data_3BXZ # _model_server_result.job_id yP7rUVCFRdnuptoGzuJonA _model_server_result.datetime_utc '2024-10-19 13:21:46' _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 3bxz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":902}' # _entry.id 3BXZ # _exptl.entry_id 3BXZ _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 128.82 _cell.angle_gamma 90 _cell.entry_id 3BXZ _cell.length_a 177.823 _cell.length_b 71.361 _cell.length_c 119.536 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BXZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _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,H,I,J _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 H N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _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 _struct_conn.pdbx_value_order metalc ? metalc1 E O1B ADP . A ADP 901 1_555 C MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc2 C MG MG . A MG 903 1_555 I O HOH . A HOH 966 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc3 C MG MG . A MG 903 1_555 I O HOH . A HOH 967 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? # _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 3BXZ _atom_sites.fract_transf_matrix[1][1] 0.005624 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004525 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014013 _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] 0.010737 _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 C 2 MG A 1 903 903 MG MG . D 3 SPD A 1 905 905 SPD SPD . E 4 ADP A 1 901 901 ADP ADP . F 2 MG B 1 904 904 MG MG . G 3 SPD B 1 906 906 SPD SPD . H 4 ADP B 1 902 902 ADP ADP . I 5 HOH A 1 906 1 HOH WAT . I 5 HOH A 2 907 3 HOH WAT . I 5 HOH A 3 908 4 HOH WAT . I 5 HOH A 4 909 5 HOH WAT . I 5 HOH A 5 910 8 HOH WAT . I 5 HOH A 6 911 9 HOH WAT . I 5 HOH A 7 912 10 HOH WAT . I 5 HOH A 8 913 11 HOH WAT . I 5 HOH A 9 914 14 HOH WAT . I 5 HOH A 10 915 22 HOH WAT . I 5 HOH A 11 916 23 HOH WAT . I 5 HOH A 12 917 32 HOH WAT . I 5 HOH A 13 918 33 HOH WAT . I 5 HOH A 14 919 34 HOH WAT . I 5 HOH A 15 920 35 HOH WAT . I 5 HOH A 16 921 36 HOH WAT . I 5 HOH A 17 922 37 HOH WAT . I 5 HOH A 18 923 39 HOH WAT . I 5 HOH A 19 924 41 HOH WAT . I 5 HOH A 20 925 42 HOH WAT . I 5 HOH A 21 926 43 HOH WAT . I 5 HOH A 22 927 44 HOH WAT . I 5 HOH A 23 928 45 HOH WAT . I 5 HOH A 24 929 48 HOH WAT . I 5 HOH A 25 930 52 HOH WAT . I 5 HOH A 26 931 53 HOH WAT . I 5 HOH A 27 932 56 HOH WAT . I 5 HOH A 28 933 57 HOH WAT . I 5 HOH A 29 934 58 HOH WAT . I 5 HOH A 30 935 60 HOH WAT . I 5 HOH A 31 936 62 HOH WAT . I 5 HOH A 32 937 64 HOH WAT . I 5 HOH A 33 938 67 HOH WAT . I 5 HOH A 34 939 70 HOH WAT . I 5 HOH A 35 940 72 HOH WAT . I 5 HOH A 36 941 73 HOH WAT . I 5 HOH A 37 942 76 HOH WAT . I 5 HOH A 38 943 77 HOH WAT . I 5 HOH A 39 944 80 HOH WAT . I 5 HOH A 40 945 82 HOH WAT . I 5 HOH A 41 946 84 HOH WAT . I 5 HOH A 42 947 85 HOH WAT . I 5 HOH A 43 948 88 HOH WAT . I 5 HOH A 44 949 89 HOH WAT . I 5 HOH A 45 950 91 HOH WAT . I 5 HOH A 46 951 93 HOH WAT . I 5 HOH A 47 952 94 HOH WAT . I 5 HOH A 48 953 95 HOH WAT . I 5 HOH A 49 954 98 HOH WAT . I 5 HOH A 50 955 99 HOH WAT . I 5 HOH A 51 956 102 HOH WAT . I 5 HOH A 52 957 104 HOH WAT . I 5 HOH A 53 958 105 HOH WAT . I 5 HOH A 54 959 107 HOH WAT . I 5 HOH A 55 960 108 HOH WAT . I 5 HOH A 56 961 109 HOH WAT . I 5 HOH A 57 962 110 HOH WAT . I 5 HOH A 58 963 111 HOH WAT . I 5 HOH A 59 964 114 HOH WAT . I 5 HOH A 60 965 116 HOH WAT . I 5 HOH A 61 966 117 HOH WAT . I 5 HOH A 62 967 118 HOH WAT . I 5 HOH A 63 968 123 HOH WAT . I 5 HOH A 64 969 125 HOH WAT . I 5 HOH A 65 970 129 HOH WAT . I 5 HOH A 66 971 130 HOH WAT . I 5 HOH A 67 972 132 HOH WAT . I 5 HOH A 68 973 134 HOH WAT . I 5 HOH A 69 974 138 HOH WAT . I 5 HOH A 70 975 140 HOH WAT . I 5 HOH A 71 976 143 HOH WAT . I 5 HOH A 72 977 144 HOH WAT . I 5 HOH A 73 978 145 HOH WAT . I 5 HOH A 74 979 146 HOH WAT . I 5 HOH A 75 980 147 HOH WAT . I 5 HOH A 76 981 148 HOH WAT . I 5 HOH A 77 982 152 HOH WAT . I 5 HOH A 78 983 153 HOH WAT . I 5 HOH A 79 984 154 HOH WAT . I 5 HOH A 80 985 155 HOH WAT . I 5 HOH A 81 986 156 HOH WAT . I 5 HOH A 82 987 157 HOH WAT . I 5 HOH A 83 988 158 HOH WAT . I 5 HOH A 84 989 161 HOH WAT . I 5 HOH A 85 990 162 HOH WAT . I 5 HOH A 86 991 164 HOH WAT . I 5 HOH A 87 992 166 HOH WAT . I 5 HOH A 88 993 169 HOH WAT . I 5 HOH A 89 994 170 HOH WAT . J 5 HOH B 1 907 2 HOH WAT . J 5 HOH B 2 908 6 HOH WAT . J 5 HOH B 3 909 7 HOH WAT . J 5 HOH B 4 910 12 HOH WAT . J 5 HOH B 5 911 13 HOH WAT . J 5 HOH B 6 912 15 HOH WAT . J 5 HOH B 7 913 16 HOH WAT . J 5 HOH B 8 914 17 HOH WAT . J 5 HOH B 9 915 18 HOH WAT . J 5 HOH B 10 916 19 HOH WAT . J 5 HOH B 11 917 20 HOH WAT . J 5 HOH B 12 918 21 HOH WAT . J 5 HOH B 13 919 24 HOH WAT . J 5 HOH B 14 920 25 HOH WAT . J 5 HOH B 15 921 26 HOH WAT . J 5 HOH B 16 922 27 HOH WAT . J 5 HOH B 17 923 28 HOH WAT . J 5 HOH B 18 924 29 HOH WAT . J 5 HOH B 19 925 30 HOH WAT . J 5 HOH B 20 926 31 HOH WAT . J 5 HOH B 21 927 38 HOH WAT . J 5 HOH B 22 928 40 HOH WAT . J 5 HOH B 23 929 46 HOH WAT . J 5 HOH B 24 930 47 HOH WAT . J 5 HOH B 25 931 49 HOH WAT . J 5 HOH B 26 932 50 HOH WAT . J 5 HOH B 27 933 51 HOH WAT . J 5 HOH B 28 934 54 HOH WAT . J 5 HOH B 29 935 55 HOH WAT . J 5 HOH B 30 936 59 HOH WAT . J 5 HOH B 31 937 61 HOH WAT . J 5 HOH B 32 938 63 HOH WAT . J 5 HOH B 33 939 65 HOH WAT . J 5 HOH B 34 940 66 HOH WAT . J 5 HOH B 35 941 68 HOH WAT . J 5 HOH B 36 942 69 HOH WAT . J 5 HOH B 37 943 71 HOH WAT . J 5 HOH B 38 944 74 HOH WAT . J 5 HOH B 39 945 75 HOH WAT . J 5 HOH B 40 946 78 HOH WAT . J 5 HOH B 41 947 79 HOH WAT . J 5 HOH B 42 948 81 HOH WAT . J 5 HOH B 43 949 83 HOH WAT . J 5 HOH B 44 950 86 HOH WAT . J 5 HOH B 45 951 87 HOH WAT . J 5 HOH B 46 952 90 HOH WAT . J 5 HOH B 47 953 92 HOH WAT . J 5 HOH B 48 954 96 HOH WAT . J 5 HOH B 49 955 97 HOH WAT . J 5 HOH B 50 956 100 HOH WAT . J 5 HOH B 51 957 101 HOH WAT . J 5 HOH B 52 958 103 HOH WAT . J 5 HOH B 53 959 106 HOH WAT . J 5 HOH B 54 960 112 HOH WAT . J 5 HOH B 55 961 113 HOH WAT . J 5 HOH B 56 962 115 HOH WAT . J 5 HOH B 57 963 119 HOH WAT . J 5 HOH B 58 964 120 HOH WAT . J 5 HOH B 59 965 121 HOH WAT . J 5 HOH B 60 966 122 HOH WAT . J 5 HOH B 61 967 124 HOH WAT . J 5 HOH B 62 968 126 HOH WAT . J 5 HOH B 63 969 127 HOH WAT . J 5 HOH B 64 970 128 HOH WAT . J 5 HOH B 65 971 131 HOH WAT . J 5 HOH B 66 972 133 HOH WAT . J 5 HOH B 67 973 135 HOH WAT . J 5 HOH B 68 974 136 HOH WAT . J 5 HOH B 69 975 137 HOH WAT . J 5 HOH B 70 976 139 HOH WAT . J 5 HOH B 71 977 141 HOH WAT . J 5 HOH B 72 978 142 HOH WAT . J 5 HOH B 73 979 149 HOH WAT . J 5 HOH B 74 980 150 HOH WAT . J 5 HOH B 75 981 151 HOH WAT . J 5 HOH B 76 982 159 HOH WAT . J 5 HOH B 77 983 160 HOH WAT . J 5 HOH B 78 984 163 HOH WAT . J 5 HOH B 79 985 165 HOH WAT . J 5 HOH B 80 986 167 HOH WAT . J 5 HOH B 81 987 168 HOH WAT . J 5 HOH B 82 988 171 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 . . . H 4 16.946 31.076 50.113 1 64.46 ? PB ADP 902 B 1 HETATM 2 O O1B ADP . . . H 4 17.627 30.353 48.982 1 67.67 ? O1B ADP 902 B 1 HETATM 3 O O2B ADP . . . H 4 18.026 31.399 51.281 1 65.48 ? O2B ADP 902 B 1 HETATM 4 O O3B ADP . . . H 4 16.315 32.319 49.569 1 65.36 ? O3B ADP 902 B 1 HETATM 5 P PA ADP . . . H 4 15.702 29.264 51.947 1 66.67 ? PA ADP 902 B 1 HETATM 6 O O1A ADP . . . H 4 16.935 29.246 52.768 1 68.41 ? O1A ADP 902 B 1 HETATM 7 O O2A ADP . . . H 4 15.343 27.959 51.44 1 69.34 ? O2A ADP 902 B 1 HETATM 8 O O3A ADP . . . H 4 15.838 30.191 50.715 1 66.15 ? O3A ADP 902 B 1 HETATM 9 O O5' ADP . . . H 4 14.482 29.835 52.665 1 70.34 ? O5' ADP 902 B 1 HETATM 10 C C5' ADP . . . H 4 14.463 31.078 53.337 1 71 ? C5' ADP 902 B 1 HETATM 11 C C4' ADP . . . H 4 13.75 30.769 54.687 1 69.82 ? C4' ADP 902 B 1 HETATM 12 O O4' ADP . . . H 4 12.577 31.574 54.778 1 70.87 ? O4' ADP 902 B 1 HETATM 13 C C3' ADP . . . H 4 13.257 29.301 54.852 1 69.29 ? C3' ADP 902 B 1 HETATM 14 O O3' ADP . . . H 4 13.841 28.676 55.98 1 69.24 ? O3' ADP 902 B 1 HETATM 15 C C2' ADP . . . H 4 11.757 29.295 55.022 1 69.6 ? C2' ADP 902 B 1 HETATM 16 O O2' ADP . . . H 4 11.379 28.653 56.248 1 72.66 ? O2' ADP 902 B 1 HETATM 17 C C1' ADP . . . H 4 11.386 30.744 54.978 1 70.68 ? C1' ADP 902 B 1 HETATM 18 N N9 ADP . . . H 4 10.33 31.088 53.943 1 71.45 ? N9 ADP 902 B 1 HETATM 19 C C8 ADP . . . H 4 10.495 31.19 52.582 1 71.53 ? C8 ADP 902 B 1 HETATM 20 N N7 ADP . . . H 4 9.306 31.535 52.02 1 71.17 ? N7 ADP 902 B 1 HETATM 21 C C5 ADP . . . H 4 8.374 31.648 52.981 1 71.33 ? C5 ADP 902 B 1 HETATM 22 C C6 ADP . . . H 4 6.996 31.992 53.057 1 71.24 ? C6 ADP 902 B 1 HETATM 23 N N6 ADP . . . H 4 6.277 32.288 51.954 1 71.25 ? N6 ADP 902 B 1 HETATM 24 N N1 ADP . . . H 4 6.361 32.005 54.307 1 72.16 ? N1 ADP 902 B 1 HETATM 25 C C2 ADP . . . H 4 7.027 31.716 55.474 1 71.57 ? C2 ADP 902 B 1 HETATM 26 N N3 ADP . . . H 4 8.348 31.398 55.423 1 70.28 ? N3 ADP 902 B 1 HETATM 27 C C4 ADP . . . H 4 9.057 31.359 54.222 1 71.6 ? C4 ADP 902 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #