data_8DYJ # _model_server_result.job_id M2cnG3sCnS_TnrUoAsrpKQ _model_server_result.datetime_utc '2024-11-25 00:34:58' _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 8dyj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":802}' # _entry.id 8DYJ # _exptl.entry_id 8DYJ _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 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 8DYJ _cell.length_a 61.025 _cell.length_b 129.358 _cell.length_c 188.422 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DYJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NE2 _struct_conn.ptnr1_label_comp_id HIS _struct_conn.ptnr1_label_seq_id 617 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id HIS _struct_conn.ptnr1_auth_seq_id 590 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id CO _struct_conn.ptnr2_label_comp_id B12 _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id B12 _struct_conn.ptnr2_auth_seq_id 801 _struct_conn.ptnr2_symmetry 1_555 _struct_conn.pdbx_ptnr1_PDB_ins_code ? _struct_conn.pdbx_ptnr1_label_alt_id ? _struct_conn.pdbx_ptnr1_standard_comp_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr3_PDB_ins_code ? _struct_conn.pdbx_ptnr3_label_alt_id ? _struct_conn.pdbx_ptnr3_label_asym_id ? _struct_conn.pdbx_ptnr3_label_atom_id ? _struct_conn.pdbx_ptnr3_label_comp_id ? _struct_conn.pdbx_ptnr3_label_seq_id ? _struct_conn.pdbx_PDB_id ? _struct_conn.pdbx_dist_value 2.264 _struct_conn.pdbx_value_order ? # _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 8DYJ _atom_sites.fract_transf_matrix[1][1] 0.016387 _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] 0.00773 _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] 0.005307 _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 B12 B 1 801 801 B12 B12 . C 3 ADP B 1 802 901 ADP ADP . D 4 HOH B 1 901 95 HOH HOH . D 4 HOH B 2 902 96 HOH HOH . D 4 HOH B 3 903 52 HOH HOH . D 4 HOH B 4 904 126 HOH HOH . D 4 HOH B 5 905 11 HOH HOH . D 4 HOH B 6 906 1 HOH HOH . D 4 HOH B 7 907 79 HOH HOH . D 4 HOH B 8 908 23 HOH HOH . D 4 HOH B 9 909 107 HOH HOH . D 4 HOH B 10 910 72 HOH HOH . D 4 HOH B 11 911 71 HOH HOH . D 4 HOH B 12 912 65 HOH HOH . D 4 HOH B 13 913 17 HOH HOH . D 4 HOH B 14 914 18 HOH HOH . D 4 HOH B 15 915 16 HOH HOH . D 4 HOH B 16 916 78 HOH HOH . D 4 HOH B 17 917 20 HOH HOH . D 4 HOH B 18 918 60 HOH HOH . D 4 HOH B 19 919 109 HOH HOH . D 4 HOH B 20 920 40 HOH HOH . D 4 HOH B 21 921 54 HOH HOH . D 4 HOH B 22 922 13 HOH HOH . D 4 HOH B 23 923 45 HOH HOH . D 4 HOH B 24 924 114 HOH HOH . D 4 HOH B 25 925 108 HOH HOH . D 4 HOH B 26 926 35 HOH HOH . D 4 HOH B 27 927 68 HOH HOH . D 4 HOH B 28 928 82 HOH HOH . D 4 HOH B 29 929 21 HOH HOH . D 4 HOH B 30 930 87 HOH HOH . D 4 HOH B 31 931 100 HOH HOH . D 4 HOH B 32 932 36 HOH HOH . D 4 HOH B 33 933 62 HOH HOH . D 4 HOH B 34 934 122 HOH HOH . D 4 HOH B 35 935 84 HOH HOH . D 4 HOH B 36 936 7 HOH HOH . D 4 HOH B 37 937 43 HOH HOH . D 4 HOH B 38 938 61 HOH HOH . D 4 HOH B 39 939 67 HOH HOH . D 4 HOH B 40 940 29 HOH HOH . D 4 HOH B 41 941 91 HOH HOH . D 4 HOH B 42 942 104 HOH HOH . D 4 HOH B 43 943 49 HOH HOH . D 4 HOH B 44 944 116 HOH HOH . D 4 HOH B 45 945 86 HOH HOH . D 4 HOH B 46 946 81 HOH HOH . D 4 HOH B 47 947 118 HOH HOH . D 4 HOH B 48 948 14 HOH HOH . D 4 HOH B 49 949 5 HOH HOH . D 4 HOH B 50 950 8 HOH HOH . D 4 HOH B 51 951 12 HOH HOH . D 4 HOH B 52 952 89 HOH HOH . D 4 HOH B 53 953 115 HOH HOH . D 4 HOH B 54 954 10 HOH HOH . D 4 HOH B 55 955 4 HOH HOH . D 4 HOH B 56 956 48 HOH HOH . D 4 HOH B 57 957 27 HOH HOH . D 4 HOH B 58 958 28 HOH HOH . D 4 HOH B 59 959 25 HOH HOH . D 4 HOH B 60 960 51 HOH HOH . D 4 HOH B 61 961 73 HOH HOH . D 4 HOH B 62 962 33 HOH HOH . D 4 HOH B 63 963 106 HOH HOH . D 4 HOH B 64 964 66 HOH HOH . D 4 HOH B 65 965 6 HOH HOH . D 4 HOH B 66 966 37 HOH HOH . D 4 HOH B 67 967 39 HOH HOH . D 4 HOH B 68 968 123 HOH HOH . D 4 HOH B 69 969 22 HOH HOH . D 4 HOH B 70 970 24 HOH HOH . D 4 HOH B 71 971 46 HOH HOH . D 4 HOH B 72 972 31 HOH HOH . D 4 HOH B 73 973 53 HOH HOH . D 4 HOH B 74 974 41 HOH HOH . D 4 HOH B 75 975 9 HOH HOH . D 4 HOH B 76 976 74 HOH HOH . D 4 HOH B 77 977 119 HOH HOH . D 4 HOH B 78 978 26 HOH HOH . D 4 HOH B 79 979 88 HOH HOH . D 4 HOH B 80 980 2 HOH HOH . D 4 HOH B 81 981 80 HOH HOH . D 4 HOH B 82 982 58 HOH HOH . D 4 HOH B 83 983 90 HOH HOH . D 4 HOH B 84 984 3 HOH HOH . D 4 HOH B 85 985 50 HOH HOH . D 4 HOH B 86 986 47 HOH HOH . D 4 HOH B 87 987 44 HOH HOH . D 4 HOH B 88 988 99 HOH HOH . D 4 HOH B 89 989 69 HOH HOH . D 4 HOH B 90 990 113 HOH HOH . D 4 HOH B 91 991 105 HOH HOH . D 4 HOH B 92 992 94 HOH HOH . D 4 HOH B 93 993 112 HOH HOH . D 4 HOH B 94 994 30 HOH HOH . D 4 HOH B 95 995 32 HOH HOH . D 4 HOH B 96 996 125 HOH HOH . D 4 HOH B 97 997 102 HOH HOH . D 4 HOH B 98 998 110 HOH HOH . D 4 HOH B 99 999 85 HOH HOH . D 4 HOH B 100 1000 83 HOH HOH . D 4 HOH B 101 1001 70 HOH HOH . D 4 HOH B 102 1002 56 HOH HOH . D 4 HOH B 103 1003 55 HOH HOH . D 4 HOH B 104 1004 76 HOH HOH . D 4 HOH B 105 1005 111 HOH HOH . D 4 HOH B 106 1006 57 HOH HOH . D 4 HOH B 107 1007 101 HOH HOH . D 4 HOH B 108 1008 64 HOH HOH . D 4 HOH B 109 1009 63 