data_4J97 # _model_server_result.job_id 1y7O1ddR5lIzfUQJZbQuxQ _model_server_result.datetime_utc '2024-10-12 13:23:50' _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 4j97 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":801}' # _entry.id 4J97 # _exptl.entry_id 4J97 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 92.39 _cell.angle_beta 112.19 _cell.angle_gamma 115.98 _cell.entry_id 4J97 _cell.length_a 70.584 _cell.length_b 70.278 _cell.length_c 85.499 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4J97 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 PISA dimeric 2 software_defined_assembly 5 PISA dimeric 2 software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,N 1 1 B,H,I,O 2 1 C,J,K,P 3 1 D,L,M,Q 4 1 A,E,F,G,N 5 1 C,J,K,P 5 2 B,H,I,O 6 1 D,L,M,Q 6 3 # 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' 1_444 x-1,y-1,z-1 1 0 0 0 1 0 0 0 1 -7.507011 -43.474467 -76.675939 3 'crystal symmetry operation' 1_445 x-1,y-1,z 1 0 0 0 1 0 0 0 1 -39.798203 -63.176198 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 H N N ? 2 J N N ? 2 L N N # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]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 ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 4J97 _atom_sites.fract_transf_matrix[1][1] 0.014168 _atom_sites.fract_transf_matrix[1][2] 0.006904 _atom_sites.fract_transf_matrix[1][3] 0.00774 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015829 _atom_sites.fract_transf_matrix[2][3] 0.004067 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.013042 _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 E 2 ACP A 1 801 801 ACP ACP . F 3 SO4 A 1 802 802 SO4 SO4 . G 3 SO4 A 1 803 803 SO4 SO4 . H 2 ACP B 1 801 801 ACP ACP . I 3 SO4 B 1 802 802 SO4 SO4 . J 2 ACP C 1 801 801 ACP ACP . K 3 SO4 C 1 802 802 SO4 SO4 . L 2 ACP D 1 801 801 ACP ACP . M 3 SO4 D 1 802 802 SO4 SO4 . N 4 HOH A 1 901 901 HOH HOH . N 4 HOH A 2 902 902 HOH HOH . N 4 HOH A 3 903 903 HOH HOH . N 4 HOH A 4 904 904 HOH HOH . N 4 HOH A 5 905 905 HOH HOH . N 4 HOH A 6 906 906 HOH HOH . N 4 HOH A 7 907 907 HOH HOH . N 4 HOH A 8 908 908 HOH HOH . N 4 HOH A 9 909 909 HOH HOH . N 4 HOH A 10 910 910 HOH HOH . N 4 HOH A 11 911 911 HOH HOH . N 4 HOH A 12 912 912 HOH HOH . N 4 HOH A 13 913 913 HOH HOH . N 4 HOH A 14 914 914 HOH HOH . N 4 HOH A 15 915 915 HOH HOH . N 4 HOH A 16 916 916 HOH HOH . N 4 HOH A 17 917 918 HOH HOH . N 4 HOH A 18 918 919 HOH HOH . N 4 HOH A 19 919 920 HOH HOH . N 4 HOH A 20 920 921 HOH HOH . N 4 HOH A 21 921 922 HOH HOH . N 4 HOH A 22 922 923 HOH HOH . N 4 HOH A 23 923 924 HOH HOH . N 4 HOH A 24 924 925 HOH HOH . N 4 HOH A 25 925 926 HOH HOH . N 4 HOH A 26 926 927 HOH HOH . N 4 HOH A 27 927 928 HOH HOH . N 4 HOH A 28 928 929 HOH HOH . N 4 HOH A 29 929 931 HOH HOH . N 4 HOH A 30 930 1 HOH HOH . O 4 HOH B 1 901 901 HOH HOH . O 4 HOH B 2 902 902 HOH HOH . O 4 HOH B 3 903 903 HOH HOH . O 4 HOH B 4 904 904 HOH HOH . O 4 HOH B 5 905 905 HOH HOH . O 4 HOH B 6 906 906 HOH HOH . O 4 HOH B 7 907 907 HOH HOH . O 4 HOH B 8 908 908 HOH HOH . O 4 HOH B 9 909 909 HOH HOH . O 4 HOH B 10 910 910 HOH HOH . O 4 HOH B 11 911 911 HOH HOH . O 4 HOH B 12 912 912 HOH HOH . O 4 HOH B 13 913 913 HOH HOH . O 4 HOH B 14 914 914 HOH HOH . O 4 HOH B 15 915 915 HOH HOH . O 4 HOH B 16 916 916 HOH HOH . O 4 HOH B 17 917 917 HOH HOH . O 4 HOH B 18 918 918 HOH HOH . O 4 HOH B 19 919 919 HOH HOH . O 4 HOH B 20 920 920 HOH HOH . O 4 HOH B 21 921 921 HOH HOH . O 4 HOH B 22 922 922 HOH HOH . O 4 HOH B 23 923 923 HOH HOH . O 4 HOH B 24 924 924 HOH HOH . O 4 HOH B 25 925 925 HOH HOH . O 4 HOH B 26 926 926 HOH HOH . O 4 HOH B 27 927 927 HOH HOH . O 4 HOH B 28 928 928 HOH HOH . O 4 HOH B 29 929 929 HOH HOH . O 4 HOH B 30 930 930 HOH HOH . O 4 HOH B 31 931 931 HOH HOH . O 4 HOH B 32 932 932 HOH HOH . O 4 HOH B 33 933 933 HOH HOH . O 4 HOH B 34 934 935 HOH HOH . O 4 HOH B 35 935 936 HOH HOH . O 4 HOH B 36 936 937 HOH HOH . O 4 HOH B 37 937 938 HOH HOH . P 4 HOH C 1 901 901 HOH HOH . P 4 HOH C 2 902 902 HOH HOH . P 4 HOH C 3 903 903 HOH HOH . P 4 HOH C 4 904 904 HOH HOH . P 4 HOH C 5 905 905 HOH HOH . P 4 HOH C 6 906 906 HOH HOH . P 4 HOH C 7 907 907 HOH HOH . P 4 HOH C 8 908 908 HOH HOH . P 4 HOH C 9 909 909 HOH HOH . P 4 HOH C 10 910 910 HOH HOH . P 4 HOH C 11 911 911 HOH HOH . P 4 HOH C 12 912 912 HOH HOH . P 4 HOH C 13 913 913 HOH HOH . P 4 HOH C 14 914 914 HOH HOH . P 4 HOH C 15 915 915 HOH HOH . P 4 HOH C 16 916 916 HOH HOH . P 4 HOH C 17 917 917 HOH HOH . P 4 HOH C 18 918 918 HOH HOH . P 4 HOH C 19 919 919 HOH HOH . P 4 HOH C 20 920 920 HOH HOH . P 4 HOH C 21 921 921 HOH HOH . P 4 HOH C 22 922 922 HOH HOH . P 4 HOH C 23 923 923 HOH HOH . P 4 HOH C 24 924 924 HOH HOH . P 4 HOH C 25 925 925 HOH HOH . P 4 HOH C 26 926 927 HOH HOH . P 4 HOH C 27 927 928 HOH HOH . P 4 HOH C 28 928 930 HOH HOH . P 4 HOH C 29 929 931 HOH HOH . P 4 HOH C 30 930 932 HOH HOH . P 4 HOH C 31 931 933 HOH HOH . Q 4 HOH D 1 901 901 HOH HOH . Q 4 HOH D 2 902 902 HOH HOH . Q 4 HOH D 3 903 903 HOH HOH . Q 4 HOH D 4 904 904 HOH HOH . Q 4 HOH D 5 905 905 HOH HOH . Q 4 HOH D 6 906 906 HOH HOH . Q 4 HOH D 7 907 907 HOH HOH . Q 4 HOH D 8 908 908 HOH HOH . Q 4 HOH D 9 909 909 HOH HOH . Q 4 HOH D 10 910 910 HOH HOH . Q 4 HOH D 11 911 911 HOH HOH . Q 4 HOH D 12 912 912 HOH HOH . Q 4 HOH D 13 913 913 HOH HOH . Q 4 HOH D 14 914 914 HOH HOH . Q 4 HOH D 15 915 915 HOH HOH . Q 4 HOH D 16 916 916 HOH HOH . Q 4 HOH D 17 917 917 HOH HOH . Q 4 HOH D 18 918 918 HOH HOH . Q 4 HOH D 19 919 919 HOH HOH . Q 4 HOH D 20 920 920 HOH HOH . Q 4 HOH D 21 921 921 HOH HOH . Q 4 HOH D 22 922 922 HOH HOH . Q 4 HOH D 23 923 924 HOH HOH . Q 4 HOH D 24 924 925 HOH HOH . Q 4 HOH D 25 925 926 HOH HOH . Q 4 HOH D 26 926 927 HOH HOH . Q 4 HOH D 27 927 928 HOH HOH . Q 4 HOH D 28 928 929 HOH HOH . Q 4 HOH D 29 929 931 HOH HOH . Q 4 HOH D 30 930 932 HOH HOH . Q 4 HOH D 31 931 933 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 PG ACP . . . J 2 -6.357 18.278 77.102 1 143.24 ? PG ACP 801 C 1 HETATM 2 O O1G ACP . . . J 2 -6.937 18.531 75.743 1 140.97 ? O1G ACP 801 C 1 HETATM 3 O O2G ACP . . . J 2 -7.505 18.317 78.171 1 134.66 ? O2G ACP 801 C 1 HETATM 4 O O3G ACP . . . J 2 -5.3 19.385 77.427 1 131.39 ? O3G ACP 801 C 1 HETATM 5 P PB ACP . . . J 2 -4.764 16.241 78.746 1 153.58 ? PB ACP 801 C 1 HETATM 6 O O1B ACP . . . J 2 -3.274 16.175 78.572 1 152.28 ? O1B ACP 801 C 1 HETATM 7 O O2B ACP . . . J 2 -5.288 14.852 79.244 1 66.87 ? O2B ACP 801 C 1 HETATM 8 C C3B ACP . . . J 2 -5.547 16.621 77.116 1 62.4 ? C3B ACP 801 C 1 HETATM 9 P PA ACP . . . J 2 -6.207 17.086 80.95 1 94.9 ? PA ACP 801 C 1 HETATM 10 O O1A ACP . . . J 2 -7.191 16.051 80.466 1 93.32 1 O1A ACP 801 C 1 HETATM 11 O O2A ACP . . . J 2 -6.949 18.374 81.251 1 94.96 ? O2A ACP 801 C 1 HETATM 12 O O3A ACP . . . J 2 -5.116 17.357 79.826 1 150.63 ? O3A ACP 801 C 1 HETATM 13 O O5' ACP . . . J 2 -5.5 16.563 82.301 1 63.74 ? O5' ACP 801 C 1 HETATM 14 C C5' ACP . . . J 2 -5.182 15.201 82.452 1 59.82 ? C5' ACP 801 C 1 HETATM 15 C C4' ACP . . . J 2 -5.697 14.714 83.745 1 53.53 ? C4' ACP 801 C 1 HETATM 16 O O4' ACP . . . J 2 -7.138 15.01 83.85 1 47.55 ? O4' ACP 801 C 1 HETATM 17 C C3' ACP . . . J 2 -5.527 13.274 83.861 1 54.25 ? C3' ACP 801 C 1 HETATM 18 O O3' ACP . . . J 2 -4.434 12.96 84.724 1 56.03 ? O3' ACP 801 C 1 HETATM 19 C C2' ACP . . . J 2 -6.734 12.728 84.391 1 53.03 ? C2' ACP 801 C 1 HETATM 20 O O2' ACP . . . J 2 -6.471 12.134 85.679 1 55.1 ? O2' ACP 801 C 1 HETATM 21 C C1' ACP . . . J 2 -7.698 13.806 84.516 1 45.43 ? C1' ACP 801 C 1 HETATM 22 N N9 ACP . . . J 2 -8.937 13.455 83.965 1 35.48 ? N9 ACP 801 C 1 HETATM 23 C C8 ACP . . . J 2 -9.425 13.794 82.764 1 28.88 ? C8 ACP 801 C 1 HETATM 24 N N7 ACP . . . J 2 -10.642 13.273 82.605 1 24.37 ? N7 ACP 801 C 1 HETATM 25 C C5 ACP . . . J 2 -10.98 12.583 83.692 1 25.39 ? C5 ACP 801 C 1 HETATM 26 C C6 ACP . . . J 2 -12.104 11.84 84.09 1 21.57 ? C6 ACP 801 C 1 HETATM 27 N N6 ACP . . . J 2 -13.252 11.698 83.212 1 18.98 ? N6 ACP 801 C 1 HETATM 28 N N1 ACP . . . J 2 -12.128 11.249 85.293 1 20.67 ? N1 ACP 801 C 1 HETATM 29 C C2 ACP . . . J 2 -11.084 11.353 86.148 1 20.05 ? C2 ACP 801 C 1 HETATM 30 N N3 ACP . . . J 2 -9.976 12.065 85.799 1 24.43 ? N3 ACP 801 C 1 HETATM 31 C C4 ACP . . . J 2 -9.897 12.684 84.591 1 31.18 ? C4 ACP 801 C 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #