data_4IY0 # _model_server_result.job_id BeKZ3qWGjn9sQnc7JR1C4g _model_server_result.datetime_utc '2025-08-31 16:46:34' _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 4iy0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 4IY0 # _exptl.entry_id 4IY0 _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 1 _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 4IY0 _cell.length_a 104.599 _cell.length_b 104.599 _cell.length_c 100.959 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4IY0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 98 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 16_554 -y+1/2,-x+1/2,-z-1/2 0 -1 0 -1 0 0 0 0 -1 52.2995 52.2995 -50.4795 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 7 n n PB O2B ADP sing 8 n n PB O3B ADP sing 9 n n PB O3A ADP sing 10 n n O2B HOB2 ADP sing 11 n n O3B HOB3 ADP sing 12 n n PA O1A ADP doub 13 n n PA O2A ADP sing 14 n n PA O3A ADP sing 15 n n PA O5' ADP sing 16 n n O2A HOA2 ADP sing 17 n n O5' C5' ADP sing 18 n n C5' C4' ADP sing 19 n n C5' "H5'1" ADP sing 20 n n C5' "H5'2" ADP sing 21 n n C4' O4' ADP sing 22 n n C4' C3' ADP sing 23 n n C4' H4' ADP sing 24 n n O4' C1' ADP sing 25 n n C3' O3' ADP sing 26 n n C3' C2' ADP sing 27 n n C3' H3' ADP sing 28 n n O3' HO3' ADP sing 29 n n C2' O2' ADP sing 30 n n C2' C1' ADP sing 31 n n C2' H2' ADP sing 32 n n O2' HO2' ADP sing 33 n n C1' N9 ADP sing 34 n n C1' H1' ADP sing 35 n n N9 C8 ADP sing 36 n y N9 C4 ADP sing 37 n y C8 N7 ADP doub 38 n y C8 H8 ADP sing 39 n n N7 C5 ADP sing 40 n y C5 C6 ADP sing 41 n y C5 C4 ADP doub 42 n y C6 N6 ADP sing 43 n n C6 N1 ADP doub 44 n y N6 HN61 ADP sing 45 n n N6 HN62 ADP sing 46 n n N1 C2 ADP sing 47 n y C2 N3 ADP doub 48 n y C2 H2 ADP sing 49 n n N3 C4 ADP sing 50 n y # _atom_sites.entry_id 4IY0 _atom_sites.fract_transf_matrix[1][1] 0.00956 _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] 0.00956 _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] 0.009905 _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 B 2 ADP A 1 601 1 ADP ADP . C 3 ACT A 1 602 5000 ACT ACT . D 3 ACT A 1 603 5001 ACT ACT . E 3 ACT A 1 604 5002 ACT ACT . F 3 ACT A 1 605 5003 ACT ACT . G 4 HOH A 1 701 1 HOH HOH . G 4 HOH A 2 702 2 HOH HOH . G 4 HOH A 3 703 3 HOH HOH . G 4 HOH A 4 704 4 HOH HOH . G 4 HOH A 5 705 5 HOH HOH . G 4 HOH A 6 706 6 HOH HOH . G 4 HOH A 7 707 7 HOH HOH . G 4 HOH A 8 708 8 HOH HOH . G 4 HOH A 9 709 9 HOH HOH . G 4 HOH A 10 710 10 HOH HOH . G 4 HOH A 11 711 11 HOH HOH . G 4 HOH A 12 712 12 HOH HOH . G 4 HOH A 13 713 13 HOH HOH . G 4 HOH A 14 714 14 HOH HOH . G 4 HOH A 15 715 15 HOH HOH . G 4 HOH A 16 716 16 HOH HOH . G 4 HOH A 17 717 17 HOH HOH . G 4 HOH A 18 718 18 HOH HOH . G 4 HOH A 19 719 19 HOH HOH . G 4 HOH A 20 720 20 HOH HOH . G 4 HOH A 21 721 21 HOH HOH . G 4 HOH A 22 722 22 HOH HOH . G 4 HOH A 23 723 23 HOH HOH . G 4 HOH A 24 724 24 HOH HOH . G 4 HOH A 25 725 25 HOH HOH . G 4 HOH A 26 726 26 HOH HOH . G 4 HOH A 27 727 27 HOH HOH . G 4 HOH A 28 728 28 HOH HOH . G 4 HOH A 29 729 29 HOH HOH . G 4 HOH A 30 730 30 HOH HOH . G 4 HOH A 31 731 31 HOH HOH . G 4 HOH A 32 732 32 HOH HOH . G 4 HOH A 33 733 33 HOH HOH . G 4 HOH A 34 734 34 HOH HOH . G 4 HOH A 35 735 35 HOH HOH . G 4 HOH A 36 736 36 HOH HOH . G 4 HOH A 37 737 37 HOH HOH . G 4 HOH A 38 738 38 HOH HOH . G 4 HOH A 39 739 39 HOH HOH . G 4 HOH A 40 740 40 HOH HOH . G 4 HOH A 41 741 41 HOH HOH . G 4 HOH A 42 742 42 HOH HOH . G 4 HOH A 43 743 43 HOH HOH . G 4 HOH A 44 744 44 HOH HOH . G 4 HOH A 45 745 45 HOH HOH . G 4 HOH A 46 746 46 HOH HOH . G 4 HOH A 47 747 47 HOH HOH . G 4 HOH A 48 748 48 HOH HOH . G 4 HOH A 49 749 49 HOH HOH . G 4 HOH A 50 750 50 HOH HOH . G 4 HOH A 51 751 51 HOH HOH . G 4 HOH A 52 752 52 HOH HOH . G 4 HOH A 53 753 53 HOH HOH . G 4 HOH A 54 754 54 HOH HOH . G 4 HOH A 55 755 55 HOH HOH . G 4 HOH A 56 756 56 HOH HOH . G 4 HOH A 57 757 57 HOH HOH . G 4 HOH A 58 758 58 HOH HOH . G 4 HOH A 59 759 59 HOH HOH . G 4 HOH A 60 760 60 HOH HOH . G 4 HOH A 61 761 61 HOH HOH . G 4 HOH A 62 762 62 HOH HOH . G 4 HOH A 63 763 63 HOH HOH . G 4 HOH A 64 764 64 HOH HOH . G 4 HOH A 65 765 65 HOH HOH . G 4 HOH A 66 766 66 HOH HOH . G 4 HOH A 67 767 67 HOH HOH . G 4 HOH A 68 768 68 HOH HOH . G 4 HOH A 69 769 69 HOH HOH . G 4 HOH A 70 770 70 HOH HOH . G 4 HOH A 71 771 71 HOH HOH . G 4 HOH A 72 772 72 HOH HOH . G 4 HOH A 73 773 73 HOH HOH . G 4 HOH A 74 774 74 HOH HOH . G 4 HOH A 75 775 75 HOH HOH . G 4 HOH A 76 776 76 HOH HOH . G 4 HOH A 77 777 77 HOH HOH . G 4 HOH A 78 778 78 HOH HOH . G 4 HOH A 79 779 79 HOH HOH . G 4 HOH A 80 780 80 HOH HOH . G 4 HOH A 81 781 81 HOH HOH . G 4 HOH A 82 782 82 HOH HOH . G 4 HOH A 83 783 83 HOH HOH . G 4 HOH A 84 784 84 HOH HOH . G 4 HOH A 85 785 85 HOH HOH . G 4 HOH A 86 786 86 HOH HOH . G 4 HOH A 87 787 87 HOH HOH . G 4 HOH A 88 788 88 HOH HOH . G 4 HOH A 89 789 89 HOH HOH . G 4 HOH A 90 790 90 HOH HOH . G 4 HOH A 91 791 91 HOH HOH . G 4 HOH A 92 792 92 HOH HOH . G 4 HOH A 93 793 93 HOH HOH . G 4 HOH A 94 794 94 HOH HOH . G 4 HOH A 95 795 95 HOH HOH . G 4 HOH A 96 796 96 HOH HOH . G 4 HOH A 97 797 97 HOH HOH . G 4 HOH A 98 798 98 HOH HOH . G 4 HOH A 99 799 99 HOH HOH . G 4 HOH A 100 800 100 HOH HOH . G 4 HOH A 101 801 101 HOH HOH . G 4 HOH A 102 802 102 HOH HOH . G 4 HOH A 103 803 103 HOH HOH . G 4 HOH A 104 804 104 HOH HOH . G 4 HOH A 105 805 105 HOH HOH . G 4 HOH A 106 806 106 HOH HOH . G 4 HOH A 107 807 107 HOH HOH . G 4 HOH A 108 808 108 HOH HOH . G 4 HOH A 109 809 109 HOH HOH . G 4 HOH A 110 810 110 HOH HOH . G 4 HOH A 111 811 111 HOH HOH . G 4 HOH A 112 812 112 HOH HOH . G 4 HOH A 113 813 113 HOH HOH . G 4 HOH A 114 814 114 HOH HOH . G 4 HOH A 115 815 115 HOH HOH . G 4 HOH A 116 816 116 HOH HOH . # 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 . . . B 2 17.678 29.642 -27.909 1 36.41 ? PB ADP 601 A 1 HETATM 2 O O1B ADP . . . B 2 17.847 30.324 -29.192 1 43.11 ? O1B ADP 601 A 1 HETATM 3 O O2B ADP . . . B 2 18.401 30.375 -26.754 1 44.59 ? O2B ADP 601 A 1 HETATM 4 O O3B ADP . . . B 2 18.025 28.203 -27.758 1 35.6 ? O3B ADP 601 A 1 HETATM 5 P PA ADP . . . B 2 15.149 30.924 -27.443 1 35.34 ? PA ADP 601 A 1 HETATM 6 O O1A ADP . . . B 2 14.286 30.548 -26.263 1 33.75 ? O1A ADP 601 A 1 HETATM 7 O O2A ADP . . . B 2 15.896 32.187 -27.543 1 34.01 ? O2A ADP 601 A 1 HETATM 8 O O3A ADP . . . B 2 16.116 29.651 -27.621 1 33.94 ? O3A ADP 601 A 1 HETATM 9 O O5' ADP . . . B 2 14.191 30.825 -28.734 1 31.13 ? O5' ADP 601 A 1 HETATM 10 C C5' ADP . . . B 2 14.516 31.318 -30.07 1 34.54 ? C5' ADP 601 A 1 HETATM 11 C C4' ADP . . . B 2 13.648 30.514 -31.07 1 34.58 ? C4' ADP 601 A 1 HETATM 12 O O4' ADP . . . B 2 14.122 29.125 -31.12 1 33.54 ? O4' ADP 601 A 1 HETATM 13 C C3' ADP . . . B 2 12.189 30.36 -30.656 1 30.28 ? C3' ADP 601 A 1 HETATM 14 O O3' ADP . . . B 2 11.405 30.485 -31.909 1 29.37 ? O3' ADP 601 A 1 HETATM 15 C C2' ADP . . . B 2 12.116 28.996 -29.968 1 33.14 ? C2' ADP 601 A 1 HETATM 16 O O2' ADP . . . B 2 10.811 28.359 -30.026 1 35.32 ? O2' ADP 601 A 1 HETATM 17 C C1' ADP . . . B 2 13.149 28.199 -30.832 1 31.95 ? C1' ADP 601 A 1 HETATM 18 N N9 ADP . . . B 2 13.781 27.068 -30.198 1 35.31 ? N9 ADP 601 A 1 HETATM 19 C C8 ADP . . . B 2 14.257 26.941 -28.897 1 32.16 ? C8 ADP 601 A 1 HETATM 20 N N7 ADP . . . B 2 14.747 25.753 -28.675 1 33.1 ? N7 ADP 601 A 1 HETATM 21 C C5 ADP . . . B 2 14.618 25.051 -29.902 1 31.76 ? C5 ADP 601 A 1 HETATM 22 C C6 ADP . . . B 2 14.962 23.69 -30.33 1 32.43 ? C6 ADP 601 A 1 HETATM 23 N N6 ADP . . . B 2 15.539 22.751 -29.512 1 27.44 ? N6 ADP 601 A 1 HETATM 24 N N1 ADP . . . B 2 14.61 23.376 -31.659 1 34.32 ? N1 ADP 601 A 1 HETATM 25 C C2 ADP . . . B 2 14.096 24.295 -32.508 1 29.32 ? C2 ADP 601 A 1 HETATM 26 N N3 ADP . . . B 2 13.758 25.548 -32.153 1 32.59 ? N3 ADP 601 A 1 HETATM 27 C C4 ADP . . . B 2 13.991 25.914 -30.858 1 34.11 ? C4 ADP 601 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 407 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #