data_7DYK # _model_server_result.job_id -Zg3x5zUmslMzrFemmohjg _model_server_result.datetime_utc '2024-11-28 15:34:04' _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 7dyk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 7DYK # _exptl.entry_id 7DYK _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 4 _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 7DYK _cell.length_a 94.847 _cell.length_b 94.847 _cell.length_c 180.56 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DYK _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_455 -y-1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -94.847 0 0 3 'crystal symmetry operation' 3_445 -x+y-1,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -47.4235 -82.139911 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 D N N ? 2 G N N ? 2 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 OG1 THR 53 A THR 53 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc2 A OG1 THR 295 A THR 295 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc3 C O2G ATP . A ATP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc4 C O2B ATP . A ATP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? metalc ? metalc5 D O2G ATP . A ATP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc6 D O1B ATP . A ATP 602 1_555 F MG MG . A MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc7 E MG MG . A MG 603 1_555 K O HOH . A HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc8 E MG MG . A MG 603 1_555 K O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc9 F MG MG . A MG 604 1_555 K O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc10 F MG MG . A MG 604 1_555 K O HOH . A HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? metalc ? metalc11 B OG1 THR 53 B THR 53 1_555 I MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc12 B OG1 THR 295 B THR 295 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc13 G O3G ATP . B ATP 601 1_555 I MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc14 G O2B ATP . B ATP 601 1_555 I MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc15 H O3G ATP . B ATP 602 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.922 ? metalc ? metalc16 H O1B ATP . B ATP 602 1_555 J MG MG . B MG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc17 J MG MG . B MG 604 1_555 L O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc18 J MG MG . B MG 604 1_555 L O HOH . B HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? # _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 7DYK _atom_sites.fract_transf_matrix[1][1] 0.010543 _atom_sites.fract_transf_matrix[1][2] 0.006087 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012174 _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] 0.005538 _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 1 601 501 ATP ATP . D 2 ATP A 1 602 601 ATP ATP . E 3 MG A 1 603 1 MG MG . F 3 MG A 1 604 2 MG MG . G 2 ATP B 1 601 501 ATP ATP . H 2 ATP B 1 602 601 ATP ATP . I 3 MG B 1 603 3 MG MG . J 3 MG B 1 604 4 MG MG . K 4 HOH A 1 701 8 HOH HOH . K 4 HOH A 2 702 10 HOH HOH . K 4 HOH A 3 703 1 HOH HOH . K 4 HOH A 4 704 9 HOH HOH . K 4 HOH A 5 705 7 HOH HOH . K 4 HOH A 6 706 3 HOH HOH . K 4 HOH A 7 707 6 HOH HOH . L 4 HOH B 1 701 12 HOH HOH . L 4 HOH B 2 702 11 HOH HOH . L 4 HOH B 3 703 2 HOH HOH . L 4 HOH B 4 704 5 HOH HOH . L 4 HOH B 5 705 4 HOH HOH . L 4 HOH B 6 706 13 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 2 -21.451 -23.361 -18.042 1 66.98 ? PG ATP 602 A 1 HETATM 2 O O1G ATP . . . D 2 -22.938 -23.094 -18.094 1 65.82 ? O1G ATP 602 A 1 HETATM 3 O O2G ATP . . . D 2 -20.784 -22.678 -16.872 1 67.35 ? O2G ATP 602 A 1 HETATM 4 O O3G ATP . . . D 2 -21.112 -24.827 -18.137 1 66.06 ? O3G ATP 602 A 1 HETATM 5 P PB ATP . . . D 2 -21.181 -21.305 -20.056 1 60.5 ? PB ATP 602 A 1 HETATM 6 O O1B ATP . . . D 2 -20.888 -20.22 -19.076 1 60.49 ? O1B ATP 602 A 1 HETATM 7 O O2B ATP . . . D 2 -22.537 -21.425 -20.661 1 60.81 ? O2B ATP 602 A 1 HETATM 8 O O3B ATP . . . D 2 -20.818 -22.7 -19.368 1 62.99 ? O3B ATP 602 A 1 HETATM 9 P PA ATP . . . D 2 -18.567 -21.474 -21.409 1 57.83 ? PA ATP 602 A 1 HETATM 10 O O1A ATP . . . D 2 -18.026 -22.009 -20.125 1 57.97 ? O1A ATP 602 A 1 HETATM 11 O O2A ATP . . . D 2 -17.952 -20.247 -21.996 1 55.74 ? O2A ATP 602 A 1 HETATM 12 O O3A ATP . . . D 2 -20.139 -21.225 -21.264 1 59.59 ? O3A ATP 602 A 1 HETATM 13 O O5' ATP . . . D 2 -18.594 -22.648 -22.495 1 56.59 ? O5' ATP 602 A 1 HETATM 14 C C5' ATP . . . D 2 -17.648 -22.609 -23.583 1 55.14 ? C5' ATP 602 A 1 HETATM 15 C C4' ATP . . . D 2 -18.196 -23.393 -24.748 1 54.3 ? C4' ATP 602 A 1 HETATM 16 O O4' ATP . . . D 2 -17.638 -22.847 -25.972 1 53.41 ? O4' ATP 602 A 1 HETATM 17 C C3' ATP . . . D 2 -17.866 -24.893 -24.772 1 52.98 ? C3' ATP 602 A 1 HETATM 18 O O3' ATP . . . D 2 -18.907 -25.682 -24.208 1 51.83 ? O3' ATP 602 A 1 HETATM 19 C C2' ATP . . . D 2 -17.716 -25.164 -26.27 1 52.42 ? C2' ATP 602 A 1 HETATM 20 O O2' ATP . . . D 2 -18.957 -25.339 -26.919 1 52.28 ? O2' ATP 602 A 1 HETATM 21 C C1' ATP . . . D 2 -17.058 -23.874 -26.742 1 51.82 ? C1' ATP 602 A 1 HETATM 22 N N9 ATP . . . D 2 -15.611 -23.823 -26.558 1 50.64 ? N9 ATP 602 A 1 HETATM 23 C C8 ATP . . . D 2 -14.908 -23.692 -25.383 1 49.94 ? C8 ATP 602 A 1 HETATM 24 N N7 ATP . . . D 2 -13.609 -23.677 -25.57 1 49.57 ? N7 ATP 602 A 1 HETATM 25 C C5 ATP . . . D 2 -13.451 -23.805 -26.943 1 49.43 ? C5 ATP 602 A 1 HETATM 26 C C6 ATP . . . D 2 -12.313 -23.855 -27.767 1 49.59 ? C6 ATP 602 A 1 HETATM 27 N N6 ATP . . . D 2 -11.068 -23.779 -27.307 1 50.16 ? N6 ATP 602 A 1 HETATM 28 N N1 ATP . . . D 2 -12.515 -23.988 -29.101 1 50.65 ? N1 ATP 602 A 1 HETATM 29 C C2 ATP . . . D 2 -13.774 -24.064 -29.556 1 50.57 ? C2 ATP 602 A 1 HETATM 30 N N3 ATP . . . D 2 -14.918 -24.027 -28.876 1 50.18 ? N3 ATP 602 A 1 HETATM 31 C C4 ATP . . . D 2 -14.681 -23.895 -27.559 1 50.21 ? C4 ATP 602 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #