data_7Y28 # _model_server_result.job_id DbSM3HJMuj8InULPT71H8A _model_server_result.datetime_utc '2025-07-05 06:27:11' _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 7y28 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2602}' # _entry.id 7Y28 # _exptl.entry_id 7Y28 _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 108.72 _cell.angle_gamma 90 _cell.entry_id 7Y28 _cell.length_a 71.563 _cell.length_b 92.38 _cell.length_c 86.059 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Y28 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,I,J,K,L,M,N _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 ? 3 D N N ? 3 I 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 OE1 GLN 222 A GLN 1237 1_555 G MG MG . A MG 2605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc2 A SG CYS 433 A CYS 1448 1_555 E ZN ZN . A ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc3 A SG CYS 438 A CYS 1453 1_555 E ZN ZN . A ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc4 A SG CYS 480 A CYS 1495 1_555 E ZN ZN . A ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.366 ? metalc ? metalc5 A SG CYS 482 A CYS 1497 1_555 E ZN ZN . A ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc6 D O1G ATP . A ATP 2602 1_555 F MG MG . A MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc7 D O2B ATP . A ATP 2602 1_555 F MG MG . A MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc8 D O2G ATP . A ATP 2602 1_555 G MG MG . A MG 2605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc9 D O1B ATP . A ATP 2602 1_555 G MG MG . A MG 2605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc10 B SG CYS 433 B CYS 1448 1_555 J ZN ZN . B ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc11 B SG CYS 438 B CYS 1453 1_555 J ZN ZN . B ZN 2603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc12 I O3G ATP . B ATP 2602 1_555 K MG MG . B MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.815 ? metalc ? metalc13 I O1B ATP . B ATP 2602 1_555 K MG MG . B MG 2604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc14 I O2B ATP . B ATP 2602 1_555 L MG MG . B MG 2605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? # _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 7Y28 _atom_sites.fract_transf_matrix[1][1] 0.013974 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004735 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010825 _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] 0.012269 _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 F96 A 1 2601 2601 F96 DW5 . D 3 ATP A 1 2602 2602 ATP ATP . E 4 ZN A 1 2603 2603 ZN ZN . F 5 MG A 1 2604 2604 MG MG . G 5 MG A 1 2605 2605 MG MG . H 2 F96 B 1 2601 2601 F96 DW5 . I 3 ATP B 1 2602 2602 ATP ATP . J 4 ZN B 1 2603 2603 ZN ZN . K 5 MG B 1 2604 2604 MG MG . L 5 MG B 1 2605 2605 MG MG . M 6 HOH A 1 2701 72 HOH HOH . M 6 HOH A 2 2702 71 HOH HOH . M 6 HOH A 3 2703 132 HOH HOH . M 6 HOH A 4 2704 60 HOH HOH . M 6 HOH A 5 2705 62 HOH HOH . M 6 HOH A 6 2706 120 HOH HOH . M 6 HOH A 7 2707 17 HOH HOH . M 6 HOH A 8 2708 41 HOH HOH . M 6 HOH A 9 2709 84 HOH HOH . M 6 HOH A 10 2710 117 HOH HOH . M 6 HOH A 11 2711 65 HOH HOH . M 6 HOH A 12 2712 32 HOH HOH . M 6 HOH A 13 2713 14 HOH HOH . M 6 HOH A 14 2714 92 HOH HOH . M 6 HOH A 15 2715 68 HOH HOH . M 6 HOH A 16 2716 12 HOH HOH . M 6 HOH A 17 2717 91 HOH HOH . M 6 HOH A 18 2718 125 HOH HOH . M 6 HOH A 19 2719 26 HOH HOH . M 6 HOH A 20 2720 78 HOH HOH . M 6 HOH A 21 2721 7 HOH HOH . M 6 HOH A 22 2722 5 HOH HOH . M 6 HOH A 23 2723 1 HOH HOH . M 6 HOH A 24 2724 97 HOH HOH . M 6 HOH A 25 2725 18 HOH HOH . M 6 HOH A 26 2726 63 HOH HOH . M 6 HOH A 27 2727 15 HOH HOH . M 6 HOH A 28 2728 50 HOH HOH . M 6 HOH A 29 2729 69 HOH HOH . M 6 HOH A 30 2730 109 HOH HOH . M 6 HOH A 31 2731 112 HOH HOH . M 6 HOH A 32 2732 57 HOH HOH . M 6 HOH A 33 2733 105 HOH HOH . M 6 HOH A 34 2734 45 HOH HOH . M 6 HOH A 35 2735 93 HOH HOH . M 6 HOH A 36 2736 47 HOH HOH . M 6 HOH A 37 2737 129 HOH HOH . M 6 HOH A 38 2738 22 HOH HOH . M 6 HOH A 39 2739 44 HOH HOH . M 6 HOH A 40 2740 29 HOH HOH . M 6 HOH A 41 2741 53 HOH HOH . M 6 HOH A 42 2742 16 HOH HOH . M 6 HOH A 43 2743 28 HOH HOH . M 6 HOH A 44 2744 23 HOH HOH . M 6 HOH A 45 2745 21 HOH HOH . M 6 HOH A 46 2746 27 HOH HOH . M 6 HOH A 47 2747 38 HOH HOH . M 6 HOH A 48 2748 4 HOH HOH . M 6 HOH A 49 2749 123 HOH HOH . M 6 HOH A 50 2750 89 HOH HOH . M 6 HOH A 51 2751 13 HOH HOH . M 6 HOH A 52 2752 2 HOH HOH . M 6 HOH A 53 2753 9 HOH HOH . M 6 HOH A 54 2754 86 HOH HOH . M 6 HOH A 55 2755 25 HOH HOH . M 6 HOH A 56 2756 43 HOH HOH . M 6 HOH A 57 2757 110 HOH HOH . M 6 HOH A 58 2758 83 HOH HOH . M 6 HOH A 59 2759 37 HOH HOH . M 6 HOH A 60 2760 107 HOH HOH . M 6 HOH A 61 2761 111 HOH HOH . M 6 HOH A 62 2762 130 HOH HOH . M 6 HOH A 63 2763 88 HOH HOH . M 6 HOH A 64 2764 61 HOH HOH . M 6 HOH A 65 2765 75 HOH HOH . M 6 HOH A 66 2766 133 HOH HOH . M 6 HOH A 67 2767 118 HOH HOH . M 6 HOH A 68 2768 58 HOH HOH . M 6 HOH A 69 2769 113 HOH HOH . M 6 HOH A 70 2770 46 HOH HOH . M 6 HOH A 71 2771 119 HOH HOH . M 6 HOH A 72 2772 70 HOH HOH . M 6 HOH A 73 2773 56 HOH HOH . M 6 HOH A 74 2774 122 HOH HOH . M 6 HOH A 75 2775 116 HOH HOH . M 6 HOH A 76 2776 128 HOH HOH . M 6 HOH A 77 2777 90 HOH HOH . N 6 HOH B 1 2701 104 HOH HOH . N 6 HOH B 2 2702 115 HOH HOH . N 6 HOH B 3 2703 102 HOH HOH . N 6 HOH B 4 2704 76 HOH HOH . N 6 HOH B 5 2705 54 HOH HOH . N 6 HOH B 6 2706 6 HOH HOH . N 6 HOH B 7 2707 8 HOH HOH . N 6 HOH B 8 2708 67 HOH HOH . N 6 HOH B 9 2709 96 HOH HOH . N 6 HOH B 10 2710 10 HOH HOH . N 6 HOH B 11 2711 31 HOH HOH . N 6 HOH B 12 2712 131 HOH HOH . N 6 HOH B 13 2713 42 HOH HOH . N 6 HOH B 14 2714 94 HOH HOH . N 6 HOH B 15 2715 55 HOH HOH . N 6 HOH B 16 2716 106 HOH HOH . N 6 HOH B 17 2717 36 HOH HOH . N 6 HOH B 18 2718 59 HOH HOH . N 6 HOH B 19 2719 11 HOH HOH . N 6 HOH B 20 2720 35 HOH HOH . N 6 HOH B 21 2721 3 HOH HOH . N 6 HOH B 22 2722 48 HOH HOH . N 6 HOH B 23 2723 66 HOH HOH . N 6 HOH B 24 2724 73 HOH HOH . N 6 HOH B 25 2725 85 HOH HOH . N 6 HOH B 26 2726 52 HOH HOH . N 6 HOH B 27 2727 49 HOH HOH . N 6 HOH B 28 2728 64 HOH HOH . N 6 HOH B 29 2729 20 HOH HOH . N 6 HOH B 30 2730 33 HOH HOH . N 6 HOH B 31 2731 34 HOH HOH . N 6 HOH B 32 2732 126 HOH HOH . N 6 HOH B 33 2733 51 HOH HOH . N 6 HOH B 34 2734 87 HOH HOH . N 6 HOH B 35 2735 81 HOH HOH . N 6 HOH B 36 2736 80 HOH HOH . N 6 HOH B 37 2737 103 HOH HOH . N 6 HOH B 38 2738 99 HOH HOH . N 6 HOH B 39 2739 74 HOH HOH . N 6 HOH B 40 2740 39 HOH HOH . N 6 HOH B 41 2741 100 HOH HOH . N 6 HOH B 42 2742 98 HOH HOH . N 6 HOH B 43 2743 124 HOH HOH . N 6 HOH B 44 2744 19 HOH HOH . N 6 HOH B 45 2745 134 HOH HOH . N 6 HOH B 46 2746 79 HOH HOH . N 6 HOH B 47 2747 95 HOH HOH . N 6 HOH B 48 2748 24 HOH HOH . N 6 HOH B 49 2749 77 HOH HOH . N 6 HOH B 50 2750 121 HOH HOH . N 6 HOH B 51 2751 108 HOH HOH . N 6 HOH B 52 2752 101 HOH HOH . N 6 HOH B 53 2753 30 HOH HOH . N 6 HOH B 54 2754 40 HOH HOH . N 6 HOH B 55 2755 127 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 . . . D 3 16.975 19.717 192.997 1 45.46 ? PG ATP 2602 A 1 HETATM 2 O O1G ATP . . . D 3 17.48 20.763 192.035 1 36.8 ? O1G ATP 2602 A 1 HETATM 3 O O2G ATP . . . D 3 15.687 20.207 193.743 1 52.3 ? O2G ATP 2602 A 1 HETATM 4 O O3G ATP . . . D 3 17.981 19.18 194.028 1 46.57 ? O3G ATP 2602 A 1 HETATM 5 P PB ATP . . . D 3 15.606 18.09 191.045 1 44.23 ? PB ATP 2602 A 1 HETATM 6 O O1B ATP . . . D 3 14.157 18.303 191.381 1 54.33 ? O1B ATP 2602 A 1 HETATM 7 O O2B ATP . . . D 3 16.181 18.872 189.865 1 32.01 ? O2B ATP 2602 A 1 HETATM 8 O O3B ATP . . . D 3 16.514 18.438 192.219 1 38.3 ? O3B ATP 2602 A 1 HETATM 9 P PA ATP . . . D 3 15.507 15.518 189.696 1 37.5 ? PA ATP 2602 A 1 HETATM 10 O O1A ATP . . . D 3 15.529 16.2 188.388 1 36.83 ? O1A ATP 2602 A 1 HETATM 11 O O2A ATP . . . D 3 14.123 14.968 190.105 1 40.27 ? O2A ATP 2602 A 1 HETATM 12 O O3A ATP . . . D 3 15.92 16.553 190.762 1 40.17 ? O3A ATP 2602 A 1 HETATM 13 O O5' ATP . . . D 3 16.635 14.401 189.779 1 46.19 ? O5' ATP 2602 A 1 HETATM 14 C C5' ATP . . . D 3 16.45 13.185 190.538 1 25.97 ? C5' ATP 2602 A 1 HETATM 15 C C4' ATP . . . D 3 17.375 13.222 191.726 1 36.8 ? C4' ATP 2602 A 1 HETATM 16 O O4' ATP . . . D 3 18.658 13.739 191.323 1 36.43 ? O4' ATP 2602 A 1 HETATM 17 C C3' ATP . . . D 3 16.915 14.121 192.868 1 32.13 ? C3' ATP 2602 A 1 HETATM 18 O O3' ATP . . . D 3 16.177 13.323 193.786 1 29.38 ? O3' ATP 2602 A 1 HETATM 19 C C2' ATP . . . D 3 18.233 14.592 193.516 1 43.8 ? C2' ATP 2602 A 1 HETATM 20 O O2' ATP . . . D 3 18.543 13.83 194.689 1 28.36 ? O2' ATP 2602 A 1 HETATM 21 C C1' ATP . . . D 3 19.289 14.381 192.417 1 36.64 ? C1' ATP 2602 A 1 HETATM 22 N N9 ATP . . . D 3 19.963 15.569 191.891 1 40.89 ? N9 ATP 2602 A 1 HETATM 23 C C8 ATP . . . D 3 19.394 16.585 191.166 1 38.08 ? C8 ATP 2602 A 1 HETATM 24 N N7 ATP . . . D 3 20.249 17.499 190.757 1 31.03 ? N7 ATP 2602 A 1 HETATM 25 C C5 ATP . . . D 3 21.476 17.025 191.218 1 36.42 ? C5 ATP 2602 A 1 HETATM 26 C C6 ATP . . . D 3 22.8 17.521 191.125 1 37.7 ? C6 ATP 2602 A 1 HETATM 27 N N6 ATP . . . D 3 23.127 18.657 190.496 1 31.2 ? N6 ATP 2602 A 1 HETATM 28 N N1 ATP . . . D 3 23.793 16.796 191.7 1 38.98 ? N1 ATP 2602 A 1 HETATM 29 C C2 ATP . . . D 3 23.488 15.659 192.327 1 34.84 ? C2 ATP 2602 A 1 HETATM 30 N N3 ATP . . . D 3 22.286 15.106 192.476 1 35.49 ? N3 ATP 2602 A 1 HETATM 31 C C4 ATP . . . D 3 21.314 15.832 191.902 1 40.73 ? C4 ATP 2602 A 1 # _model_server_stats.io_time_ms 132 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 51 _model_server_stats.query_time_ms 574 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 31 #