data_3VX4 # _model_server_result.job_id iOX-ALeGnFhlYVH1KDJ6AA _model_server_result.datetime_utc '2024-12-26 18:42:40' _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 3vx4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 3VX4 # _exptl.entry_id 3VX4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 3VX4 _cell.length_a 129.611 _cell.length_b 129.611 _cell.length_c 72.425 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VX4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 171 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,G,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 75 A THR 568 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc2 A OE1 GLN 116 A GLN 609 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? metalc ? metalc3 C O2B ATP . A ATP 801 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? metalc ? metalc4 C O3G ATP . A ATP 801 1_555 D MG MG . A MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc5 D MG MG . A MG 802 1_555 G O HOH . A HOH 920 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc6 D MG MG . A MG 802 1_555 G O HOH . A HOH 964 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? metalc ? metalc7 B OG1 THR 75 D THR 568 1_555 F MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc8 B OE1 GLN 116 D GLN 609 1_555 F MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? metalc ? metalc9 E O3G ATP . D ATP 801 1_555 F MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc10 E O2B ATP . D ATP 801 1_555 F MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc11 F MG MG . D MG 802 1_555 H O HOH . D HOH 977 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc12 F MG MG . D MG 802 1_555 H O HOH . D HOH 982 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 3VX4 _atom_sites.fract_transf_matrix[1][1] 0.007715 _atom_sites.fract_transf_matrix[1][2] 0.004454 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008909 _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] 0.013807 _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 C 2 ATP A 1 801 762 ATP ATP . D 3 MG A 1 802 763 MG MG . E 2 ATP D 1 801 762 ATP ATP . F 3 MG D 1 802 763 MG MG . G 4 HOH A 1 901 4 HOH HOH . G 4 HOH A 2 902 11 HOH HOH . G 4 HOH A 3 903 12 HOH HOH . G 4 HOH A 4 904 16 HOH HOH . G 4 HOH A 5 905 17 HOH HOH . G 4 HOH A 6 906 21 HOH HOH . G 4 HOH A 7 907 24 HOH HOH . G 4 HOH A 8 908 26 HOH HOH . G 4 HOH A 9 909 27 HOH HOH . G 4 HOH A 10 910 28 HOH HOH . G 4 HOH A 11 911 29 HOH HOH . G 4 HOH A 12 912 32 HOH HOH . G 4 HOH A 13 913 33 HOH HOH . G 4 HOH A 14 914 34 HOH HOH . G 4 HOH A 15 915 39 HOH HOH . G 4 HOH A 16 916 40 HOH HOH . G 4 HOH A 17 917 42 HOH HOH . G 4 HOH A 18 918 46 HOH HOH . G 4 HOH A 19 919 51 HOH HOH . G 4 HOH A 20 920 53 HOH HOH . G 4 HOH A 21 921 54 HOH HOH . G 4 HOH A 22 922 57 HOH HOH . G 4 HOH A 23 923 59 HOH HOH . G 4 HOH A 24 924 60 HOH HOH . G 4 HOH A 25 925 61 HOH HOH . G 4 HOH A 26 926 66 HOH HOH . G 4 HOH A 27 927 68 HOH HOH . G 4 HOH A 28 928 72 HOH HOH . G 4 HOH A 29 929 74 HOH HOH . G 4 HOH A 30 930 77 HOH HOH . G 4 HOH A 31 931 80 HOH HOH . G 4 HOH A 32 932 84 HOH HOH . G 4 HOH A 33 933 85 HOH HOH . G 4 HOH A 34 934 86 HOH HOH . G 4 HOH A 35 935 89 HOH HOH . G 4 HOH A 36 936 91 HOH HOH . G 4 HOH A 37 937 96 HOH HOH . G 4 HOH A 38 938 99 HOH HOH . G 4 HOH A 39 939 100 HOH HOH . G 4 HOH A 40 940 101 HOH HOH . G 4 HOH A 41 941 105 HOH HOH . G 4 HOH A 42 942 107 HOH HOH . G 4 HOH A 43 943 108 HOH HOH . G 4 HOH A 44 944 109 HOH HOH . G 4 HOH A 45 945 110 HOH HOH . G 4 HOH A 46 946 111 HOH HOH . G 4 HOH A 47 947 113 HOH HOH . G 4 HOH A 48 948 122 HOH HOH . G 4 HOH A 49 949 123 HOH HOH . G 4 HOH A 50 950 124 HOH HOH . G 4 HOH A 51 951 127 HOH HOH . G 4 HOH A 52 952 129 HOH HOH . G 4 HOH A 53 953 130 HOH HOH . G 4 HOH A 54 954 132 HOH HOH . G 4 HOH A 55 955 135 HOH HOH . G 4 HOH A 56 956 137 HOH HOH . G 4 HOH A 57 957 138 HOH HOH . G 4 HOH A 58 958 139 HOH HOH . G 4 HOH A 59 959 141 HOH HOH . G 4 HOH A 60 960 142 HOH HOH . G 4 HOH A 61 961 144 HOH HOH . G 4 HOH A 62 962 145 HOH HOH . G 4 HOH A 63 963 146 HOH HOH . G 4 HOH A 64 964 148 HOH HOH . H 4 HOH D 1 901 1 HOH HOH . H 4 HOH D 2 902 2 HOH HOH . H 4 HOH D 3 903 3 HOH HOH . H 4 HOH D 4 904 5 HOH HOH . H 4 HOH D 5 905 6 HOH HOH . H 4 HOH D 6 906 7 HOH HOH . H 4 HOH D 7 907 8 HOH HOH . H 4 HOH D 8 908 9 HOH HOH . H 4 HOH D 9 909 10 HOH HOH . H 4 HOH D 10 910 13 HOH HOH . H 4 HOH D 11 911 14 HOH HOH . H 4 HOH D 12 912 15 HOH HOH . H 4 HOH D 13 913 18 HOH HOH . H 4 HOH D 14 914 19 HOH HOH . H 4 HOH D 15 915 20 HOH HOH . H 4 HOH D 16 916 22 HOH HOH . H 4 HOH D 17 917 23 HOH HOH . H 4 HOH D 18 918 25 HOH HOH . H 4 HOH D 19 919 30 HOH HOH . H 4 HOH D 20 920 31 HOH HOH . H 4 HOH D 21 921 35 HOH HOH . H 4 HOH D 22 922 36 HOH HOH . H 4 HOH D 23 923 37 HOH HOH . H 4 HOH D 24 924 38 HOH HOH . H 4 HOH D 25 925 41 HOH HOH . H 4 HOH D 26 926 43 HOH HOH . H 4 HOH D 27 927 44 HOH HOH . H 4 HOH D 28 928 45 HOH HOH . H 4 HOH D 29 929 47 HOH HOH . H 4 HOH D 30 930 48 HOH HOH . H 4 HOH D 31 931 49 HOH HOH . H 4 HOH D 32 932 50 HOH HOH . H 4 HOH D 33 933 52 HOH HOH . H 4 HOH D 34 934 55 HOH HOH . H 4 HOH D 35 935 56 HOH HOH . H 4 HOH D 36 936 58 HOH HOH . H 4 HOH D 37 937 62 HOH HOH . H 4 HOH D 38 938 63 HOH HOH . H 4 HOH D 39 939 64 HOH HOH . H 4 HOH D 40 940 65 HOH HOH . H 4 HOH D 41 941 67 HOH HOH . H 4 HOH D 42 942 69 HOH HOH . H 4 HOH D 43 943 70 HOH HOH . H 4 HOH D 44 944 71 HOH HOH . H 4 HOH D 45 945 73 HOH HOH . H 4 HOH D 46 946 75 HOH HOH . H 4 HOH D 47 947 76 HOH HOH . H 4 HOH D 48 948 78 HOH HOH . H 4 HOH D 49 949 79 HOH HOH . H 4 HOH D 50 950 81 HOH HOH . H 4 HOH D 51 951 82 HOH HOH . H 4 HOH D 52 952 83 HOH HOH . H 4 HOH D 53 953 87 HOH HOH . H 4 HOH D 54 954 88 HOH HOH . H 4 HOH D 55 955 90 HOH HOH . H 4 HOH D 56 956 92 HOH HOH . H 4 HOH D 57 957 93 HOH HOH . H 4 HOH D 58 958 94 HOH HOH . H 4 HOH D 59 959 95 HOH HOH . H 4 HOH D 60 960 97 HOH HOH . H 4 HOH D 61 961 98 HOH HOH . H 4 HOH D 62 962 102 HOH HOH . H 4 HOH D 63 963 103 HOH HOH . H 4 HOH D 64 964 104 HOH HOH . H 4 HOH D 65 965 106 HOH HOH . H 4 HOH D 66 966 112 HOH HOH . H 4 HOH D 67 967 114 HOH HOH . H 4 HOH D 68 968 115 HOH HOH . H 4 HOH D 69 969 116 HOH HOH . H 4 HOH D 70 970 117 HOH HOH . H 4 HOH D 71 971 118 HOH HOH . H 4 HOH D 72 972 119 HOH HOH . H 4 HOH D 73 973 120 HOH HOH . H 4 HOH D 74 974 121 HOH HOH . H 4 HOH D 75 975 125 HOH HOH . H 4 HOH D 76 976 126 HOH HOH . H 4 HOH D 77 977 128 HOH HOH . H 4 HOH D 78 978 131 HOH HOH . H 4 HOH D 79 979 133 HOH HOH . H 4 HOH D 80 980 134 HOH HOH . H 4 HOH D 81 981 136 HOH HOH . H 4 HOH D 82 982 140 HOH HOH . H 4 HOH D 83 983 143 HOH HOH . H 4 HOH D 84 984 147 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 ATP . . . E 2 48.363 13.97 9.839 1 9.58 ? PG ATP 801 D 1 HETATM 2 O O1G ATP . . . E 2 49.697 14.625 9.941 1 9.49 ? O1G ATP 801 D 1 HETATM 3 O O2G ATP . . . E 2 47.717 14.109 8.477 1 9.62 ? O2G ATP 801 D 1 HETATM 4 O O3G ATP . . . E 2 47.462 14.162 10.978 1 9.07 ? O3G ATP 801 D 1 HETATM 5 P PB ATP . . . E 2 49.089 11.371 11.168 1 10.93 ? PB ATP 801 D 1 HETATM 6 O O1B ATP . . . E 2 50.562 11.397 11.362 1 10.64 ? O1B ATP 801 D 1 HETATM 7 O O2B ATP . . . E 2 48.206 11.675 12.318 1 11.16 ? O2B ATP 801 D 1 HETATM 8 O O3B ATP . . . E 2 48.742 12.354 9.874 1 10.28 ? O3B ATP 801 D 1 HETATM 9 P PA ATP . . . E 2 47.54 8.981 11.385 1 14.4 ? PA ATP 801 D 1 HETATM 10 O O1A ATP . . . E 2 48.063 8.563 12.748 1 13.64 ? O1A ATP 801 D 1 HETATM 11 O O2A ATP . . . E 2 46.266 9.74 11.303 1 14.09 ? O2A ATP 801 D 1 HETATM 12 O O3A ATP . . . E 2 48.664 9.865 10.607 1 11.98 ? O3A ATP 801 D 1 HETATM 13 O O5' ATP . . . E 2 47.294 7.623 10.496 1 14.59 ? O5' ATP 801 D 1 HETATM 14 C C5' ATP . . . E 2 48.328 6.946 9.751 1 14.98 ? C5' ATP 801 D 1 HETATM 15 C C4' ATP . . . E 2 47.685 5.868 8.836 1 15.16 ? C4' ATP 801 D 1 HETATM 16 O O4' ATP . . . E 2 46.459 5.336 9.498 1 15.77 ? O4' ATP 801 D 1 HETATM 17 C C3' ATP . . . E 2 47.163 6.476 7.529 1 14.61 ? C3' ATP 801 D 1 HETATM 18 O O3' ATP . . . E 2 47.244 5.5 6.464 1 13.88 ? O3' ATP 801 D 1 HETATM 19 C C2' ATP . . . E 2 45.743 6.74 7.89 1 14.72 ? C2' ATP 801 D 1 HETATM 20 O O2' ATP . . . E 2 44.927 6.886 6.783 1 14.5 ? O2' ATP 801 D 1 HETATM 21 C C1' ATP . . . E 2 45.394 5.531 8.578 1 15.51 ? C1' ATP 801 D 1 HETATM 22 N N9 ATP . . . E 2 44.254 5.727 9.418 1 16.63 ? N9 ATP 801 D 1 HETATM 23 C C8 ATP . . . E 2 44.01 6.73 10.253 1 16.58 ? C8 ATP 801 D 1 HETATM 24 N N7 ATP . . . E 2 42.861 6.512 10.824 1 16.04 ? N7 ATP 801 D 1 HETATM 25 C C5 ATP . . . E 2 42.396 5.382 10.35 1 17.23 ? C5 ATP 801 D 1 HETATM 26 C C6 ATP . . . E 2 41.285 4.745 10.614 1 18.39 ? C6 ATP 801 D 1 HETATM 27 N N6 ATP . . . E 2 40.505 5.337 11.506 1 18.95 ? N6 ATP 801 D 1 HETATM 28 N N1 ATP . . . E 2 40.972 3.565 10.012 1 18.72 ? N1 ATP 801 D 1 HETATM 29 C C2 ATP . . . E 2 41.873 3.002 9.071 1 18.03 ? C2 ATP 801 D 1 HETATM 30 N N3 ATP . . . E 2 43.047 3.704 8.808 1 17.32 ? N3 ATP 801 D 1 HETATM 31 C C4 ATP . . . E 2 43.264 4.884 9.467 1 17.35 ? C4 ATP 801 D 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 31 #