data_5DYG # _model_server_result.job_id Z7-V6UHl2KSHsGF-xo83EQ _model_server_result.datetime_utc '2025-06-29 12:50:21' _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 5dyg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":800}' # _entry.id 5DYG # _exptl.entry_id 5DYG _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 120 _cell.entry_id 5DYG _cell.length_a 145.584 _cell.length_b 145.584 _cell.length_c 84.002 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DYG _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_555 y,-x+y,z 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 0 0 0 6 'crystal symmetry operation' 6_555 x-y,x,z 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 0 0 0 # _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 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 5DYG _atom_sites.fract_transf_matrix[1][1] 0.006869 _atom_sites.fract_transf_matrix[1][2] 0.003966 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007932 _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] 0.011904 _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 1 800 800 ADP ADP . C 3 HOH A 1 901 25 HOH HOH . C 3 HOH A 2 902 31 HOH HOH . C 3 HOH A 3 903 107 HOH HOH . C 3 HOH A 4 904 61 HOH HOH . C 3 HOH A 5 905 100 HOH HOH . C 3 HOH A 6 906 85 HOH HOH . C 3 HOH A 7 907 45 HOH HOH . C 3 HOH A 8 908 35 HOH HOH . C 3 HOH A 9 909 63 HOH HOH . C 3 HOH A 10 910 46 HOH HOH . C 3 HOH A 11 911 41 HOH HOH . C 3 HOH A 12 912 48 HOH HOH . C 3 HOH A 13 913 87 HOH HOH . C 3 HOH A 14 914 66 HOH HOH . C 3 HOH A 15 915 76 HOH HOH . C 3 HOH A 16 916 64 HOH HOH . C 3 HOH A 17 917 52 HOH HOH . C 3 HOH A 18 918 89 HOH HOH . C 3 HOH A 19 919 71 HOH HOH . C 3 HOH A 20 920 26 HOH HOH . C 3 HOH A 21 921 42 HOH HOH . C 3 HOH A 22 922 74 HOH HOH . C 3 HOH A 23 923 88 HOH HOH . C 3 HOH A 24 924 10 HOH HOH . C 3 HOH A 25 925 17 HOH HOH . C 3 HOH A 26 926 58 HOH HOH . C 3 HOH A 27 927 40 HOH HOH . C 3 HOH A 28 928 60 HOH HOH . C 3 HOH A 29 929 43 HOH HOH . C 3 HOH A 30 930 14 HOH HOH . C 3 HOH A 31 931 51 HOH HOH . C 3 HOH A 32 932 106 HOH HOH . C 3 HOH A 33 933 59 HOH HOH . C 3 HOH A 34 934 12 HOH HOH . C 3 HOH A 35 935 2 HOH HOH . C 3 HOH A 36 936 5 HOH HOH . C 3 HOH A 37 937 1 HOH HOH . C 3 HOH A 38 938 50 HOH HOH . C 3 HOH A 39 939 33 HOH HOH . C 3 HOH A 40 940 68 HOH HOH . C 3 HOH A 41 941 56 HOH HOH . C 3 HOH A 42 942 94 HOH HOH . C 3 HOH A 43 943 9 HOH HOH . C 3 HOH A 44 944 11 HOH HOH . C 3 HOH A 45 945 97 HOH HOH . C 3 HOH A 46 946 90 HOH HOH . C 3 HOH A 47 947 53 HOH HOH . C 3 HOH A 48 948 65 HOH HOH . C 3 HOH A 49 949 6 HOH HOH . C 3 HOH A 50 950 16 HOH HOH . C 3 HOH A 51 951 80 HOH HOH . C 3 HOH A 52 952 44 HOH HOH . C 3 HOH A 53 953 54 HOH HOH . C 3 HOH A 54 954 105 HOH HOH . C 3 HOH A 55 955 84 HOH HOH . C 3 HOH A 56 956 67 HOH HOH . C 3 HOH A 57 957 98 HOH HOH . C 3 HOH A 58 958 72 HOH HOH . C 3 HOH A 59 959 22 HOH HOH . C 3 HOH A 60 960 20 HOH HOH . C 3 HOH A 61 961 47 HOH HOH . C 3 HOH A 62 962 15 HOH HOH . C 3 HOH A 63 963 86 HOH HOH . C 3 HOH A 64 964 77 HOH HOH . C 3 HOH A 65 965 82 HOH HOH . C 3 HOH A 66 966 21 HOH HOH . C 3 HOH A 67 967 30 HOH HOH . C 3 HOH A 68 968 57 HOH HOH . C 3 HOH A 69 969 4 HOH HOH . C 3 HOH A 70 970 23 HOH HOH . C 3 HOH A 71 971 91 HOH HOH . C 3 HOH A 72 972 99 HOH HOH . C 3 HOH A 73 973 8 HOH HOH . C 3 HOH A 74 974 18 HOH HOH . C 3 HOH A 75 975 78 HOH HOH . C 3 HOH A 76 976 7 HOH HOH . C 3 HOH A 77 977 96 HOH HOH . C 3 HOH A 78 978 103 HOH HOH . C 3 HOH A 79 979 95 HOH HOH . C 3 HOH A 80 980 27 HOH HOH . C 3 HOH A 81 981 36 HOH HOH . C 3 HOH A 82 982 93 HOH HOH . C 3 HOH A 83 983 81 HOH HOH . C 3 HOH A 84 984 34 HOH HOH . C 3 HOH A 85 985 104 HOH HOH . C 3 HOH A 86 986 24 HOH HOH . C 3 HOH A 87 987 79 HOH HOH . C 3 HOH A 88 988 3 HOH HOH . C 3 HOH A 89 989 102 HOH HOH . C 3 HOH A 90 990 32 HOH HOH . C 3 HOH A 91 991 73 HOH HOH . C 3 HOH A 92 992 92 HOH HOH . C 3 HOH A 93 993 83 HOH HOH . C 3 HOH A 94 994 13 HOH HOH . C 3 HOH A 95 995 108 HOH HOH . C 3 HOH A 96 996 28 HOH HOH . C 3 HOH A 97 997 29 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 -30.372 -11.861 16.694 1 33.69 ? PB ADP 800 A 1 HETATM 2 O O1B ADP . . . B 2 -30.136 -12.677 15.419 1 30.28 ? O1B ADP 800 A 1 HETATM 3 O O2B ADP . . . B 2 -30.028 -12.751 17.908 1 27.5 ? O2B ADP 800 A 1 HETATM 4 O O3B ADP . . . B 2 -29.783 -10.453 16.68 1 35.6 ? O3B ADP 800 A 1 HETATM 5 P PA ADP . . . B 2 -32.778 -11.545 18.251 1 35.34 ? PA ADP 800 A 1 HETATM 6 O O1A ADP . . . B 2 -33.176 -12.968 18.487 1 26.29 ? O1A ADP 800 A 1 HETATM 7 O O2A ADP . . . B 2 -32.108 -10.71 19.332 1 31.13 ? O2A ADP 800 A 1 HETATM 8 O O3A ADP . . . B 2 -31.978 -11.413 16.795 1 32.66 ? O3A ADP 800 A 1 HETATM 9 O O5' ADP . . . B 2 -34.156 -10.767 18.076 1 37 ? O5' ADP 800 A 1 HETATM 10 C C5' ADP . . . B 2 -34.675 -9.975 17.042 1 34.49 ? C5' ADP 800 A 1 HETATM 11 C C4' ADP . . . B 2 -36.183 -10.027 17.267 1 31.29 ? C4' ADP 800 A 1 HETATM 12 O O4' ADP . . . B 2 -36.864 -10.078 16.008 1 27.25 ? O4' ADP 800 A 1 HETATM 13 C C3' ADP . . . B 2 -36.619 -11.278 18.043 1 30.91 ? C3' ADP 800 A 1 HETATM 14 O O3' ADP . . . B 2 -36.649 -10.966 19.433 1 33.3 ? O3' ADP 800 A 1 HETATM 15 C C2' ADP . . . B 2 -37.964 -11.555 17.499 1 27.91 ? C2' ADP 800 A 1 HETATM 16 O O2' ADP . . . B 2 -38.798 -10.565 18.09 1 33 ? O2' ADP 800 A 1 HETATM 17 C C1' ADP . . . B 2 -37.815 -11.125 16.055 1 27.09 ? C1' ADP 800 A 1 HETATM 18 N N9 ADP . . . B 2 -37.373 -12.214 15.223 1 23.34 ? N9 ADP 800 A 1 HETATM 19 C C8 ADP . . . B 2 -36.187 -12.392 14.669 1 22.64 ? C8 ADP 800 A 1 HETATM 20 N N7 ADP . . . B 2 -36.197 -13.527 13.926 1 22.96 ? N7 ADP 800 A 1 HETATM 21 C C5 ADP . . . B 2 -37.399 -14.087 14.027 1 22.6 ? C5 ADP 800 A 1 HETATM 22 C C6 ADP . . . B 2 -38.062 -15.29 13.524 1 23.52 ? C6 ADP 800 A 1 HETATM 23 N N6 ADP . . . B 2 -37.385 -16.165 12.72 1 22.46 ? N6 ADP 800 A 1 HETATM 24 N N1 ADP . . . B 2 -39.367 -15.481 13.881 1 21.39 ? N1 ADP 800 A 1 HETATM 25 C C2 ADP . . . B 2 -40.017 -14.614 14.665 1 23.07 ? C2 ADP 800 A 1 HETATM 26 N N3 ADP . . . B 2 -39.446 -13.511 15.159 1 21.5 ? N3 ADP 800 A 1 HETATM 27 C C4 ADP . . . B 2 -38.17 -13.212 14.894 1 23.28 ? C4 ADP 800 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #