data_7Z8M # _model_server_result.job_id DLYFIUXC-YzW1C6q5Ea3lA _model_server_result.datetime_utc '2025-03-09 02:37:24' _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 7z8m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":800}' # _entry.id 7Z8M # _exptl.entry_id 7Z8M _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 12 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 7Z8M _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Z8M _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 nonameric _pdbx_struct_assembly.oligomeric_count 9 _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 _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 ? 12 O N N ? 12 Q N N ? 12 S 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 D SG CYS 30 Y CYS 30 1_555 J ZN ZN . Y ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc2 D SG CYS 33 Y CYS 33 1_555 J ZN ZN . Y ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc3 D SG CYS 51 Y CYS 51 1_555 K ZN ZN . Y ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc4 D SG CYS 54 Y CYS 54 1_555 K ZN ZN . Y ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc5 D SG CYS 70 Y CYS 70 1_555 K ZN ZN . Y ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc6 D SG CYS 73 Y CYS 73 1_555 K ZN ZN . Y ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc7 D SG CYS 76 Y CYS 76 1_555 L ZN ZN . Y ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc8 D SG CYS 79 Y CYS 79 1_555 L ZN ZN . Y ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc9 D SG CYS 111 Y CYS 111 1_555 L ZN ZN . Y ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc10 D SG CYS 114 Y CYS 114 1_555 L ZN ZN . Y ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc11 D SG CYS 284 Y CYS 284 1_555 J ZN ZN . Y ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc12 D SG CYS 287 Y CYS 287 1_555 J ZN ZN . Y ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc13 M O2G ATP . J ATP 800 1_555 N MG MG . J MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? metalc ? metalc14 O O3B ADP . G ADP 800 1_555 P MG MG . G MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.929 ? metalc ? metalc15 Q O1B ADP . H ADP 800 1_555 R MG MG . H MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc16 S O2B ADP . I ADP 800 1_555 T MG MG . I MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? metalc ? metalc17 S O3B ADP . I ADP 800 1_555 T MG MG . I MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? # _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 7Z8M _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 J 9 ZN Y 1 501 501 ZN ZN . K 9 ZN Y 1 502 502 ZN ZN . L 9 ZN Y 1 503 503 ZN ZN . M 10 ATP J 1 800 800 ATP ATP . N 11 MG J 1 801 801 MG MG . O 12 ADP G 1 800 800 ADP ADP . P 11 MG G 1 801 801 MG MG . Q 12 ADP H 1 800 800 ADP ADP . R 11 MG H 1 801 801 MG MG . S 12 ADP I 1 800 800 ADP ADP . T 11 MG I 1 801 801 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 12 677.472 521.015 392.143 1 44.01 ? PB ADP 800 G 1 HETATM 2 O O1B ADP . . . O 12 677.038 520.426 390.825 1 45.71 ? O1B ADP 800 G 1 HETATM 3 O O2B ADP . . . O 12 678.936 520.853 392.458 1 40.35 ? O2B ADP 800 G 1 HETATM 4 O O3B ADP . . . O 12 676.561 520.709 393.305 1 44.46 ? O3B ADP 800 G 1 HETATM 5 P PA ADP . . . O 12 678.19 523.642 392.75 1 36.28 ? PA ADP 800 G 1 HETATM 6 O O1A ADP . . . O 12 679.637 523.434 392.392 1 40.07 ? O1A ADP 800 G 1 HETATM 7 O O2A ADP . . . O 12 677.738 523.607 394.187 1 39.31 ? O2A ADP 800 G 1 HETATM 8 O O3A ADP . . . O 12 677.315 522.593 391.908 1 37.89 ? O3A ADP 800 G 1 HETATM 9 O O5' ADP . . . O 12 677.713 525.022 392.09 1 39.2 ? O5' ADP 800 G 1 HETATM 10 C C5' ADP . . . O 12 678.661 525.895 391.494 1 37.49 ? C5' ADP 800 G 1 HETATM 11 C C4' ADP . . . O 12 677.919 527.082 390.903 1 37.4 ? C4' ADP 800 G 1 HETATM 12 O O4' ADP . . . O 12 677.547 527.99 391.94 1 36.58 ? O4' ADP 800 G 1 HETATM 13 C C3' ADP . . . O 12 678.77 527.856 389.914 1 39.62 ? C3' ADP 800 G 1 HETATM 14 O O3' ADP . . . O 12 678.267 527.679 388.59 1 42.49 ? O3' ADP 800 G 1 HETATM 15 C C2' ADP . . . O 12 678.676 529.307 390.33 1 39.99 ? C2' ADP 800 G 1 HETATM 16 O O2' ADP . . . O 12 678.209 530.113 389.247 1 44.74 ? O2' ADP 800 G 1 HETATM 17 C C1' ADP . . . O 12 677.696 529.335 391.49 1 37.28 ? C1' ADP 800 G 1 HETATM 18 N N9 ADP . . . O 12 678.199 530.204 392.58 1 37.39 ? N9 ADP 800 G 1 HETATM 19 C C8 ADP . . . O 12 679.181 529.901 393.447 1 41.11 ? C8 ADP 800 G 1 HETATM 20 N N7 ADP . . . O 12 679.385 530.927 394.312 1 40.92 ? N7 ADP 800 G 1 HETATM 21 C C5 ADP . . . O 12 678.52 531.905 393.998 1 37.95 ? C5 ADP 800 G 1 HETATM 22 C C6 ADP . . . O 12 678.205 533.255 394.508 1 37.24 ? C6 ADP 800 G 1 HETATM 23 N N6 ADP . . . O 12 678.874 533.781 395.56 1 39.92 ? N6 ADP 800 G 1 HETATM 24 N N1 ADP . . . O 12 677.226 533.944 393.889 1 37.4 ? N1 ADP 800 G 1 HETATM 25 C C2 ADP . . . O 12 676.548 533.44 392.844 1 37.23 ? C2 ADP 800 G 1 HETATM 26 N N3 ADP . . . O 12 676.788 532.221 392.334 1 34.19 ? N3 ADP 800 G 1 HETATM 27 C C4 ADP . . . O 12 677.742 531.422 392.856 1 36.06 ? C4 ADP 800 G 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #