data_2NCD # _model_server_result.job_id iC0Ln5oqt1UXWgQJvQuDKA _model_server_result.datetime_utc '2025-07-26 20:12:08' _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 2ncd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":800}' # _entry.id 2NCD # _exptl.entry_id 2NCD _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 120 _cell.entry_id 2NCD _cell.length_a 123 _cell.length_b 123 _cell.length_c 121.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NCD _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # 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' 9_555 -x,-x+y,-z+2/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 80.733333 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id F _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 2NCD _atom_sites.fract_transf_matrix[1][1] 0.00813 _atom_sites.fract_transf_matrix[1][2] 0.004694 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009388 _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] 0.008258 _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 SO4 A 1 1110 1110 SO4 SO4 . C 2 SO4 A 1 1111 1111 SO4 SO4 . D 2 SO4 A 1 1112 1112 SO4 SO4 . E 2 SO4 A 1 1113 1113 SO4 SO4 . F 3 ADP A 1 800 800 ADP ADP . G 4 HOH A 1 901 901 HOH HOH . G 4 HOH A 2 902 902 HOH HOH . G 4 HOH A 3 903 903 HOH HOH . G 4 HOH A 4 904 904 HOH HOH . G 4 HOH A 5 905 905 HOH HOH . G 4 HOH A 6 906 906 HOH HOH . G 4 HOH A 7 907 907 HOH HOH . G 4 HOH A 8 908 908 HOH HOH . G 4 HOH A 9 909 909 HOH HOH . G 4 HOH A 10 910 910 HOH HOH . G 4 HOH A 11 911 911 HOH HOH . G 4 HOH A 12 912 912 HOH HOH . G 4 HOH A 13 913 913 HOH HOH . G 4 HOH A 14 914 914 HOH HOH . G 4 HOH A 15 915 915 HOH HOH . G 4 HOH A 16 916 916 HOH HOH . G 4 HOH A 17 917 917 HOH HOH . G 4 HOH A 18 918 918 HOH HOH . G 4 HOH A 19 919 919 HOH HOH . G 4 HOH A 20 920 920 HOH HOH . G 4 HOH A 21 921 921 HOH HOH . G 4 HOH A 22 922 922 HOH HOH . G 4 HOH A 23 923 923 HOH HOH . G 4 HOH A 24 924 924 HOH HOH . G 4 HOH A 25 925 925 HOH HOH . G 4 HOH A 26 926 926 HOH HOH . G 4 HOH A 27 927 927 HOH HOH . G 4 HOH A 28 928 928 HOH HOH . G 4 HOH A 29 929 929 HOH HOH . G 4 HOH A 30 930 930 HOH HOH . G 4 HOH A 31 931 931 HOH HOH . G 4 HOH A 32 932 932 HOH HOH . G 4 HOH A 33 933 933 HOH HOH . G 4 HOH A 34 934 934 HOH HOH . G 4 HOH A 35 935 935 HOH HOH . G 4 HOH A 36 936 936 HOH HOH . G 4 HOH A 37 937 937 HOH HOH . G 4 HOH A 38 938 938 HOH HOH . G 4 HOH A 39 939 939 HOH HOH . G 4 HOH A 40 940 940 HOH HOH . G 4 HOH A 41 941 941 HOH HOH . G 4 HOH A 42 942 942 HOH HOH . G 4 HOH A 43 943 943 HOH HOH . G 4 HOH A 44 944 944 HOH HOH . G 4 HOH A 45 945 945 HOH HOH . G 4 HOH A 46 946 946 HOH HOH . G 4 HOH A 47 947 947 HOH HOH . G 4 HOH A 48 948 948 HOH HOH . G 4 HOH A 49 949 949 HOH HOH . G 4 HOH A 50 950 950 HOH HOH . G 4 HOH A 51 951 951 HOH HOH . G 4 HOH A 52 952 952 HOH HOH . G 4 HOH A 53 953 953 HOH HOH . G 4 HOH A 54 954 954 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 . . . F 3 5.977 50.774 50.045 1 100 ? PB ADP 800 A 1 HETATM 2 O O1B ADP . . . F 3 7.255 50.919 50.791 1 100 ? O1B ADP 800 A 1 HETATM 3 O O2B ADP . . . F 3 5.817 49.569 49.19 1 98.42 ? O2B ADP 800 A 1 HETATM 4 O O3B ADP . . . F 3 4.798 51.093 50.874 1 100 ? O3B ADP 800 A 1 HETATM 5 P PA ADP . . . F 3 5.871 52.475 47.389 1 100 ? PA ADP 800 A 1 HETATM 6 O O1A ADP . . . F 3 6.51 51.415 46.566 1 100 ? O1A ADP 800 A 1 HETATM 7 O O2A ADP . . . F 3 4.476 52.927 47.169 1 100 ? O2A ADP 800 A 1 HETATM 8 O O3A ADP . . . F 3 6.003 52.033 49.032 1 100 ? O3A ADP 800 A 1 HETATM 9 O O5' ADP . . . F 3 6.657 53.837 46.883 1 100 ? O5' ADP 800 A 1 HETATM 10 C C5' ADP . . . F 3 6.638 54.544 45.602 1 100 ? C5' ADP 800 A 1 HETATM 11 C C4' ADP . . . F 3 7.906 54.99 44.777 1 96.27 ? C4' ADP 800 A 1 HETATM 12 O O4' ADP . . . F 3 8.32 54.097 43.658 1 100 ? O4' ADP 800 A 1 HETATM 13 C C3' ADP . . . F 3 7.671 56.327 44.055 1 90.27 ? C3' ADP 800 A 1 HETATM 14 O O3' ADP . . . F 3 8.751 57.249 44.243 1 90.76 ? O3' ADP 800 A 1 HETATM 15 C C2' ADP . . . F 3 7.35 55.992 42.596 1 85.69 ? C2' ADP 800 A 1 HETATM 16 O O2' ADP . . . F 3 8.095 56.77 41.651 1 83.22 ? O2' ADP 800 A 1 HETATM 17 C C1' ADP . . . F 3 7.612 54.488 42.412 1 81.5 ? C1' ADP 800 A 1 HETATM 18 N N9 ADP . . . F 3 6.454 53.701 41.784 1 63.18 ? N9 ADP 800 A 1 HETATM 19 C C8 ADP . . . F 3 5.626 52.784 42.339 1 54.11 ? C8 ADP 800 A 1 HETATM 20 N N7 ADP . . . F 3 4.643 52.372 41.548 1 48.25 ? N7 ADP 800 A 1 HETATM 21 C C5 ADP . . . F 3 4.915 53.024 40.442 1 46.93 ? C5 ADP 800 A 1 HETATM 22 C C6 ADP . . . F 3 4.169 52.972 39.266 1 43.42 ? C6 ADP 800 A 1 HETATM 23 N N6 ADP . . . F 3 3.039 52.284 39.214 1 39.68 ? N6 ADP 800 A 1 HETATM 24 N N1 ADP . . . F 3 4.59 53.73 38.217 1 44.38 ? N1 ADP 800 A 1 HETATM 25 C C2 ADP . . . F 3 5.69 54.508 38.284 1 52.2 ? C2 ADP 800 A 1 HETATM 26 N N3 ADP . . . F 3 6.39 54.551 39.436 1 51.88 ? N3 ADP 800 A 1 HETATM 27 C C4 ADP . . . F 3 6.028 53.838 40.532 1 51.64 ? C4 ADP 800 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #