data_6AZ0 # _model_server_result.job_id LIJaEWPzcub4rmIn5nqDsQ _model_server_result.datetime_utc '2025-07-08 06:08:32' _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 6az0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":801}' # _entry.id 6AZ0 # _exptl.entry_id 6AZ0 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 6AZ0 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6AZ0 _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 heptameric _pdbx_struct_assembly.oligomeric_count 7 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id T _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 NE2 HIS 262 A HIS 540 1_555 I ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc2 A NE2 HIS 266 A HIS 544 1_555 I ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc3 A OD1 ASP 340 A ASP 618 1_555 I ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc4 A OD2 ASP 340 A ASP 618 1_555 I ZN ZN . A ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc5 H O2G ATP . A ATP 801 1_555 J MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc6 H O3G ATP . A ATP 801 1_555 J MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc7 H O2B ATP . A ATP 801 1_555 J MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc8 H O2A ATP . A ATP 801 1_555 J MG MG . A MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc9 B OD2 ASP 102 B ASP 380 1_555 M MG MG . B MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.912 ? metalc ? metalc10 B NE2 HIS 262 B HIS 540 1_555 L ZN ZN . B ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc11 B NE2 HIS 266 B HIS 544 1_555 L ZN ZN . B ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc12 B OD1 ASP 340 B ASP 618 1_555 L ZN ZN . B ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc13 B OD2 ASP 340 B ASP 618 1_555 L ZN ZN . B ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc14 K O2B ATP . B ATP 801 1_555 M MG MG . B MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc15 C OG1 THR 50 C THR 328 1_555 P MG MG . C MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc16 C NE2 HIS 262 C HIS 540 1_555 O ZN ZN . C ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc17 C NE2 HIS 266 C HIS 544 1_555 O ZN ZN . C ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc18 C OD1 ASP 340 C ASP 618 1_555 O ZN ZN . C ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc19 C OD2 ASP 340 C ASP 618 1_555 O ZN ZN . C ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc20 N O2B ATP . C ATP 801 1_555 P MG MG . C MG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc21 D OG1 THR 50 D THR 328 1_555 R MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc22 D NE2 HIS 262 D HIS 540 1_555 Q ZN ZN . D ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc23 D NE2 HIS 266 D HIS 544 1_555 Q ZN ZN . D ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc24 D OD2 ASP 340 D ASP 618 1_555 Q ZN ZN . D ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc25 R MG MG . D MG 802 1_555 S O2B ATP . D ATP 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc26 E NE2 HIS 262 E HIS 540 1_555 U ZN ZN . E ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc27 E NE2 HIS 266 E HIS 544 1_555 U ZN ZN . E ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc28 E OD1 ASP 340 E ASP 618 1_555 U ZN ZN . E ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc29 E OD2 ASP 340 E ASP 618 1_555 U ZN ZN . E ZN 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc30 F NE2 HIS 262 F HIS 540 1_555 V ZN ZN . F ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc31 F NE2 HIS 266 F HIS 544 1_555 V ZN ZN . F ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? # _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 6AZ0 _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 H 3 ATP A 1 801 800 ATP ATP . I 4 ZN A 1 802 999 ZN ZN . J 5 MG A 1 803 899 MG MG . K 3 ATP B 1 801 802 ATP ATP . L 4 ZN B 1 802 999 ZN ZN . M 5 MG B 1 803 899 MG MG . N 3 ATP C 1 801 801 ATP ATP . O 4 ZN C 1 802 999 ZN ZN . P 5 MG C 1 803 899 MG MG . Q 4 ZN D 1 801 999 ZN ZN . R 5 MG D 1 802 899 MG MG . S 3 ATP D 1 803 799 ATP ATP . T 6 ADP E 1 801 799 ADP ADP . U 4 ZN E 1 802 999 ZN ZN . V 4 ZN F 1 801 999 ZN ZN . # 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 . . . T 6 98.99 51.06 79.149 1 84.36 ? PB ADP 801 E 1 HETATM 2 O O1B ADP . . . T 6 99.622 51.344 77.817 1 84.36 ? O1B ADP 801 E 1 HETATM 3 O O2B ADP . . . T 6 99.898 51.356 80.31 1 84.36 ? O2B ADP 801 E 1 HETATM 4 O O3B ADP . . . T 6 97.59 51.594 79.284 1 84.36 ? O3B ADP 801 E 1 HETATM 5 P PA ADP . . . T 6 98.724 48.58 80.487 1 84.36 ? PA ADP 801 E 1 HETATM 6 O O1A ADP . . . T 6 97.311 48.623 81.002 1 84.36 ? O1A ADP 801 E 1 HETATM 7 O O2A ADP . . . T 6 99.883 48.945 81.377 1 84.36 ? O2A ADP 801 E 1 HETATM 8 O O3A ADP . . . T 6 98.801 49.461 79.144 1 84.36 ? O3A ADP 801 E 1 HETATM 9 O O5' ADP . . . T 6 98.966 47.092 79.958 1 84.36 ? O5' ADP 801 E 1 HETATM 10 C C5' ADP . . . T 6 98.055 46.539 79.021 1 84.36 ? C5' ADP 801 E 1 HETATM 11 C C4' ADP . . . T 6 98.587 45.205 78.496 1 84.36 ? C4' ADP 801 E 1 HETATM 12 O O4' ADP . . . T 6 99.707 45.423 77.637 1 84.36 ? O4' ADP 801 E 1 HETATM 13 C C3' ADP . . . T 6 99.05 44.244 79.583 1 84.36 ? C3' ADP 801 E 1 HETATM 14 O O3' ADP . . . T 6 98.296 43.037 79.516 1 84.36 ? O3' ADP 801 E 1 HETATM 15 C C2' ADP . . . T 6 100.503 43.964 79.288 1 84.36 ? C2' ADP 801 E 1 HETATM 16 O O2' ADP . . . T 6 100.807 42.582 79.425 1 84.36 ? O2' ADP 801 E 1 HETATM 17 C C1' ADP . . . T 6 100.703 44.431 77.871 1 84.36 ? C1' ADP 801 E 1 HETATM 18 N N9 ADP . . . T 6 102.047 44.992 77.67 1 84.36 ? N9 ADP 801 E 1 HETATM 19 C C8 ADP . . . T 6 102.31 46.191 77.139 1 84.36 ? C8 ADP 801 E 1 HETATM 20 N N7 ADP . . . T 6 103.641 46.408 77.067 1 84.36 ? N7 ADP 801 E 1 HETATM 21 C C5 ADP . . . T 6 104.237 45.317 77.551 1 84.36 ? C5 ADP 801 E 1 HETATM 22 C C6 ADP . . . T 6 105.623 44.898 77.762 1 84.36 ? C6 ADP 801 E 1 HETATM 23 N N6 ADP . . . T 6 106.615 45.732 77.414 1 84.36 ? N6 ADP 801 E 1 HETATM 24 N N1 ADP . . . T 6 105.845 43.686 78.298 1 84.36 ? N1 ADP 801 E 1 HETATM 25 C C2 ADP . . . T 6 104.831 42.875 78.635 1 84.36 ? C2 ADP 801 E 1 HETATM 26 N N3 ADP . . . T 6 103.539 43.195 78.47 1 84.36 ? N3 ADP 801 E 1 HETATM 27 C C4 ADP . . . T 6 103.188 44.382 77.945 1 84.36 ? C4 ADP 801 E 1 HETATM 28 H "H5'1" ADP . . . T 6 97.082 46.403 79.493 1 84.36 ? "H5'1" ADP 801 E 1 HETATM 29 H "H5'2" ADP . . . T 6 97.92 47.244 78.202 1 84.36 ? "H5'2" ADP 801 E 1 HETATM 30 H H4' ADP . . . T 6 97.786 44.711 77.931 1 84.36 ? H4' ADP 801 E 1 HETATM 31 H H3' ADP . . . T 6 98.956 44.686 80.58 1 84.36 ? H3' ADP 801 E 1 HETATM 32 H HO3' ADP . . . T 6 98.456 42.524 80.316 1 84.36 ? HO3' ADP 801 E 1 HETATM 33 H H2' ADP . . . T 6 101.139 44.558 79.943 1 84.36 ? H2' ADP 801 E 1 HETATM 34 H HO2' ADP . . . T 6 100.744 42.348 80.359 1 84.36 ? HO2' ADP 801 E 1 HETATM 35 H H1' ADP . . . T 6 100.562 43.588 77.192 1 84.36 ? H1' ADP 801 E 1 HETATM 36 H H8 ADP . . . T 6 101.56 46.894 76.82 1 84.36 ? H8 ADP 801 E 1 HETATM 37 H HN61 ADP . . . T 6 107.576 45.47 77.549 1 84.36 ? HN61 ADP 801 E 1 HETATM 38 H HN62 ADP . . . T 6 106.381 46.627 77.021 1 84.36 ? HN62 ADP 801 E 1 HETATM 39 H H2 ADP . . . T 6 105.068 41.914 79.062 1 84.36 ? H2 ADP 801 E 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 418 _model_server_stats.query_time_ms 1577 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 39 #