data_8DGC # _model_server_result.job_id 1pnwl7WdsihwOvCOtLBnVQ _model_server_result.datetime_utc '2025-07-03 23:14:41' _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 8dgc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":2101}' # _entry.id 8DGC # _exptl.entry_id 8DGC _exptl.method 'ELECTRON MICROSCOPY' # _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 8 _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 8DGC _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DGC _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_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,O,P,Q,R,S,T,U,V,W,X _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 ? _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 I N N ? 3 K N N ? 3 M N N ? 3 O N N ? 3 Q N N ? 3 S N N ? 3 U N N ? 3 W 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 OG SER 294 A SER 294 1_555 J MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc2 I O1G ATP . A ATP 2101 1_555 J MG MG . A MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc3 B OG SER 294 B SER 294 1_555 L MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc4 K O1G ATP . B ATP 2101 1_555 L MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc5 K O2B ATP . B ATP 2101 1_555 L MG MG . B MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc6 C OG SER 294 C SER 294 1_555 N MG MG . C MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc7 M O1G ATP . C ATP 2101 1_555 N MG MG . C MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc8 D OG SER 294 D SER 294 1_555 P MG MG . D MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc9 O O1G ATP . D ATP 2101 1_555 P MG MG . D MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc10 O O2B ATP . D ATP 2101 1_555 P MG MG . D MG 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc11 Q O2G ATP . E ATP 601 1_555 R MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc12 Q O2B ATP . E ATP 601 1_555 R MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc13 Q O3B ATP . E ATP 601 1_555 R MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc14 S O2G ATP . F ATP 601 1_555 T MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc15 S O2B ATP . F ATP 601 1_555 T MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc16 S O3B ATP . F ATP 601 1_555 T MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? metalc ? metalc17 U O2G ATP . G ATP 601 1_555 V MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc18 U O2B ATP . G ATP 601 1_555 V MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc19 U O3B ATP . G ATP 601 1_555 V MG MG . G MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? metalc ? metalc20 W O2G ATP . H ATP 601 1_555 X MG MG . H MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc21 W O2B ATP . H ATP 601 1_555 X MG MG . H MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc22 W O3B ATP . H ATP 601 1_555 X MG MG . H MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? # _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 8DGC _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 I 3 ATP A 1 2101 2101 ATP ATP . J 4 MG A 1 2102 2102 MG MG . K 3 ATP B 1 2101 2101 ATP ATP . L 4 MG B 1 2102 2102 MG MG . M 3 ATP C 1 2101 2101 ATP ATP . N 4 MG C 1 2102 2102 MG MG . O 3 ATP D 1 2101 2101 ATP ATP . P 4 MG D 1 2102 2102 MG MG . Q 3 ATP E 1 601 601 ATP ATP . R 4 MG E 1 602 602 MG MG . S 3 ATP F 1 601 601 ATP ATP . T 4 MG F 1 602 602 MG MG . U 3 ATP G 1 601 601 ATP ATP . V 4 MG G 1 602 602 MG MG . W 3 ATP H 1 601 601 ATP ATP . X 4 MG H 1 602 602 MG MG . # 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 . . . K 3 150.409 188.46 90.309 1 55.04 ? PG ATP 2101 B 1 HETATM 2 O O1G ATP . . . K 3 150.375 187.693 89.04 1 64.33 ? O1G ATP 2101 B 1 HETATM 3 O O2G ATP . . . K 3 149.12 188.392 91.091 1 63.39 ? O2G ATP 2101 B 1 HETATM 4 O O3G ATP . . . K 3 151.575 188.087 91.208 1 67.76 ? O3G ATP 2101 B 1 HETATM 5 P PB ATP . . . K 3 151.587 190.946 89.258 1 63.17 ? PB ATP 2101 B 1 HETATM 6 O O1B ATP . . . K 3 152.799 191.222 90.045 1 67.02 ? O1B ATP 2101 B 1 HETATM 7 O O2B ATP . . . K 3 151.826 190.319 87.895 1 71.89 ? O2B ATP 2101 B 1 HETATM 8 O O3B ATP . . . K 3 150.607 190 90.02 1 63.18 ? O3B ATP 2101 B 1 HETATM 9 P PA ATP . . . K 3 149.979 192.935 87.819 1 58.71 ? PA ATP 2101 B 1 HETATM 10 O O1A ATP . . . K 3 148.88 192.107 87.286 1 63.04 ? O1A ATP 2101 B 1 HETATM 11 O O2A ATP . . . K 3 151.068 193.261 86.812 1 65.38 ? O2A ATP 2101 B 1 HETATM 12 O O3A ATP . . . K 3 150.692 192.237 89.035 1 65.77 ? O3A ATP 2101 B 1 HETATM 13 O O5' ATP . . . K 3 149.442 194.286 88.428 1 67.94 ? O5' ATP 2101 B 1 HETATM 14 C C5' ATP . . . K 3 148.103 194.389 88.953 1 67.62 ? C5' ATP 2101 B 1 HETATM 15 C C4' ATP . . . K 3 147.657 195.827 88.916 1 62.08 ? C4' ATP 2101 B 1 HETATM 16 O O4' ATP . . . K 3 148.8 196.688 89.058 1 65.28 ? O4' ATP 2101 B 1 HETATM 17 C C3' ATP . . . K 3 146.965 196.258 87.623 1 62.08 ? C3' ATP 2101 B 1 HETATM 18 O O3' ATP . . . K 3 145.553 196.333 87.779 1 66.86 ? O3' ATP 2101 B 1 HETATM 19 C C2' ATP . . . K 3 147.563 197.641 87.311 1 59.13 ? C2' ATP 2101 B 1 HETATM 20 O O2' ATP . . . K 3 146.563 198.646 87.21 1 60.27 ? O2' ATP 2101 B 1 HETATM 21 C C1' ATP . . . K 3 148.454 197.935 88.519 1 56.19 ? C1' ATP 2101 B 1 HETATM 22 N N9 ATP . . . K 3 149.68 198.641 88.173 1 57.66 ? N9 ATP 2101 B 1 HETATM 23 C C8 ATP . . . K 3 150.969 198.198 88.312 1 65.73 ? C8 ATP 2101 B 1 HETATM 24 N N7 ATP . . . K 3 151.875 199.053 87.907 1 61.05 ? N7 ATP 2101 B 1 HETATM 25 C C5 ATP . . . K 3 151.13 200.139 87.479 1 59.79 ? C5 ATP 2101 B 1 HETATM 26 C C6 ATP . . . K 3 151.495 201.381 86.934 1 63.24 ? C6 ATP 2101 B 1 HETATM 27 N N6 ATP . . . K 3 152.759 201.753 86.721 1 66.41 ? N6 ATP 2101 B 1 HETATM 28 N N1 ATP . . . K 3 150.505 202.237 86.607 1 68.52 ? N1 ATP 2101 B 1 HETATM 29 C C2 ATP . . . K 3 149.24 201.871 86.818 1 67.18 ? C2 ATP 2101 B 1 HETATM 30 N N3 ATP . . . K 3 148.776 200.729 87.325 1 61.51 ? N3 ATP 2101 B 1 HETATM 31 C C4 ATP . . . K 3 149.776 199.899 87.637 1 60.38 ? C4 ATP 2101 B 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 96 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #