data_6YO0 # _model_server_result.job_id oge0rczKMCliz_zpefIWmQ _model_server_result.datetime_utc '2025-03-03 12:15:43' _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 6yo0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":900}' # _entry.id 6YO0 # _exptl.entry_id 6YO0 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 6YO0 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YO0 _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 PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,O,P,Q,R,S,T,U,V _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 ? 11 O N N ? 11 U 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 covale ? covale1 E N LYS 206 B1 LYS 206 1_555 Q O2B ATP . B1 ATP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? covale ? covale2 E NH2 ARG 404 B1 ARG 404 1_555 U O2A ADP . E1 ADP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? covale ? covale3 Q O3G ATP . B1 ATP 900 1_555 F NH1 ARG 375 F1 ARG 375 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? metalc ? metalc1 C OG1 THR 207 C1 THR 207 1_555 N MG MG . C1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc2 M O3G ATP . C1 ATP 900 1_555 N MG MG . C1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc3 M O1B ATP . C1 ATP 900 1_555 N MG MG . C1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc4 D OG1 THR 182 D1 THR 182 1_555 P MG MG . D1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc5 D OE2 GLU 207 D1 GLU 207 1_555 P MG MG . D1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc6 O O3B ADP . D1 ADP 900 1_555 P MG MG . D1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? metalc ? metalc7 E OG1 THR 207 B1 THR 207 1_555 R MG MG . B1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc8 Q O1G ATP . B1 ATP 900 1_555 R MG MG . B1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc9 Q O3B ATP . B1 ATP 900 1_555 R MG MG . B1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc10 G OG1 THR 207 A1 THR 207 1_555 T MG MG . A1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc11 S O3G ATP . A1 ATP 900 1_555 T MG MG . A1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc12 S O1B ATP . A1 ATP 900 1_555 T MG MG . A1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? metalc ? metalc13 H OG1 THR 182 E1 THR 182 1_555 V MG MG . E1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc14 U O2B ADP . E1 ADP 900 1_555 V MG MG . E1 MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6YO0 _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 M 9 ATP C1 1 900 900 ATP ATP . N 10 MG C1 1 1001 1001 MG MG . O 11 ADP D1 1 900 900 ADP ADP . P 10 MG D1 1 1001 1001 MG MG . Q 9 ATP B1 1 900 900 ATP ATP . R 10 MG B1 1 1001 1001 MG MG . S 9 ATP A1 1 900 900 ATP ATP . T 10 MG A1 1 1001 1001 MG MG . U 11 ADP E1 1 900 900 ADP ADP . V 10 MG E1 1 1001 1001 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 PB ADP . . . O 11 213.331 272.036 348.018 1 71.32 ? PB ADP 900 D1 1 HETATM 2 O O1B ADP . . . O 11 212.882 270.623 348.308 1 71.32 ? O1B ADP 900 D1 1 HETATM 3 O O2B ADP . . . O 11 212.196 272.996 348.308 1 71.32 ? O2B ADP 900 D1 1 HETATM 4 O O3B ADP . . . O 11 214.518 272.371 348.881 1 71.32 ? O3B ADP 900 D1 1 HETATM 5 P PA ADP . . . O 11 214.853 271.129 345.788 1 71.32 ? PA ADP 900 D1 1 HETATM 6 O O1A ADP . . . O 11 216.095 271.881 345.412 1 71.32 ? O1A ADP 900 D1 1 HETATM 7 O O2A ADP . . . O 11 215.204 270.062 346.786 1 71.32 ? O2A ADP 900 D1 1 HETATM 8 O O3A ADP . . . O 11 213.75 272.142 346.442 1 71.32 ? O3A ADP 900 D1 1 HETATM 9 O O5' ADP . . . O 11 214.204 270.409 344.461 1 71.32 ? O5' ADP 900 D1 1 HETATM 10 C C5' ADP . . . O 11 214.829 269.239 344.085 1 71.32 ? C5' ADP 900 D1 1 HETATM 11 C C4' ADP . . . O 11 214.141 268.622 342.911 1 71.32 ? C4' ADP 900 D1 1 HETATM 12 O O4' ADP . . . O 11 214.316 269.335 341.831 1 71.32 ? O4' ADP 900 D1 1 HETATM 13 C C3' ADP . . . O 11 214.8 267.11 342.636 1 71.32 ? C3' ADP 900 D1 1 HETATM 14 O O3' ADP . . . O 11 213.759 266.18 342.178 1 71.32 ? O3' ADP 900 D1 1 HETATM 15 C C2' ADP . . . O 11 215.639 267.265 341.747 1 71.32 ? C2' ADP 900 D1 1 HETATM 16 O O2' ADP . . . O 11 215.792 265.98 340.962 1 71.32 ? O2' ADP 900 D1 1 HETATM 17 C C1' ADP . . . O 11 215.008 268.424 340.836 1 71.32 ? C1' ADP 900 D1 1 HETATM 18 N N9 ADP . . . O 11 215.949 268.996 340.1 1 71.32 ? N9 ADP 900 D1 1 HETATM 19 C C8 ADP . . . O 11 216.342 269.994 340.898 1 71.32 ? C8 ADP 900 D1 1 HETATM 20 N N7 ADP . . . O 11 217.31 270.672 340.28 1 71.32 ? N7 ADP 900 D1 1 HETATM 21 C C5 ADP . . . O 11 217.526 270.092 339.081 1 71.32 ? C5 ADP 900 D1 1 HETATM 22 C C6 ADP . . . O 11 218.4 270.384 338.058 1 71.32 ? C6 ADP 900 D1 1 HETATM 23 N N6 ADP . . . O 11 219.399 271.421 337.905 1 71.32 ? N6 ADP 900 D1 1 HETATM 24 N N1 ADP . . . O 11 218.41 269.645 336.968 1 71.32 ? N1 ADP 900 D1 1 HETATM 25 C C2 ADP . . . O 11 217.569 268.606 336.855 1 71.32 ? C2 ADP 900 D1 1 HETATM 26 N N3 ADP . . . O 11 216.714 268.319 337.855 1 71.32 ? N3 ADP 900 D1 1 HETATM 27 C C4 ADP . . . O 11 216.701 269.073 338.971 1 71.32 ? C4 ADP 900 D1 1 HETATM 28 H "H5'1" ADP . . . O 11 214.797 268.626 344.831 1 71.32 ? "H5'1" ADP 900 D1 1 HETATM 29 H "H5'2" ADP . . . O 11 215.753 269.435 343.878 1 71.32 ? "H5'2" ADP 900 D1 1 HETATM 30 H H4' ADP . . . O 11 213.196 268.534 343.094 1 71.32 ? H4' ADP 900 D1 1 HETATM 31 H H3' ADP . . . O 11 215.227 266.776 343.438 1 71.32 ? H3' ADP 900 D1 1 HETATM 32 H HO3' ADP . . . O 11 214.124 265.52 341.787 1 71.32 ? HO3' ADP 900 D1 1 HETATM 33 H H2' ADP . . . O 11 216.484 267.542 342.126 1 71.32 ? H2' ADP 900 D1 1 HETATM 34 H HO2' ADP . . . O 11 215.935 265.339 341.501 1 71.32 ? HO2' ADP 900 D1 1 HETATM 35 H H1' ADP . . . O 11 214.34 268.037 340.253 1 71.32 ? H1' ADP 900 D1 1 HETATM 36 H H8 ADP . . . O 11 216.024 270.202 341.74 1 71.32 ? H8 ADP 900 D1 1 HETATM 37 H HN61 ADP . . . O 11 219.439 272.065 338.472 1 71.32 ? HN61 ADP 900 D1 1 HETATM 38 H HN62 ADP . . . O 11 219.95 271.395 337.246 1 71.32 ? HN62 ADP 900 D1 1 HETATM 39 H H2 ADP . . . O 11 217.576 268.085 336.086 1 71.32 ? H2 ADP 900 D1 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 79 _model_server_stats.query_time_ms 540 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 39 #