data_5XDR # _model_server_result.job_id nAOO7_iK3FBI_FJzSN475g _model_server_result.datetime_utc '2024-12-12 19:24:09' _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 5xdr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 5XDR # _exptl.entry_id 5XDR _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 5XDR _cell.length_a 81.919 _cell.length_b 89.377 _cell.length_c 211.078 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XDR _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 A OG1 THR 62 A THR 167 1_555 E MG MG . A MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc2 B O3B ADP . A ADP 801 1_555 E MG MG . A MG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc3 E MG MG . A MG 804 1_555 F O HOH . A HOH 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? metalc ? metalc4 E MG MG . A MG 804 1_555 F O HOH . A HOH 922 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc5 E MG MG . A MG 804 1_555 F O HOH . A HOH 926 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? metalc ? metalc6 E MG MG . A MG 804 1_555 F O HOH . A HOH 936 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? # _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 5XDR _atom_sites.fract_transf_matrix[1][1] 0.012207 _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] 0.011189 _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] 0.004738 _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 1 801 1750 ADP ADP . C 3 SO4 A 1 802 1 SO4 SO4 . D 3 SO4 A 1 803 2 SO4 SO4 . E 4 MG A 1 804 1 MG MG . F 5 HOH A 1 901 48 HOH HOH . F 5 HOH A 2 902 4 HOH HOH . F 5 HOH A 3 903 72 HOH HOH . F 5 HOH A 4 904 81 HOH HOH . F 5 HOH A 5 905 77 HOH HOH . F 5 HOH A 6 906 58 HOH HOH . F 5 HOH A 7 907 62 HOH HOH . F 5 HOH A 8 908 10 HOH HOH . F 5 HOH A 9 909 21 HOH HOH . F 5 HOH A 10 910 1 HOH HOH . F 5 HOH A 11 911 15 HOH HOH . F 5 HOH A 12 912 32 HOH HOH . F 5 HOH A 13 913 74 HOH HOH . F 5 HOH A 14 914 23 HOH HOH . F 5 HOH A 15 915 9 HOH HOH . F 5 HOH A 16 916 44 HOH HOH . F 5 HOH A 17 917 11 HOH HOH . F 5 HOH A 18 918 2 HOH HOH . F 5 HOH A 19 919 17 HOH HOH . F 5 HOH A 20 920 76 HOH HOH . F 5 HOH A 21 921 49 HOH HOH . F 5 HOH A 22 922 78 HOH HOH . F 5 HOH A 23 923 30 HOH HOH . F 5 HOH A 24 924 61 HOH HOH . F 5 HOH A 25 925 68 HOH HOH . F 5 HOH A 26 926 3 HOH HOH . F 5 HOH A 27 927 16 HOH HOH . F 5 HOH A 28 928 5 HOH HOH . F 5 HOH A 29 929 35 HOH HOH . F 5 HOH A 30 930 24 HOH HOH . F 5 HOH A 31 931 31 HOH HOH . F 5 HOH A 32 932 51 HOH HOH . F 5 HOH A 33 933 29 HOH HOH . F 5 HOH A 34 934 28 HOH HOH . F 5 HOH A 35 935 83 HOH HOH . F 5 HOH A 36 936 80 HOH HOH . F 5 HOH A 37 937 7 HOH HOH . F 5 HOH A 38 938 13 HOH HOH . F 5 HOH A 39 939 47 HOH HOH . F 5 HOH A 40 940 63 HOH HOH . F 5 HOH A 41 941 60 HOH HOH . F 5 HOH A 42 942 56 HOH HOH . F 5 HOH A 43 943 67 HOH HOH . F 5 HOH A 44 944 87 HOH HOH . F 5 HOH A 45 945 12 HOH HOH . F 5 HOH A 46 946 52 HOH HOH . F 5 HOH A 47 947 37 HOH HOH . F 5 HOH A 48 948 22 HOH HOH . F 5 HOH A 49 949 38 HOH HOH . F 5 HOH A 50 950 86 HOH HOH . F 5 HOH A 51 951 19 HOH HOH . F 5 HOH A 52 952 33 HOH HOH . F 5 HOH A 53 953 79 HOH HOH . F 5 HOH A 54 954 26 HOH HOH . F 5 HOH A 55 955 64 HOH HOH . F 5 HOH A 56 956 18 HOH HOH . F 5 HOH A 57 957 88 HOH HOH . F 5 HOH A 58 958 54 HOH HOH . F 5 HOH A 59 959 41 HOH HOH . F 5 HOH A 60 960 46 HOH HOH . F 5 HOH A 61 961 45 HOH HOH . F 5 HOH A 62 962 34 HOH HOH . F 5 HOH A 63 963 20 HOH HOH . F 5 HOH A 64 964 55 HOH HOH . F 5 HOH A 65 965 8 HOH HOH . F 5 HOH A 66 966 42 HOH HOH . F 5 HOH A 67 967 65 HOH HOH . F 5 HOH A 68 968 40 HOH HOH . F 5 HOH A 69 969 73 HOH HOH . F 5 HOH A 70 970 69 HOH HOH . F 5 HOH A 71 971 39 HOH HOH . F 5 HOH A 72 972 53 HOH HOH . F 5 HOH A 73 973 14 HOH HOH . F 5 HOH A 74 974 27 HOH HOH . F 5 HOH A 75 975 6 HOH HOH . F 5 HOH A 76 976 71 HOH HOH . F 5 HOH A 77 977 66 HOH HOH . F 5 HOH A 78 978 36 HOH HOH . F 5 HOH A 79 979 50 HOH HOH . F 5 HOH A 80 980 25 HOH HOH . F 5 HOH A 81 981 57 HOH HOH . F 5 HOH A 82 982 91 HOH HOH . F 5 HOH A 83 983 84 HOH HOH . F 5 HOH A 84 984 70 HOH HOH . F 5 HOH A 85 985 43 HOH HOH . F 5 HOH A 86 986 59 HOH HOH . F 5 HOH A 87 987 89 HOH HOH . F 5 HOH A 88 988 94 HOH HOH . F 5 HOH A 89 989 82 HOH HOH . F 5 HOH A 90 990 93 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 19.763 -24.676 8.029 1 58.88 ? PB ADP 801 A 1 HETATM 2 O O1B ADP . . . B 2 19.128 -23.865 6.939 1 57.05 ? O1B ADP 801 A 1 HETATM 3 O O2B ADP . . . B 2 18.785 -25.536 8.796 1 62.6 ? O2B ADP 801 A 1 HETATM 4 O O3B ADP . . . B 2 20.703 -23.881 8.894 1 62.97 ? O3B ADP 801 A 1 HETATM 5 P PA ADP . . . B 2 22.201 -26.122 7.674 1 61.84 ? PA ADP 801 A 1 HETATM 6 O O1A ADP . . . B 2 23.172 -25.129 7.099 1 60.96 ? O1A ADP 801 A 1 HETATM 7 O O2A ADP . . . B 2 22.274 -26.374 9.164 1 66.75 ? O2A ADP 801 A 1 HETATM 8 O O3A ADP . . . B 2 20.692 -25.741 7.265 1 61.32 ? O3A ADP 801 A 1 HETATM 9 O O5' ADP . . . B 2 22.276 -27.528 6.906 1 70.82 ? O5' ADP 801 A 1 HETATM 10 C C5' ADP . . . B 2 23.434 -27.98 6.219 1 73.95 ? C5' ADP 801 A 1 HETATM 11 C C4' ADP . . . B 2 23.343 -29.475 5.888 1 77.26 ? C4' ADP 801 A 1 HETATM 12 O O4' ADP . . . B 2 24.638 -30.07 6.048 1 77.88 ? O4' ADP 801 A 1 HETATM 13 C C3' ADP . . . B 2 22.369 -30.308 6.727 1 81.04 ? C3' ADP 801 A 1 HETATM 14 O O3' ADP . . . B 2 21.122 -30.522 6.057 1 82.52 ? O3' ADP 801 A 1 HETATM 15 C C2' ADP . . . B 2 23.116 -31.604 6.958 1 81.99 ? C2' ADP 801 A 1 HETATM 16 O O2' ADP . . . B 2 22.807 -32.521 5.906 1 84.65 ? O2' ADP 801 A 1 HETATM 17 C C1' ADP . . . B 2 24.586 -31.215 6.903 1 79.52 ? C1' ADP 801 A 1 HETATM 18 N N9 ADP . . . B 2 25.124 -30.844 8.241 1 77.28 ? N9 ADP 801 A 1 HETATM 19 C C8 ADP . . . B 2 24.764 -29.765 8.971 1 76.12 ? C8 ADP 801 A 1 HETATM 20 N N7 ADP . . . B 2 25.443 -29.711 10.139 1 78.18 ? N7 ADP 801 A 1 HETATM 21 C C5 ADP . . . B 2 26.26 -30.773 10.174 1 77.1 ? C5 ADP 801 A 1 HETATM 22 C C6 ADP . . . B 2 27.253 -31.306 11.135 1 78.31 ? C6 ADP 801 A 1 HETATM 23 N N6 ADP . . . B 2 27.482 -30.658 12.305 1 79.5 ? N6 ADP 801 A 1 HETATM 24 N N1 ADP . . . B 2 27.907 -32.45 10.798 1 79.6 ? N1 ADP 801 A 1 HETATM 25 C C2 ADP . . . B 2 27.672 -33.097 9.628 1 78.66 ? C2 ADP 801 A 1 HETATM 26 N N3 ADP . . . B 2 26.778 -32.655 8.713 1 77.97 ? N3 ADP 801 A 1 HETATM 27 C C4 ADP . . . B 2 26.053 -31.521 8.921 1 77.12 ? C4 ADP 801 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 214 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 27 #