HOH HOH . D 4 HOH B 110 1010 120 HOH HOH . D 4 HOH B 111 1011 124 HOH HOH . D 4 HOH B 112 1012 15 HOH HOH . D 4 HOH B 113 1013 59 HOH HOH . D 4 HOH B 114 1014 92 HOH HOH . D 4 HOH B 115 1015 75 HOH HOH . D 4 HOH B 116 1016 121 HOH HOH . D 4 HOH B 117 1017 97 HOH HOH . D 4 HOH B 118 1018 103 HOH HOH . D 4 HOH B 119 1019 42 HOH HOH . D 4 HOH B 120 1020 77 HOH HOH . D 4 HOH B 121 1021 98 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 . . . C 3 20.2 12.141 18.112 1 65.9 ? PB ADP 802 B 1 HETATM 2 O O1B ADP . . . C 3 20.252 13.346 17.173 1 63.92 ? O1B ADP 802 B 1 HETATM 3 O O2B ADP . . . C 3 19.719 10.803 17.666 1 68.85 ? O2B ADP 802 B 1 HETATM 4 O O3B ADP . . . C 3 19.839 12.492 19.539 1 63.32 ? O3B ADP 802 B 1 HETATM 5 P PA ADP . . . C 3 22.125 10.841 19.639 1 61.19 ? PA ADP 802 B 1 HETATM 6 O O1A ADP . . . C 3 23.488 10.898 20.344 1 62.59 ? O1A ADP 802 B 1 HETATM 7 O O2A ADP . . . C 3 20.931 10.468 20.404 1 61.37 ? O2A ADP 802 B 1 HETATM 8 O O3A ADP . . . C 3 21.968 11.724 18.371 1 66.01 ? O3A ADP 802 B 1 HETATM 9 O O5' ADP . . . C 3 22.265 9.115 18.997 1 62.96 ? O5' ADP 802 B 1 HETATM 10 C C5' ADP . . . C 3 23.552 8.935 18.592 1 60.12 ? C5' ADP 802 B 1 HETATM 11 C C4' ADP . . . C 3 23.455 8.223 17.246 1 57.83 ? C4' ADP 802 B 1 HETATM 12 O O4' ADP . . . C 3 23.609 9.221 16.204 1 58.14 ? O4' ADP 802 B 1 HETATM 13 C C3' ADP . . . C 3 24.612 7.207 17.053 1 58.26 ? C3' ADP 802 B 1 HETATM 14 O O3' ADP . . . C 3 24.129 5.919 17.29 1 59.38 ? O3' ADP 802 B 1 HETATM 15 C C2' ADP . . . C 3 25.029 7.379 15.604 1 59.41 ? C2' ADP 802 B 1 HETATM 16 O O2' ADP . . . C 3 24.217 6.662 14.72 1 56.99 ? O2' ADP 802 B 1 HETATM 17 C C1' ADP . . . C 3 24.734 8.889 15.389 1 58.82 ? C1' ADP 802 B 1 HETATM 18 N N9 ADP . . . C 3 25.895 9.716 15.841 1 61.86 ? N9 ADP 802 B 1 HETATM 19 C C8 ADP . . . C 3 26.453 9.867 17.115 1 64.56 ? C8 ADP 802 B 1 HETATM 20 N N7 ADP . . . C 3 27.491 10.699 17.149 1 65.13 ? N7 ADP 802 B 1 HETATM 21 C C5 ADP . . . C 3 27.616 11.117 15.821 1 65.04 ? C5 ADP 802 B 1 HETATM 22 C C6 ADP . . . C 3 28.521 11.997 15.203 1 63.99 ? C6 ADP 802 B 1 HETATM 23 N N6 ADP . . . C 3 29.495 12.61 15.937 1 62.05 ? N6 ADP 802 B 1 HETATM 24 N N1 ADP . . . C 3 28.439 12.251 13.862 1 63.59 ? N1 ADP 802 B 1 HETATM 25 C C2 ADP . . . C 3 27.437 11.595 13.204 1 65.11 ? C2 ADP 802 B 1 HETATM 26 N N3 ADP . . . C 3 26.501 10.736 13.641 1 65.26 ? N3 ADP 802 B 1 HETATM 27 C C4 ADP . . . C 3 26.623 10.507 14.994 1 64.97 ? C4 ADP 802 B 1 # _model_server_stats.io_time_ms 83 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #