data_1XDP # _model_server_result.job_id RIlDK9kHXrjkq6wMeqNqew _model_server_result.datetime_utc '2025-03-06 03:22:52' _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 1xdp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _entry.id 1XDP # _exptl.entry_id 1XDP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _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 90 _cell.entry_id 1XDP _cell.length_a 152 _cell.length_b 152 _cell.length_c 150 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XDP _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,B,C,D,E,F,G,H,I,J 2 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' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -152 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 H 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 NH2 ARG 374 A ARG 375 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc2 A NH2 ARG 374 A ARG 375 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc3 A NH1 ARG 404 A ARG 405 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.904 ? metalc ? metalc4 A NE ARG 404 A ARG 405 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc5 A NH1 ARG 404 A ARG 405 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc6 E O2A ATP . A ATP 701 1_555 C MG MG . A MG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc7 E O1G ATP . A ATP 701 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc8 C MG MG . A MG 702 1_555 D MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.118 ? metalc ? metalc9 B NH2 ARG 52 B ARG 53 1_555 G MG MG . B MG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc10 B NH1 ARG 404 B ARG 405 1_555 F MG MG . B MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.116 ? metalc ? metalc11 H O1G ATP . B ATP 704 1_555 F MG MG . B MG 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc12 H O2A ATP . B ATP 704 1_555 G MG MG . B MG 706 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc13 F MG MG . B MG 705 1_555 J O HOH . B HOH 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.077 ? metalc ? metalc14 G MG MG . B MG 706 1_555 J O HOH . B HOH 743 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? # _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 1XDP _atom_sites.fract_transf_matrix[1][1] 0.006579 _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] 0.006579 _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] 0.006667 _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 MG A 1 702 702 MG MG . D 2 MG A 1 703 703 MG MG . E 3 ATP A 1 701 701 ATP ATP . F 2 MG B 1 705 705 MG MG . G 2 MG B 1 706 706 MG MG . H 3 ATP B 1 704 704 ATP ATP . I 4 HOH A 1 704 2 HOH TIP . I 4 HOH A 2 705 3 HOH TIP . I 4 HOH A 3 706 5 HOH TIP . I 4 HOH A 4 707 9 HOH TIP . I 4 HOH A 5 708 10 HOH TIP . I 4 HOH A 6 709 11 HOH TIP . I 4 HOH A 7 710 13 HOH TIP . I 4 HOH A 8 711 14 HOH TIP . I 4 HOH A 9 712 16 HOH TIP . I 4 HOH A 10 713 17 HOH TIP . I 4 HOH A 11 714 19 HOH TIP . I 4 HOH A 12 715 21 HOH TIP . I 4 HOH A 13 716 22 HOH TIP . I 4 HOH A 14 717 27 HOH TIP . I 4 HOH A 15 718 28 HOH TIP . I 4 HOH A 16 719 30 HOH TIP . I 4 HOH A 17 720 31 HOH TIP . I 4 HOH A 18 721 32 HOH TIP . I 4 HOH A 19 722 34 HOH TIP . I 4 HOH A 20 723 36 HOH TIP . I 4 HOH A 21 724 37 HOH TIP . I 4 HOH A 22 725 38 HOH TIP . I 4 HOH A 23 726 40 HOH TIP . I 4 HOH A 24 727 41 HOH TIP . I 4 HOH A 25 728 42 HOH TIP . I 4 HOH A 26 729 45 HOH TIP . I 4 HOH A 27 730 46 HOH TIP . I 4 HOH A 28 731 48 HOH TIP . I 4 HOH A 29 732 50 HOH TIP . I 4 HOH A 30 733 51 HOH TIP . I 4 HOH A 31 734 55 HOH TIP . I 4 HOH A 32 735 56 HOH TIP . I 4 HOH A 33 736 60 HOH TIP . I 4 HOH A 34 737 61 HOH TIP . I 4 HOH A 35 738 62 HOH TIP . I 4 HOH A 36 739 64 HOH TIP . I 4 HOH A 37 740 65 HOH TIP . I 4 HOH A 38 741 66 HOH TIP . I 4 HOH A 39 742 67 HOH TIP . I 4 HOH A 40 743 68 HOH TIP . I 4 HOH A 41 744 71 HOH TIP . I 4 HOH A 42 745 72 HOH TIP . I 4 HOH A 43 746 75 HOH TIP . I 4 HOH A 44 747 76 HOH TIP . I 4 HOH A 45 748 78 HOH TIP . I 4 HOH A 46 749 79 HOH TIP . I 4 HOH A 47 750 80 HOH TIP . I 4 HOH A 48 751 82 HOH TIP . I 4 HOH A 49 752 84 HOH TIP . I 4 HOH A 50 753 85 HOH TIP . I 4 HOH A 51 754 87 HOH TIP . I 4 HOH A 52 755 88 HOH TIP . I 4 HOH A 53 756 89 HOH TIP . I 4 HOH A 54 757 90 HOH TIP . I 4 HOH A 55 758 91 HOH TIP . I 4 HOH A 56 759 92 HOH TIP . I 4 HOH A 57 760 96 HOH TIP . I 4 HOH A 58 761 97 HOH TIP . I 4 HOH A 59 762 98 HOH TIP . I 4 HOH A 60 763 103 HOH TIP . I 4 HOH A 61 764 105 HOH TIP . I 4 HOH A 62 765 106 HOH TIP . I 4 HOH A 63 766 109 HOH TIP . I 4 HOH A 64 767 113 HOH TIP . I 4 HOH A 65 768 114 HOH TIP . I 4 HOH A 66 769 115 HOH TIP . I 4 HOH A 67 770 116 HOH TIP . I 4 HOH A 68 771 117 HOH TIP . I 4 HOH A 69 772 118 HOH TIP . I 4 HOH A 70 773 122 HOH TIP . I 4 HOH A 71 774 123 HOH TIP . I 4 HOH A 72 775 125 HOH TIP . I 4 HOH A 73 776 126 HOH TIP . I 4 HOH A 74 777 127 HOH TIP . I 4 HOH A 75 778 129 HOH TIP . I 4 HOH A 76 779 130 HOH TIP . J 4 HOH B 1 707 1 HOH TIP . J 4 HOH B 2 708 4 HOH TIP . J 4 HOH B 3 709 6 HOH TIP . J 4 HOH B 4 710 7 HOH TIP . J 4 HOH B 5 711 8 HOH TIP . J 4 HOH B 6 712 12 HOH TIP . J 4 HOH B 7 713 15 HOH TIP . J 4 HOH B 8 714 18 HOH TIP . J 4 HOH B 9 715 20 HOH TIP . J 4 HOH B 10 716 23 HOH TIP . J 4 HOH B 11 717 24 HOH TIP . J 4 HOH B 12 718 25 HOH TIP . J 4 HOH B 13 719 26 HOH TIP . J 4 HOH B 14 720 29 HOH TIP . J 4 HOH B 15 721 33 HOH TIP . J 4 HOH B 16 722 39 HOH TIP . J 4 HOH B 17 723 43 HOH TIP . J 4 HOH B 18 724 44 HOH TIP . J 4 HOH B 19 725 47 HOH TIP . J 4 HOH B 20 726 49 HOH TIP . J 4 HOH B 21 727 52 HOH TIP . J 4 HOH B 22 728 53 HOH TIP . J 4 HOH B 23 729 54 HOH TIP . J 4 HOH B 24 730 57 HOH TIP . J 4 HOH B 25 731 58 HOH TIP . J 4 HOH B 26 732 59 HOH TIP . J 4 HOH B 27 733 63 HOH TIP . J 4 HOH B 28 734 69 HOH TIP . J 4 HOH B 29 735 70 HOH TIP . J 4 HOH B 30 736 73 HOH TIP . J 4 HOH B 31 737 74 HOH TIP . J 4 HOH B 32 738 77 HOH TIP . J 4 HOH B 33 739 81 HOH TIP . J 4 HOH B 34 740 83 HOH TIP . J 4 HOH B 35 741 86 HOH TIP . J 4 HOH B 36 742 93 HOH TIP . J 4 HOH B 37 743 94 HOH TIP . J 4 HOH B 38 744 95 HOH TIP . J 4 HOH B 39 745 99 HOH TIP . J 4 HOH B 40 746 100 HOH TIP . J 4 HOH B 41 747 101 HOH TIP . J 4 HOH B 42 748 102 HOH TIP . J 4 HOH B 43 749 104 HOH TIP . J 4 HOH B 44 750 107 HOH TIP . J 4 HOH B 45 751 108 HOH TIP . J 4 HOH B 46 752 110 HOH TIP . J 4 HOH B 47 753 111 HOH TIP . J 4 HOH B 48 754 112 HOH TIP . J 4 HOH B 49 755 119 HOH TIP . J 4 HOH B 50 756 120 HOH TIP . J 4 HOH B 51 757 121 HOH TIP . J 4 HOH B 52 758 124 HOH TIP . J 4 HOH B 53 759 128 HOH TIP . J 4 HOH B 54 760 131 HOH TIP . # 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 3 -31.181 -82.12 38.966 1 70.46 ? PG ATP 701 A 1 HETATM 2 O O1G ATP . . . E 3 -30.084 -81.904 37.853 1 71.75 ? O1G ATP 701 A 1 HETATM 3 O O2G ATP . . . E 3 -32.17 -83.318 38.78 1 71.55 ? O2G ATP 701 A 1 HETATM 4 O O3G ATP . . . E 3 -30.507 -82.177 40.367 1 71.36 ? O3G ATP 701 A 1 HETATM 5 P PB ATP . . . E 3 -31.703 -79.18 39.082 1 70.77 ? PB ATP 701 A 1 HETATM 6 O O1B ATP . . . E 3 -32.596 -78.133 39.765 1 71.99 ? O1B ATP 701 A 1 HETATM 7 O O2B ATP . . . E 3 -30.268 -78.84 38.596 1 71.38 ? O2B ATP 701 A 1 HETATM 8 O O3B ATP . . . E 3 -32.114 -80.767 39.192 1 69.75 ? O3B ATP 701 A 1 HETATM 9 P PA ATP . . . E 3 -33.012 -79.633 36.227 1 71.12 ? PA ATP 701 A 1 HETATM 10 O O1A ATP . . . E 3 -34.514 -79.868 36 1 70.35 ? O1A ATP 701 A 1 HETATM 11 O O2A ATP . . . E 3 -31.809 -80.242 35.268 1 71.4 ? O2A ATP 701 A 1 HETATM 12 O O3A ATP . . . E 3 -32.461 -78.813 37.529 1 71.15 ? O3A ATP 701 A 1 HETATM 13 O O5' ATP . . . E 3 -33.337 -78.238 35.541 1 69.18 ? O5' ATP 701 A 1 HETATM 14 C C5' ATP . . . E 3 -32.701 -77.359 35.078 1 68.14 ? C5' ATP 701 A 1 HETATM 15 C C4' ATP . . . E 3 -32.332 -76.011 34.396 1 67.34 ? C4' ATP 701 A 1 HETATM 16 O O4' ATP . . . E 3 -33.181 -75.478 33.265 1 66.31 ? O4' ATP 701 A 1 HETATM 17 C C3' ATP . . . E 3 -32.33 -75.313 35.625 1 67.31 ? C3' ATP 701 A 1 HETATM 18 O O3' ATP . . . E 3 -31.027 -75.217 36.314 1 67.74 ? O3' ATP 701 A 1 HETATM 19 C C2' ATP . . . E 3 -33.148 -73.973 35.323 1 66.51 ? C2' ATP 701 A 1 HETATM 20 O O2' ATP . . . E 3 -32.454 -72.802 35.666 1 66.97 ? O2' ATP 701 A 1 HETATM 21 C C1' ATP . . . E 3 -33.615 -74.139 33.743 1 65.54 ? C1' ATP 701 A 1 HETATM 22 N N9 ATP . . . E 3 -35.097 -73.827 33.42 1 63.13 ? N9 ATP 701 A 1 HETATM 23 C C8 ATP . . . E 3 -35.839 -74.316 32.282 1 62.37 ? C8 ATP 701 A 1 HETATM 24 N N7 ATP . . . E 3 -37.1 -73.835 32.289 1 61.97 ? N7 ATP 701 A 1 HETATM 25 C C5 ATP . . . E 3 -37.198 -73.034 33.415 1 61.46 ? C5 ATP 701 A 1 HETATM 26 C C6 ATP . . . E 3 -38.307 -72.226 34.018 1 60.6 ? C6 ATP 701 A 1 HETATM 27 N N6 ATP . . . E 3 -39.553 -72.219 33.388 1 59.51 ? N6 ATP 701 A 1 HETATM 28 N N1 ATP . . . E 3 -38.041 -71.484 35.196 1 59.72 ? N1 ATP 701 A 1 HETATM 29 C C2 ATP . . . E 3 -36.804 -71.504 35.757 1 60.05 ? C2 ATP 701 A 1 HETATM 30 N N3 ATP . . . E 3 -35.685 -72.208 35.348 1 60.49 ? N3 ATP 701 A 1 HETATM 31 C C4 ATP . . . E 3 -35.993 -72.975 34.12 1 61.96 ? C4 ATP 701 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 31 #