ADP . . . I 2 -22.354 41.139 145.427 1 117.56 ? O3B ADP 801 B 1 HETATM 5 P PA ADP . . . I 2 -20.044 43.611 145.831 1 163.01 ? PA ADP 801 B 1 HETATM 6 O O1A ADP . . . I 2 -20.571 44.961 145.568 1 129.65 ? O1A ADP 801 B 1 HETATM 7 O O2A ADP . . . I 2 -20.28 43.097 147.206 1 153.12 ? O2A ADP 801 B 1 HETATM 8 O O3A ADP . . . I 2 -20.477 42.628 144.773 1 143.71 ? O3A ADP 801 B 1 HETATM 9 O O5' ADP . . . I 2 -18.43 43.783 145.738 1 120.82 ? O5' ADP 801 B 1 HETATM 10 C C5' ADP . . . I 2 -17.748 44.649 146.663 1 45.38 ? C5' ADP 801 B 1 HETATM 11 C C4' ADP . . . I 2 -16.489 45.385 146.145 1 36.96 ? C4' ADP 801 B 1 HETATM 12 O O4' ADP . . . I 2 -16.925 46.433 145.248 1 63.38 ? O4' ADP 801 B 1 HETATM 13 C C3' ADP . . . I 2 -15.546 46.071 147.185 1 77.37 ? C3' ADP 801 B 1 HETATM 14 O O3' ADP . . . I 2 -14.448 45.219 147.565 1 39.44 ? O3' ADP 801 B 1 HETATM 15 C C2' ADP . . . I 2 -15.091 47.326 146.423 1 94.16 ? C2' ADP 801 B 1 HETATM 16 O O2' ADP . . . I 2 -13.927 47.049 145.634 1 63.99 ? O2' ADP 801 B 1 HETATM 17 C C1' ADP . . . I 2 -16.306 47.687 145.589 1 97.99 ? C1' ADP 801 B 1 HETATM 18 N N9 ADP . . . I 2 -17.283 48.643 146.268 1 123.03 ? N9 ADP 801 B 1 HETATM 19 C C8 ADP . . . I 2 -18.45 48.417 147.009 1 120.18 ? C8 ADP 801 B 1 HETATM 20 N N7 ADP . . . I 2 -19.061 49.505 147.461 1 114.92 ? N7 ADP 801 B 1 HETATM 21 C C5 ADP . . . I 2 -18.262 50.552 146.976 1 97.52 ? C5 ADP 801 B 1 HETATM 22 C C6 ADP . . . I 2 -18.326 52 147.117 1 98.78 ? C6 ADP 801 B 1 HETATM 23 N N6 ADP . . . I 2 -19.315 52.657 147.755 1 43.52 ? N6 ADP 801 B 1 HETATM 24 N N1 ADP . . . I 2 -17.341 52.738 146.511 1 114.38 ? N1 ADP 801 B 1 HETATM 25 C C2 ADP . . . I 2 -16.341 52.107 145.856 1 99.55 ? C2 ADP 801 B 1 HETATM 26 N N3 ADP . . . I 2 -16.154 50.786 145.658 1 79.85 ? N3 ADP 801 B 1 HETATM 27 C C4 ADP . . . I 2 -17.147 50.037 146.276 1 103.74 ? C4 ADP 801 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 399 _model_server_stats.encode_time_ms 50 _model_server_stats.element_count 27 #