data_6PEN # _model_server_result.job_id 11n7MiRkduwOiP6EB7HaxQ _model_server_result.datetime_utc '2024-11-25 14:16:37' _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 6pen # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":701}' # _entry.id 6PEN # _exptl.entry_id 6PEN _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 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 6PEN _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PEN _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 _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 H N N ? 3 K N N ? 3 N N N ? 3 Q N N ? 3 T 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 A OG1 THR 271 A THR 389 1_555 J MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc2 A OD2 ASP 323 A ASP 441 1_555 J MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc3 H O3B ADP . A ADP 701 1_555 I BE BEF . A BEF 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.596 ? metalc ? metalc4 H O1B ADP . A ADP 701 1_555 J MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? metalc ? metalc5 H O2B ADP . A ADP 701 1_555 J MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc6 I F1 BEF . A BEF 702 1_555 J MG MG . A MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc7 B OG1 THR 271 B THR 389 1_555 M MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc8 B OD2 ASP 323 B ASP 441 1_555 M MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc9 K O3B ADP . B ADP 701 1_555 L BE BEF . B BEF 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.597 ? metalc ? metalc10 K O1B ADP . B ADP 701 1_555 M MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? metalc ? metalc11 K O2B ADP . B ADP 701 1_555 M MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc12 L F1 BEF . B BEF 702 1_555 M MG MG . B MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc13 C OG1 THR 271 C THR 389 1_555 P MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc14 N O3B ADP . C ADP 701 1_555 O BE BEF . C BEF 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.595 ? metalc ? metalc15 N O1B ADP . C ADP 701 1_555 P MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? metalc ? metalc16 N O2B ADP . C ADP 701 1_555 P MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc17 O F1 BEF . C BEF 702 1_555 P MG MG . C MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc18 D OG1 THR 271 D THR 389 1_555 S MG MG . D MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.913 ? metalc ? metalc19 Q O3B ADP . D ADP 701 1_555 R BE BEF . D BEF 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.58 ? metalc ? metalc20 Q O1B ADP . D ADP 701 1_555 S MG MG . D MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc21 Q O2B ADP . D ADP 701 1_555 S MG MG . D MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc22 R F1 BEF . D BEF 702 1_555 S MG MG . D MG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? # _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 6PEN _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 ADP A 1 701 711 ADP ADP . I 4 BEF A 1 702 712 BEF BEF . J 5 MG A 1 703 713 MG MG . K 3 ADP B 1 701 711 ADP ADP . L 4 BEF B 1 702 712 BEF BEF . M 5 MG B 1 703 713 MG MG . N 3 ADP C 1 701 711 ADP ADP . O 4 BEF C 1 702 712 BEF BEF . P 5 MG C 1 703 713 MG MG . Q 3 ADP D 1 701 711 ADP ADP . R 4 BEF D 1 702 712 BEF BEF . S 5 MG D 1 703 713 MG MG . T 3 ADP E 1 701 711 ADP ADP . # 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 . . . H 3 103.952 131.442 139.772 1 84.36 ? PB ADP 701 A 1 HETATM 2 O O1B ADP . . . H 3 104.305 130.269 138.845 1 84.36 ? O1B ADP 701 A 1 HETATM 3 O O2B ADP . . . H 3 103.946 132.722 139.035 1 84.36 ? O2B ADP 701 A 1 HETATM 4 O O3B ADP . . . H 3 105.008 131.376 140.956 1 84.36 ? O3B ADP 701 A 1 HETATM 5 P PA ADP . . . H 3 101.235 130.556 139.977 1 84.36 ? PA ADP 701 A 1 HETATM 6 O O1A ADP . . . H 3 101.526 130.02 138.565 1 84.36 ? O1A ADP 701 A 1 HETATM 7 O O2A ADP . . . H 3 100.178 131.589 139.996 1 84.36 ? O2A ADP 701 A 1 HETATM 8 O O3A ADP . . . H 3 102.573 131.204 140.51 1 84.36 ? O3A ADP 701 A 1 HETATM 9 O O5' ADP . . . H 3 101.062 129.364 140.983 1 84.36 ? O5' ADP 701 A 1 HETATM 10 C C5' ADP . . . H 3 101.564 128.056 140.652 1 84.36 ? C5' ADP 701 A 1 HETATM 11 C C4' ADP . . . H 3 100.4 127.192 140.26 1 84.36 ? C4' ADP 701 A 1 HETATM 12 O O4' ADP . . . H 3 99.879 126.529 141.436 1 84.36 ? O4' ADP 701 A 1 HETATM 13 C C3' ADP . . . H 3 99.212 127.931 139.637 1 84.36 ? C3' ADP 701 A 1 HETATM 14 O O3' ADP . . . H 3 99.344 128 138.223 1 84.36 ? O3' ADP 701 A 1 HETATM 15 C C2' ADP . . . H 3 98.042 127.049 140.069 1 84.36 ? C2' ADP 701 A 1 HETATM 16 O O2' ADP . . . H 3 97.894 125.92 139.231 1 84.36 ? O2' ADP 701 A 1 HETATM 17 C C1' ADP . . . H 3 98.473 126.688 141.491 1 84.36 ? C1' ADP 701 A 1 HETATM 18 N N9 ADP . . . H 3 98.188 127.702 142.496 1 84.36 ? N9 ADP 701 A 1 HETATM 19 C C8 ADP . . . H 3 99.099 128.525 143.099 1 84.36 ? C8 ADP 701 A 1 HETATM 20 N N7 ADP . . . H 3 98.577 129.351 143.973 1 84.36 ? N7 ADP 701 A 1 HETATM 21 C C5 ADP . . . H 3 97.224 129.049 143.943 1 84.36 ? C5 ADP 701 A 1 HETATM 22 C C6 ADP . . . H 3 96.122 129.571 144.642 1 84.36 ? C6 ADP 701 A 1 HETATM 23 N N6 ADP . . . H 3 96.211 130.553 145.546 1 84.36 ? N6 ADP 701 A 1 HETATM 24 N N1 ADP . . . H 3 94.902 129.046 144.375 1 84.36 ? N1 ADP 701 A 1 HETATM 25 C C2 ADP . . . H 3 94.807 128.062 143.469 1 84.36 ? C2 ADP 701 A 1 HETATM 26 N N3 ADP . . . H 3 95.779 127.491 142.75 1 84.36 ? N3 ADP 701 A 1 HETATM 27 C C4 ADP . . . H 3 96.97 128.032 143.034 1 84.36 ? C4 ADP 701 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 27 #