data_5ES7 # _model_server_result.job_id yj6syWXuZAy0yQguhQi2aQ _model_server_result.datetime_utc '2024-10-12 11:15:51' _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 5es7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":703}' # _entry.id 5ES7 # _exptl.entry_id 5ES7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 5ES7 _cell.length_a 160.943 _cell.length_b 160.943 _cell.length_c 137.581 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ES7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 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 _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" # 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 PG O1G APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 5ES7 _atom_sites.fract_transf_matrix[1][1] 0.006213 _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] 0.006213 _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] 0.007268 _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 FON A 1 701 586 FON FON . C 3 VAL A 1 702 587 VAL VLN . D 4 APC A 1 703 588 APC APC . E 5 HOH A 1 801 38 HOH HOH . E 5 HOH A 2 802 76 HOH HOH . E 5 HOH A 3 803 14 HOH HOH . E 5 HOH A 4 804 33 HOH HOH . E 5 HOH A 5 805 83 HOH HOH . E 5 HOH A 6 806 6 HOH HOH . E 5 HOH A 7 807 12 HOH HOH . E 5 HOH A 8 808 62 HOH HOH . E 5 HOH A 9 809 13 HOH HOH . E 5 HOH A 10 810 52 HOH HOH . E 5 HOH A 11 811 5 HOH HOH . E 5 HOH A 12 812 11 HOH HOH . E 5 HOH A 13 813 25 HOH HOH . E 5 HOH A 14 814 7 HOH HOH . E 5 HOH A 15 815 79 HOH HOH . E 5 HOH A 16 816 1 HOH HOH . E 5 HOH A 17 817 75 HOH HOH . E 5 HOH A 18 818 66 HOH HOH . E 5 HOH A 19 819 4 HOH HOH . E 5 HOH A 20 820 43 HOH HOH . E 5 HOH A 21 821 19 HOH HOH . E 5 HOH A 22 822 60 HOH HOH . E 5 HOH A 23 823 59 HOH HOH . E 5 HOH A 24 824 28 HOH HOH . E 5 HOH A 25 825 57 HOH HOH . E 5 HOH A 26 826 2 HOH HOH . E 5 HOH A 27 827 68 HOH HOH . E 5 HOH A 28 828 24 HOH HOH . E 5 HOH A 29 829 56 HOH HOH . E 5 HOH A 30 830 29 HOH HOH . E 5 HOH A 31 831 42 HOH HOH . E 5 HOH A 32 832 30 HOH HOH . E 5 HOH A 33 833 10 HOH HOH . E 5 HOH A 34 834 81 HOH HOH . E 5 HOH A 35 835 49 HOH HOH . E 5 HOH A 36 836 63 HOH HOH . E 5 HOH A 37 837 73 HOH HOH . E 5 HOH A 38 838 45 HOH HOH . E 5 HOH A 39 839 48 HOH HOH . E 5 HOH A 40 840 36 HOH HOH . E 5 HOH A 41 841 34 HOH HOH . E 5 HOH A 42 842 82 HOH HOH . E 5 HOH A 43 843 80 HOH HOH . E 5 HOH A 44 844 8 HOH HOH . E 5 HOH A 45 845 74 HOH HOH . E 5 HOH A 46 846 46 HOH HOH . E 5 HOH A 47 847 67 HOH HOH . E 5 HOH A 48 848 61 HOH HOH . E 5 HOH A 49 849 9 HOH HOH . E 5 HOH A 50 850 53 HOH HOH . E 5 HOH A 51 851 51 HOH HOH . E 5 HOH A 52 852 54 HOH HOH . E 5 HOH A 53 853 18 HOH HOH . E 5 HOH A 54 854 27 HOH HOH . E 5 HOH A 55 855 64 HOH HOH . E 5 HOH A 56 856 55 HOH HOH . E 5 HOH A 57 857 77 HOH HOH . E 5 HOH A 58 858 17 HOH HOH . E 5 HOH A 59 859 58 HOH HOH . E 5 HOH A 60 860 22 HOH HOH . E 5 HOH A 61 861 69 HOH HOH . E 5 HOH A 62 862 3 HOH HOH . E 5 HOH A 63 863 20 HOH HOH . E 5 HOH A 64 864 70 HOH HOH . E 5 HOH A 65 865 78 HOH HOH . E 5 HOH A 66 866 47 HOH HOH . E 5 HOH A 67 867 72 HOH HOH . E 5 HOH A 68 868 40 HOH HOH . E 5 HOH A 69 869 41 HOH HOH . E 5 HOH A 70 870 35 HOH HOH . E 5 HOH A 71 871 31 HOH HOH . E 5 HOH A 72 872 21 HOH HOH . E 5 HOH A 73 873 50 HOH HOH . E 5 HOH A 74 874 32 HOH HOH . E 5 HOH A 75 875 65 HOH HOH . E 5 HOH A 76 876 23 HOH HOH . E 5 HOH A 77 877 44 HOH HOH . E 5 HOH A 78 878 71 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 PA APC . . . D 4 186.892 -15.077 19.221 0.7 188.1 ? PA APC 703 A 1 HETATM 2 O O1A APC . . . D 4 185.977 -14.92 18.045 0.7 131.54 ? O1A APC 703 A 1 HETATM 3 O O2A APC . . . D 4 187.637 -16.395 19.103 0.7 153.58 -1 O2A APC 703 A 1 HETATM 4 C C3A APC . . . D 4 185.887 -15.084 20.785 0.7 130.42 ? C3A APC 703 A 1 HETATM 5 O O5' APC . . . D 4 187.996 -13.814 19.248 0.7 133.55 ? O5' APC 703 A 1 HETATM 6 C C5' APC . . . D 4 187.632 -12.508 18.896 0.7 112.39 ? C5' APC 703 A 1 HETATM 7 C C4' APC . . . D 4 186.424 -12.145 19.672 0.7 129.02 ? C4' APC 703 A 1 HETATM 8 O O4' APC . . . D 4 186.677 -12.232 20.921 0.7 134.64 ? O4' APC 703 A 1 HETATM 9 C C3' APC . . . D 4 185.947 -10.553 19.509 0.7 114.98 ? C3' APC 703 A 1 HETATM 10 O O3' APC . . . D 4 185.362 -10.311 18.2 0.7 109.71 ? O3' APC 703 A 1 HETATM 11 C C2' APC . . . D 4 185.07 -10.415 20.422 0.7 120.78 ? C2' APC 703 A 1 HETATM 12 O O2' APC . . . D 4 183.698 -10.695 19.88 0.7 101.45 ? O2' APC 703 A 1 HETATM 13 C C1' APC . . . D 4 185.448 -11.49 21.514 0.7 132.62 ? C1' APC 703 A 1 HETATM 14 N N9 APC . . . D 4 185.71 -10.958 22.711 0.7 123.93 ? N9 APC 703 A 1 HETATM 15 C C8 APC . . . D 4 186.877 -10.628 23.238 0.7 106.84 ? C8 APC 703 A 1 HETATM 16 N N7 APC . . . D 4 186.688 -10.143 24.472 0.7 107.39 ? N7 APC 703 A 1 HETATM 17 C C5 APC . . . D 4 185.374 -10.161 24.749 0.7 113.53 ? C5 APC 703 A 1 HETATM 18 C C6 APC . . . D 4 184.536 -9.803 25.827 0.7 96.06 ? C6 APC 703 A 1 HETATM 19 N N6 APC . . . D 4 185.061 -9.245 27.066 0.7 98.94 ? N6 APC 703 A 1 HETATM 20 N N1 APC . . . D 4 183.235 -9.971 25.724 0.7 97.62 ? N1 APC 703 A 1 HETATM 21 C C2 APC . . . D 4 182.695 -10.484 24.619 0.7 103.3 ? C2 APC 703 A 1 HETATM 22 N N3 APC . . . D 4 183.44 -10.823 23.598 0.7 87.76 ? N3 APC 703 A 1 HETATM 23 C C4 APC . . . D 4 184.767 -10.681 23.626 0.7 103.5 ? C4 APC 703 A 1 HETATM 24 H H3A1 APC . . . D 4 186.115 -15.879 21.291 0.7 156.5 ? H3A1 APC 703 A 1 HETATM 25 H H3A2 APC . . . D 4 184.949 -15.13 20.545 0.7 156.5 ? H3A2 APC 703 A 1 HETATM 26 H "H5'1" APC . . . D 4 188.354 -11.898 19.115 0.7 134.87 ? "H5'1" APC 703 A 1 HETATM 27 H "H5'2" APC . . . D 4 187.44 -12.463 17.946 0.7 134.87 ? "H5'2" APC 703 A 1 HETATM 28 H H4' APC . . . D 4 185.711 -12.715 19.45 0.7 154.82 ? H4' APC 703 A 1 HETATM 29 H H3' APC . . . D 4 186.673 -9.977 19.662 0.7 137.98 ? H3' APC 703 A 1 HETATM 30 H HO3' APC . . . D 4 185.151 -9.491 18.131 0.7 131.65 ? HO3' APC 703 A 1 HETATM 31 H H2' APC . . . D 4 185.114 -9.551 20.787 0.7 144.93 ? H2' APC 703 A 1 HETATM 32 H HO2' APC . . . D 4 183.612 -11.53 19.746 0.7 121.74 ? HO2' APC 703 A 1 HETATM 33 H H1' APC . . . D 4 184.737 -12.099 21.597 0.7 159.14 ? H1' APC 703 A 1 HETATM 34 H H8 APC . . . D 4 187.701 -10.721 22.818 0.7 128.2 ? H8 APC 703 A 1 HETATM 35 H HN61 APC . . . D 4 185.744 -9.615 27.453 0.7 118.73 ? HN61 APC 703 A 1 HETATM 36 H HN62 APC . . . D 4 184.691 -8.543 27.417 0.7 118.73 ? HN62 APC 703 A 1 HETATM 37 H H2 APC . . . D 4 181.774 -10.595 24.568 0.7 123.96 ? H2 APC 703 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 37 #