data_9DVA # _model_server_result.job_id RHcfzQ85g0mVWwQW1IVa0w _model_server_result.datetime_utc '2024-12-19 04:17:51' _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 9dva # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":401}' # _entry.id 9DVA # _exptl.entry_id 9DVA _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 5 _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 9DVA _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DVA _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_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 _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 ? 4 I N N ? 4 K N N ? 4 M N N ? 4 O N N ? 4 Q 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 A C GLU 72 A GLU 72 1_555 A N HIC 73 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C HIC 73 A HIC 73 1_555 A N GLY 74 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C GLU 72 B GLU 72 1_555 B N HIC 73 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 B C HIC 73 B HIC 73 1_555 B N GLY 74 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 C C GLU 72 C GLU 72 1_555 C N HIC 73 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale6 C C HIC 73 C HIC 73 1_555 C N GLY 74 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale7 D C GLU 72 D GLU 72 1_555 D N HIC 73 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 D C HIC 73 D HIC 73 1_555 D N GLY 74 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 E C GLU 72 E GLU 72 1_555 E N HIC 73 E HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale10 E C HIC 73 E HIC 73 1_555 E N GLY 74 E GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 I O2B ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc2 I O3A ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc3 K O2B ADP . B ADP 401 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.657 ? metalc ? metalc4 M O3B ADP . C ADP 401 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc5 O O3B ADP . D ADP 401 1_555 P MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc6 Q O2B ADP . E ADP 401 1_555 R MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? # _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 ? # 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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 9DVA _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 4 ADP A 1 401 401 ADP ADP . J 5 MG A 1 402 402 MG MG . K 4 ADP B 1 401 401 ADP ADP . L 5 MG B 1 402 402 MG MG . M 4 ADP C 1 401 401 ADP ADP . N 5 MG C 1 402 402 MG MG . O 4 ADP D 1 401 401 ADP ADP . P 5 MG D 1 402 402 MG MG . Q 4 ADP E 1 401 401 ADP ADP . R 5 MG E 1 402 402 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 4 175.682 229.611 267.209 1 70.71 ? PB ADP 401 D 1 HETATM 2 O O1B ADP . . . O 4 177.16 229.325 267.208 1 70.71 ? O1B ADP 401 D 1 HETATM 3 O O2B ADP . . . O 4 175.288 230.824 266.405 1 70.71 -1 O2B ADP 401 D 1 HETATM 4 O O3B ADP . . . O 4 175.034 229.536 268.57 1 70.71 ? O3B ADP 401 D 1 HETATM 5 P PA ADP . . . O 4 175.292 226.857 266.862 1 70.71 ? PA ADP 401 D 1 HETATM 6 O O1A ADP . . . O 4 173.975 226.128 266.783 1 70.71 -1 O1A ADP 401 D 1 HETATM 7 O O2A ADP . . . O 4 176.041 226.901 268.17 1 70.71 ? O2A ADP 401 D 1 HETATM 8 O O3A ADP . . . O 4 175.037 228.377 266.4 1 70.71 ? O3A ADP 401 D 1 HETATM 9 O O5' ADP . . . O 4 176.259 226.246 265.73 1 70.71 ? O5' ADP 401 D 1 HETATM 10 C C5' ADP . . . O 4 177.078 227.074 264.912 1 70.71 ? C5' ADP 401 D 1 HETATM 11 C C4' ADP . . . O 4 178.335 226.306 264.519 1 70.71 ? C4' ADP 401 D 1 HETATM 12 O O4' ADP . . . O 4 178.197 224.912 264.797 1 70.71 ? O4' ADP 401 D 1 HETATM 13 C C3' ADP . . . O 4 178.653 226.421 263.038 1 70.71 ? C3' ADP 401 D 1 HETATM 14 O O3' ADP . . . O 4 179.769 227.291 262.847 1 70.71 ? O3' ADP 401 D 1 HETATM 15 C C2' ADP . . . O 4 179.026 225.022 262.593 1 70.71 ? C2' ADP 401 D 1 HETATM 16 O O2' ADP . . . O 4 180.341 225.016 262.036 1 70.71 ? O2' ADP 401 D 1 HETATM 17 C C1' ADP . . . O 4 178.988 224.182 263.858 1 70.71 ? C1' ADP 401 D 1 HETATM 18 N N9 ADP . . . O 4 178.416 222.842 263.581 1 70.71 ? N9 ADP 401 D 1 HETATM 19 C C8 ADP . . . O 4 177.126 222.559 263.327 1 70.71 ? C8 ADP 401 D 1 HETATM 20 N N7 ADP . . . O 4 176.951 221.23 263.113 1 70.71 ? N7 ADP 401 D 1 HETATM 21 C C5 ADP . . . O 4 178.154 220.64 263.228 1 70.71 ? C5 ADP 401 D 1 HETATM 22 C C6 ADP . . . O 4 178.685 219.262 263.123 1 70.71 ? C6 ADP 401 D 1 HETATM 23 N N6 ADP . . . O 4 177.871 218.217 262.843 1 70.71 ? N6 ADP 401 D 1 HETATM 24 N N1 ADP . . . O 4 180.009 219.081 263.315 1 70.71 ? N1 ADP 401 D 1 HETATM 25 C C2 ADP . . . O 4 180.829 220.11 263.594 1 70.71 ? C2 ADP 401 D 1 HETATM 26 N N3 ADP . . . O 4 180.417 221.384 263.703 1 70.71 ? N3 ADP 401 D 1 HETATM 27 C C4 ADP . . . O 4 179.115 221.708 263.534 1 70.71 ? C4 ADP 401 D 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #