data_4K33 # _model_server_result.job_id NFa--E-KjiXo1rWys5sIRw _model_server_result.datetime_utc '2024-12-26 19:18:15' _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 4k33 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":801}' # _entry.id 4K33 # _exptl.entry_id 4K33 _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 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 4K33 _cell.length_a 54.226 _cell.length_b 61.427 _cell.length_c 100.666 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4K33 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 _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 OD1 ASN 188 A ASN 622 1_555 C MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc2 A OD2 ASP 201 A ASP 635 1_555 C MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc3 B O2B ACP . A ACP 801 1_555 C MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc4 B O2A ACP . A ACP 801 1_555 C MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc5 B O1B ACP . A ACP 801 1_555 D MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.909 ? metalc ? metalc6 B O2G ACP . A ACP 801 1_555 D MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc7 C MG MG . A MG 802 1_555 E O HOH . A HOH 943 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc8 C MG MG . A MG 802 1_555 E O HOH . A HOH 944 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc9 D MG MG . A MG 803 1_555 E O HOH . A HOH 939 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc10 D MG MG . A MG 803 1_555 E O HOH . A HOH 940 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc11 D MG MG . A MG 803 1_555 E O HOH . A HOH 941 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc12 D MG MG . A MG 803 1_555 E O HOH . A HOH 963 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.83 ? # _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 4K33 _atom_sites.fract_transf_matrix[1][1] 0.018441 _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] 0.016279 _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] 0.009934 _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 ACP A 1 801 801 ACP ACP . C 3 MG A 1 802 802 MG MG . D 3 MG A 1 803 803 MG MG . E 4 HOH A 1 901 901 HOH HOH . E 4 HOH A 2 902 902 HOH HOH . E 4 HOH A 3 903 903 HOH HOH . E 4 HOH A 4 904 904 HOH HOH . E 4 HOH A 5 905 905 HOH HOH . E 4 HOH A 6 906 906 HOH HOH . E 4 HOH A 7 907 907 HOH HOH . E 4 HOH A 8 908 908 HOH HOH . E 4 HOH A 9 909 909 HOH HOH . E 4 HOH A 10 910 910 HOH HOH . E 4 HOH A 11 911 911 HOH HOH . E 4 HOH A 12 912 912 HOH HOH . E 4 HOH A 13 913 913 HOH HOH . E 4 HOH A 14 914 915 HOH HOH . E 4 HOH A 15 915 916 HOH HOH . E 4 HOH A 16 916 917 HOH HOH . E 4 HOH A 17 917 918 HOH HOH . E 4 HOH A 18 918 919 HOH HOH . E 4 HOH A 19 919 920 HOH HOH . E 4 HOH A 20 920 921 HOH HOH . E 4 HOH A 21 921 922 HOH HOH . E 4 HOH A 22 922 923 HOH HOH . E 4 HOH A 23 923 924 HOH HOH . E 4 HOH A 24 924 925 HOH HOH . E 4 HOH A 25 925 926 HOH HOH . E 4 HOH A 26 926 927 HOH HOH . E 4 HOH A 27 927 928 HOH HOH . E 4 HOH A 28 928 929 HOH HOH . E 4 HOH A 29 929 930 HOH HOH . E 4 HOH A 30 930 931 HOH HOH . E 4 HOH A 31 931 933 HOH HOH . E 4 HOH A 32 932 934 HOH HOH . E 4 HOH A 33 933 935 HOH HOH . E 4 HOH A 34 934 936 HOH HOH . E 4 HOH A 35 935 937 HOH HOH . E 4 HOH A 36 936 938 HOH HOH . E 4 HOH A 37 937 939 HOH HOH . E 4 HOH A 38 938 940 HOH HOH . E 4 HOH A 39 939 941 HOH HOH . E 4 HOH A 40 940 942 HOH HOH . E 4 HOH A 41 941 943 HOH HOH . E 4 HOH A 42 942 944 HOH HOH . E 4 HOH A 43 943 945 HOH HOH . E 4 HOH A 44 944 946 HOH HOH . E 4 HOH A 45 945 947 HOH HOH . E 4 HOH A 46 946 948 HOH HOH . E 4 HOH A 47 947 949 HOH HOH . E 4 HOH A 48 948 950 HOH HOH . E 4 HOH A 49 949 951 HOH HOH . E 4 HOH A 50 950 952 HOH HOH . E 4 HOH A 51 951 953 HOH HOH . E 4 HOH A 52 952 954 HOH HOH . E 4 HOH A 53 953 955 HOH HOH . E 4 HOH A 54 954 956 HOH HOH . E 4 HOH A 55 955 957 HOH HOH . E 4 HOH A 56 956 958 HOH HOH . E 4 HOH A 57 957 959 HOH HOH . E 4 HOH A 58 958 961 HOH HOH . E 4 HOH A 59 959 962 HOH HOH . E 4 HOH A 60 960 964 HOH HOH . E 4 HOH A 61 961 965 HOH HOH . E 4 HOH A 62 962 966 HOH HOH . E 4 HOH A 63 963 967 HOH HOH . E 4 HOH A 64 964 968 HOH HOH . E 4 HOH A 65 965 969 HOH HOH . E 4 HOH A 66 966 970 HOH HOH . E 4 HOH A 67 967 971 HOH HOH . E 4 HOH A 68 968 972 HOH HOH . E 4 HOH A 69 969 973 HOH HOH . E 4 HOH A 70 970 974 HOH HOH . E 4 HOH A 71 971 975 HOH HOH . E 4 HOH A 72 972 976 HOH HOH . E 4 HOH A 73 973 977 HOH HOH . E 4 HOH A 74 974 978 HOH HOH . E 4 HOH A 75 975 979 HOH HOH . E 4 HOH A 76 976 980 HOH HOH . E 4 HOH A 77 977 981 HOH HOH . E 4 HOH A 78 978 982 HOH HOH . E 4 HOH A 79 979 983 HOH HOH . E 4 HOH A 80 980 984 HOH HOH . E 4 HOH A 81 981 985 HOH HOH . E 4 HOH A 82 982 986 HOH HOH . E 4 HOH A 83 983 987 HOH HOH . E 4 HOH A 84 984 988 HOH HOH . E 4 HOH A 85 985 989 HOH HOH . E 4 HOH A 86 986 990 HOH HOH . E 4 HOH A 87 987 991 HOH HOH . E 4 HOH A 88 988 992 HOH HOH . E 4 HOH A 89 989 993 HOH HOH . E 4 HOH A 90 990 994 HOH HOH . E 4 HOH A 91 991 995 HOH HOH . E 4 HOH A 92 992 996 HOH HOH . E 4 HOH A 93 993 997 HOH HOH . E 4 HOH A 94 994 998 HOH HOH . E 4 HOH A 95 995 999 HOH HOH . E 4 HOH A 96 996 1000 HOH HOH . E 4 HOH A 97 997 1001 HOH HOH . E 4 HOH A 98 998 1002 HOH HOH . E 4 HOH A 99 999 1003 HOH HOH . E 4 HOH A 100 1000 1004 HOH HOH . E 4 HOH A 101 1001 1005 HOH HOH . E 4 HOH A 102 1002 1006 HOH HOH . E 4 HOH A 103 1003 1007 HOH HOH . E 4 HOH A 104 1004 1008 HOH HOH . E 4 HOH A 105 1005 1009 HOH HOH . E 4 HOH A 106 1006 1010 HOH HOH . E 4 HOH A 107 1007 1011 HOH HOH . E 4 HOH A 108 1008 1012 HOH HOH . E 4 HOH A 109 1009 1013 HOH HOH . E 4 HOH A 110 1010 1014 HOH HOH . E 4 HOH A 111 1011 1015 HOH HOH . E 4 HOH A 112 1012 1016 HOH HOH . E 4 HOH A 113 1013 1017 HOH HOH . E 4 HOH A 114 1014 1018 HOH HOH . E 4 HOH A 115 1015 1019 HOH HOH . E 4 HOH A 116 1016 1020 HOH HOH . E 4 HOH A 117 1017 1021 HOH HOH . E 4 HOH A 118 1018 1022 HOH HOH . E 4 HOH A 119 1019 1023 HOH HOH . E 4 HOH A 120 1020 1025 HOH HOH . E 4 HOH A 121 1021 1026 HOH HOH . E 4 HOH A 122 1022 1027 HOH HOH . E 4 HOH A 123 1023 1028 HOH HOH . E 4 HOH A 124 1024 1 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 . . . B 2 26.188 7.162 30.055 1 39.33 ? PG ACP 801 A 1 HETATM 2 O O1G ACP . . . B 2 25.696 6.102 29.096 1 39.24 ? O1G ACP 801 A 1 HETATM 3 O O2G ACP . . . B 2 25.015 8.134 30.434 1 26.26 ? O2G ACP 801 A 1 HETATM 4 O O3G ACP . . . B 2 27.345 7.963 29.355 1 50.21 ? O3G ACP 801 A 1 HETATM 5 P PB ACP . . . B 2 25.56 5.897 32.757 1 33.18 ? PB ACP 801 A 1 HETATM 6 O O1B ACP . . . B 2 24.637 7.058 32.959 1 30.05 ? O1B ACP 801 A 1 HETATM 7 O O2B ACP . . . B 2 24.726 4.638 32.318 1 23.72 ? O2B ACP 801 A 1 HETATM 8 C C3B ACP . . . B 2 26.868 6.324 31.539 1 34.4 ? C3B ACP 801 A 1 HETATM 9 P PA ACP . . . B 2 25.914 4.517 35.119 1 30.48 ? PA ACP 801 A 1 HETATM 10 O O1A ACP . . . B 2 25.593 5.225 36.418 1 29.29 ? O1A ACP 801 A 1 HETATM 11 O O2A ACP . . . B 2 24.67 3.785 34.589 1 25.83 ? O2A ACP 801 A 1 HETATM 12 O O3A ACP . . . B 2 26.391 5.593 34.069 1 31.96 ? O3A ACP 801 A 1 HETATM 13 O O5' ACP . . . B 2 27.14 3.485 35.39 1 37.12 ? O5' ACP 801 A 1 HETATM 14 C C5' ACP . . . B 2 27.813 2.896 34.294 1 32.79 ? C5' ACP 801 A 1 HETATM 15 C C4' ACP . . . B 2 28.629 1.762 34.775 1 31.56 ? C4' ACP 801 A 1 HETATM 16 O O4' ACP . . . B 2 29.606 2.225 35.783 1 33.24 ? O4' ACP 801 A 1 HETATM 17 C C3' ACP . . . B 2 27.818 0.785 35.482 1 34.95 ? C3' ACP 801 A 1 HETATM 18 O O3' ACP . . . B 2 27.178 -0.133 34.602 1 34.5 ? O3' ACP 801 A 1 HETATM 19 C C2' ACP . . . B 2 28.726 0.125 36.37 1 40.16 ? C2' ACP 801 A 1 HETATM 20 O O2' ACP . . . B 2 29.476 -0.894 35.657 1 43.8 ? O2' ACP 801 A 1 HETATM 21 C C1' ACP . . . B 2 29.606 1.179 36.845 1 31.79 ? C1' ACP 801 A 1 HETATM 22 N N9 ACP . . . B 2 29.121 1.728 38.03 1 32.59 ? N9 ACP 801 A 1 HETATM 23 C C8 ACP . . . B 2 28.23 2.729 38.156 1 33.69 ? C8 ACP 801 A 1 HETATM 24 N N7 ACP . . . B 2 28.009 2.987 39.45 1 34.18 ? N7 ACP 801 A 1 HETATM 25 C C5 ACP . . . B 2 28.749 2.172 40.206 1 32.41 ? C5 ACP 801 A 1 HETATM 26 C C6 ACP . . . B 2 28.919 1.988 41.585 1 31.55 ? C6 ACP 801 A 1 HETATM 27 N N6 ACP . . . B 2 28.193 2.798 42.546 1 30.69 ? N6 ACP 801 A 1 HETATM 28 N N1 ACP . . . B 2 29.758 1.048 42.048 1 36.72 ? N1 ACP 801 A 1 HETATM 29 C C2 ACP . . . B 2 30.455 0.259 41.192 1 38.06 ? C2 ACP 801 A 1 HETATM 30 N N3 ACP . . . B 2 30.312 0.405 39.837 1 36.12 ? N3 ACP 801 A 1 HETATM 31 C C4 ACP . . . B 2 29.472 1.341 39.319 1 34.92 ? C4 ACP 801 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #