data_1DGK # _model_server_result.job_id JjmRbJbv2ummA0BtAmZrYw _model_server_result.datetime_utc '2024-11-18 09:37:34' _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 1dgk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":921}' # _entry.id 1DGK # _exptl.entry_id 1DGK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 90 _cell.entry_id 1DGK _cell.length_a 145.78 _cell.length_b 146.83 _cell.length_c 58.59 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DGK _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _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,E,F,G _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 ? 4 E N N ? 4 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 1DGK _atom_sites.fract_transf_matrix[1][1] 0.00686 _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] 0.00681 _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] 0.01707 _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 GLC N 1 918 915 GLC GLC . C 2 GLC N 1 919 917 GLC GLC . D 3 PO4 N 1 920 916 PO4 PO4 . E 4 ADP N 1 921 918 ADP ADP . F 4 ADP N 1 922 919 ADP ADP . G 5 HOH N 1 923 1 HOH WAT . G 5 HOH N 2 924 2 HOH WAT . G 5 HOH N 3 925 3 HOH WAT . G 5 HOH N 4 926 4 HOH WAT . G 5 HOH N 5 927 5 HOH WAT . G 5 HOH N 6 928 6 HOH WAT . G 5 HOH N 7 929 7 HOH WAT . G 5 HOH N 8 930 8 HOH WAT . G 5 HOH N 9 931 9 HOH WAT . G 5 HOH N 10 932 10 HOH WAT . G 5 HOH N 11 933 11 HOH WAT . G 5 HOH N 12 934 12 HOH WAT . G 5 HOH N 13 935 13 HOH WAT . G 5 HOH N 14 936 14 HOH WAT . G 5 HOH N 15 937 15 HOH WAT . G 5 HOH N 16 938 16 HOH WAT . G 5 HOH N 17 939 17 HOH WAT . G 5 HOH N 18 940 18 HOH WAT . G 5 HOH N 19 941 19 HOH WAT . G 5 HOH N 20 942 20 HOH WAT . G 5 HOH N 21 943 21 HOH WAT . G 5 HOH N 22 944 22 HOH WAT . G 5 HOH N 23 945 23 HOH WAT . G 5 HOH N 24 946 24 HOH WAT . G 5 HOH N 25 947 25 HOH WAT . G 5 HOH N 26 948 26 HOH WAT . G 5 HOH N 27 949 27 HOH WAT . G 5 HOH N 28 950 28 HOH WAT . G 5 HOH N 29 951 29 HOH WAT . G 5 HOH N 30 952 30 HOH WAT . G 5 HOH N 31 953 31 HOH WAT . G 5 HOH N 32 954 32 HOH WAT . G 5 HOH N 33 955 33 HOH WAT . G 5 HOH N 34 956 34 HOH WAT . G 5 HOH N 35 957 35 HOH WAT . G 5 HOH N 36 958 36 HOH WAT . G 5 HOH N 37 959 37 HOH WAT . G 5 HOH N 38 960 38 HOH WAT . G 5 HOH N 39 961 39 HOH WAT . G 5 HOH N 40 962 40 HOH WAT . G 5 HOH N 41 963 41 HOH WAT . G 5 HOH N 42 964 42 HOH WAT . G 5 HOH N 43 965 43 HOH WAT . G 5 HOH N 44 966 44 HOH WAT . G 5 HOH N 45 967 45 HOH WAT . G 5 HOH N 46 968 46 HOH WAT . G 5 HOH N 47 969 47 HOH WAT . G 5 HOH N 48 970 48 HOH WAT . G 5 HOH N 49 971 49 HOH WAT . G 5 HOH N 50 972 50 HOH WAT . G 5 HOH N 51 973 51 HOH WAT . G 5 HOH N 52 974 52 HOH WAT . G 5 HOH N 53 975 53 HOH WAT . G 5 HOH N 54 976 54 HOH WAT . G 5 HOH N 55 977 55 HOH WAT . G 5 HOH N 56 978 56 HOH WAT . G 5 HOH N 57 979 57 HOH WAT . G 5 HOH N 58 980 58 HOH WAT . G 5 HOH N 59 981 59 HOH WAT . G 5 HOH N 60 982 60 HOH WAT . G 5 HOH N 61 983 61 HOH WAT . G 5 HOH N 62 984 62 HOH WAT . G 5 HOH N 63 985 63 HOH WAT . G 5 HOH N 64 986 64 HOH WAT . G 5 HOH N 65 987 65 HOH WAT . G 5 HOH N 66 988 66 HOH WAT . G 5 HOH N 67 989 67 HOH WAT . G 5 HOH N 68 990 68 HOH WAT . G 5 HOH N 69 991 69 HOH WAT . G 5 HOH N 70 992 70 HOH WAT . G 5 HOH N 71 993 71 HOH WAT . G 5 HOH N 72 994 72 HOH WAT . G 5 HOH N 73 995 73 HOH WAT . G 5 HOH N 74 996 74 HOH WAT . G 5 HOH N 75 997 75 HOH WAT . G 5 HOH N 76 998 76 HOH WAT . G 5 HOH N 77 999 77 HOH WAT . G 5 HOH N 78 1000 78 HOH WAT . G 5 HOH N 79 1001 79 HOH WAT . G 5 HOH N 80 1002 80 HOH WAT . G 5 HOH N 81 1003 81 HOH WAT . G 5 HOH N 82 1004 82 HOH WAT . G 5 HOH N 83 1005 83 HOH WAT . G 5 HOH N 84 1006 84 HOH WAT . G 5 HOH N 85 1007 85 HOH WAT . G 5 HOH N 86 1008 86 HOH WAT . G 5 HOH N 87 1009 87 HOH WAT . G 5 HOH N 88 1010 88 HOH WAT . G 5 HOH N 89 1011 89 HOH WAT . G 5 HOH N 90 1012 90 HOH WAT . G 5 HOH N 91 1013 91 HOH WAT . G 5 HOH N 92 1014 92 HOH WAT . G 5 HOH N 93 1015 93 HOH WAT . G 5 HOH N 94 1016 94 HOH WAT . # 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 . . . E 4 94.814 59.654 -16.381 1 70.9 ? PB ADP 921 N 1 HETATM 2 O O1B ADP . . . E 4 94.602 60.956 -15.654 1 71.61 ? O1B ADP 921 N 1 HETATM 3 O O2B ADP . . . E 4 93.558 59.517 -17.187 1 70.11 ? O2B ADP 921 N 1 HETATM 4 O O3B ADP . . . E 4 95.964 59.838 -17.315 1 69.67 ? O3B ADP 921 N 1 HETATM 5 P PA ADP . . . E 4 95.035 58.428 -13.761 1 63.78 ? PA ADP 921 N 1 HETATM 6 O O1A ADP . . . E 4 95.975 57.386 -13.253 1 66.08 ? O1A ADP 921 N 1 HETATM 7 O O2A ADP . . . E 4 95.529 59.611 -13.083 1 63.2 ? O2A ADP 921 N 1 HETATM 8 O O3A ADP . . . E 4 95.035 58.48 -15.336 1 66.25 ? O3A ADP 921 N 1 HETATM 9 O O5' ADP . . . E 4 93.539 57.986 -13.408 1 65.15 ? O5' ADP 921 N 1 HETATM 10 C C5' ADP . . . E 4 92.937 56.789 -13.953 1 64.5 ? C5' ADP 921 N 1 HETATM 11 C C4' ADP . . . E 4 91.971 56.036 -13.1 1 64.93 ? C4' ADP 921 N 1 HETATM 12 O O4' ADP . . . E 4 90.745 56.632 -12.689 1 64.89 ? O4' ADP 921 N 1 HETATM 13 C C3' ADP . . . E 4 91.668 54.598 -13.456 1 65.58 ? C3' ADP 921 N 1 HETATM 14 O O3' ADP . . . E 4 92.343 53.633 -12.614 1 65.52 ? O3' ADP 921 N 1 HETATM 15 C C2' ADP . . . E 4 90.123 54.531 -13.402 1 65.39 ? C2' ADP 921 N 1 HETATM 16 O O2' ADP . . . E 4 89.68 53.227 -12.974 1 65.91 ? O2' ADP 921 N 1 HETATM 17 C C1' ADP . . . E 4 89.785 55.65 -12.403 1 64.44 ? C1' ADP 921 N 1 HETATM 18 N N9 ADP . . . E 4 88.509 56.284 -12.625 1 63.58 ? N9 ADP 921 N 1 HETATM 19 C C8 ADP . . . E 4 87.881 56.558 -13.794 1 64.05 ? C8 ADP 921 N 1 HETATM 20 N N7 ADP . . . E 4 86.691 57.032 -13.701 1 64.44 ? N7 ADP 921 N 1 HETATM 21 C C5 ADP . . . E 4 86.485 57.085 -12.4 1 63.55 ? C5 ADP 921 N 1 HETATM 22 C C6 ADP . . . E 4 85.369 57.536 -11.744 1 63.26 ? C6 ADP 921 N 1 HETATM 23 N N6 ADP . . . E 4 84.263 58.013 -12.3 1 64.53 ? N6 ADP 921 N 1 HETATM 24 N N1 ADP . . . E 4 85.447 57.508 -10.404 1 62.56 ? N1 ADP 921 N 1 HETATM 25 C C2 ADP . . . E 4 86.602 57.038 -9.826 1 62.75 ? C2 ADP 921 N 1 HETATM 26 N N3 ADP . . . E 4 87.717 56.579 -10.353 1 62.62 ? N3 ADP 921 N 1 HETATM 27 C C4 ADP . . . E 4 87.573 56.646 -11.682 1 63.04 ? C4 ADP 921 N 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #