data_9B14 # _model_server_result.job_id KyvqXvyCvsE4_D3VA85XYg _model_server_result.datetime_utc '2025-03-02 23:51:22' _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 9b14 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"EA","auth_seq_id":402}' # _entry.id 9B14 # _exptl.entry_id 9B14 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 9B14 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9B14 _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,Y,Z,AA,BA,CA,DA,EA,FA _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 J N N ? 3 M N N ? 3 P N N ? 3 S N N ? 3 V N N ? 3 Y N N ? 3 BA N N ? 3 EA 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 J O3B ADP . A ADP 402 1_555 K MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.8 ? metalc ? metalc2 J O2A ADP . A ADP 402 1_555 K MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? metalc ? metalc3 M O3B ADP . B ADP 402 1_555 N MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc4 M O2A ADP . B ADP 402 1_555 N MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc5 P O3B ADP . C ADP 402 1_555 Q MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.864 ? metalc ? metalc6 P O2A ADP . C ADP 402 1_555 Q MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? metalc ? metalc7 S O3B ADP . D ADP 402 1_555 T MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc8 S O2A ADP . D ADP 402 1_555 T MG MG . D MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc9 V O3B ADP . E ADP 402 1_555 W MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc10 V O2A ADP . E ADP 402 1_555 W MG MG . E MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc11 Y O3B ADP . F ADP 402 1_555 Z MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc12 Y O2A ADP . F ADP 402 1_555 Z MG MG . F MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc13 BA O3B ADP . G ADP 402 1_555 CA MG MG . G MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc14 BA O2A ADP . G ADP 402 1_555 CA MG MG . G MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc15 EA O3B ADP . H ADP 402 1_555 FA MG MG . H MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? metalc ? metalc16 EA O2A ADP . H ADP 402 1_555 FA MG MG . H MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? # _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 9B14 _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 2 CRN A 1 401 401 CRN CRN . J 3 ADP A 1 402 402 ADP ADP . K 4 MG A 1 403 1 MG MG . L 2 CRN B 1 401 401 CRN CRN . M 3 ADP B 1 402 402 ADP ADP . N 4 MG B 1 403 2 MG MG . O 2 CRN C 1 401 401 CRN CRN . P 3 ADP C 1 402 402 ADP ADP . Q 4 MG C 1 403 3 MG MG . R 2 CRN D 1 401 401 CRN CRN . S 3 ADP D 1 402 402 ADP ADP . T 4 MG D 1 403 4 MG MG . U 2 CRN E 1 401 401 CRN CRN . V 3 ADP E 1 402 402 ADP ADP . W 4 MG E 1 403 5 MG MG . X 2 CRN F 1 401 401 CRN CRN . Y 3 ADP F 1 402 402 ADP ADP . Z 4 MG F 1 403 6 MG MG . AA 2 CRN G 1 401 401 CRN CRN . BA 3 ADP G 1 402 402 ADP ADP . CA 4 MG G 1 403 7 MG MG . DA 2 CRN H 1 401 404 CRN CRN . EA 3 ADP H 1 402 402 ADP ADP . FA 4 MG H 1 403 8 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 . . . EA 3 93.085 125.539 151.79 1 121.11 ? PB ADP 402 H 1 HETATM 2 O O1B ADP . . . EA 3 93.391 126.829 152.507 1 128.97 ? O1B ADP 402 H 1 HETATM 3 O O2B ADP . . . EA 3 93.491 124.288 152.523 1 108.98 ? O2B ADP 402 H 1 HETATM 4 O O3B ADP . . . EA 3 93.443 125.552 150.326 1 117.77 ? O3B ADP 402 H 1 HETATM 5 P PA ADP . . . EA 3 90.689 126.169 150.567 1 109.51 ? PA ADP 402 H 1 HETATM 6 O O1A ADP . . . EA 3 89.981 127.391 151.09 1 116.43 ? O1A ADP 402 H 1 HETATM 7 O O2A ADP . . . EA 3 91.648 126.259 149.409 1 113.28 ? O2A ADP 402 H 1 HETATM 8 O O3A ADP . . . EA 3 91.482 125.466 151.771 1 112.51 ? O3A ADP 402 H 1 HETATM 9 O O5' ADP . . . EA 3 89.602 125.038 150.232 1 108.95 ? O5' ADP 402 H 1 HETATM 10 C C5' ADP . . . EA 3 89.611 124.388 148.966 1 110.49 ? C5' ADP 402 H 1 HETATM 11 C C4' ADP . . . EA 3 88.544 123.306 148.96 1 108.99 ? C4' ADP 402 H 1 HETATM 12 O O4' ADP . . . EA 3 88.547 122.593 150.198 1 104.05 ? O4' ADP 402 H 1 HETATM 13 C C3' ADP . . . EA 3 87.156 123.896 148.789 1 112.9 ? C3' ADP 402 H 1 HETATM 14 O O3' ADP . . . EA 3 86.58 123.433 147.565 1 115.12 ? O3' ADP 402 H 1 HETATM 15 C C2' ADP . . . EA 3 86.355 123.414 149.979 1 110.48 ? C2' ADP 402 H 1 HETATM 16 O O2' ADP . . . EA 3 85.07 122.931 149.584 1 115.18 ? O2' ADP 402 H 1 HETATM 17 C C1' ADP . . . EA 3 87.203 122.315 150.591 1 103.65 ? C1' ADP 402 H 1 HETATM 18 N N9 ADP . . . EA 3 87.056 122.297 152.064 1 99.25 ? N9 ADP 402 H 1 HETATM 19 C C8 ADP . . . EA 3 87.758 123.037 152.94 1 103.01 ? C8 ADP 402 H 1 HETATM 20 N N7 ADP . . . EA 3 87.365 122.768 154.211 1 103.41 ? N7 ADP 402 H 1 HETATM 21 C C5 ADP . . . EA 3 86.396 121.841 154.154 1 103.52 ? C5 ADP 402 H 1 HETATM 22 C C6 ADP . . . EA 3 85.55 121.116 155.125 1 111.17 ? C6 ADP 402 H 1 HETATM 23 N N6 ADP . . . EA 3 85.665 121.334 156.453 1 117.09 ? N6 ADP 402 H 1 HETATM 24 N N1 ADP . . . EA 3 84.658 120.227 154.646 1 112.67 ? N1 ADP 402 H 1 HETATM 25 C C2 ADP . . . EA 3 84.525 119.992 153.33 1 112.38 ? C2 ADP 402 H 1 HETATM 26 N N3 ADP . . . EA 3 85.262 120.618 152.398 1 108.67 ? N3 ADP 402 H 1 HETATM 27 C C4 ADP . . . EA 3 86.196 121.534 152.737 1 101.69 ? C4 ADP 402 H 1 HETATM 28 H "H5'1" ADP . . . EA 3 89.414 125.112 148.173 1 110.85 ? "H5'1" ADP 402 H 1 HETATM 29 H "H5'2" ADP . . . EA 3 90.592 123.942 148.787 1 108.58 ? "H5'2" ADP 402 H 1 HETATM 30 H H4' ADP . . . EA 3 88.741 122.616 148.128 1 108.1 ? H4' ADP 402 H 1 HETATM 31 H H3' ADP . . . EA 3 87.215 124.993 148.804 1 114.27 ? H3' ADP 402 H 1 HETATM 32 H HO3' ADP . . . EA 3 85.743 123.892 147.406 1 116.1 ? HO3' ADP 402 H 1 HETATM 33 H H2' ADP . . . EA 3 86.252 124.235 150.702 1 112.3 ? H2' ADP 402 H 1 HETATM 34 H HO2' ADP . . . EA 3 84.529 123.678 149.291 1 115.31 ? HO2' ADP 402 H 1 HETATM 35 H H1' ADP . . . EA 3 86.886 121.35 150.172 1 107.09 ? H1' ADP 402 H 1 HETATM 36 H H8 ADP . . . EA 3 88.528 123.748 152.669 1 106.53 ? H8 ADP 402 H 1 HETATM 37 H HN61 ADP . . . EA 3 85.076 120.826 157.095 1 117.21 ? HN61 ADP 402 H 1 HETATM 38 H HN62 ADP . . . EA 3 86.337 122.003 156.802 1 114.53 ? HN62 ADP 402 H 1 HETATM 39 H H2 ADP . . . EA 3 83.789 119.266 153.006 1 113.05 ? H2 ADP 402 H 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #