data_9F1U # _model_server_result.job_id -QwLaV448o02XPB-hCbugw _model_server_result.datetime_utc '2025-03-03 03:12:16' _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 9f1u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1101}' # _entry.id 9F1U # _exptl.entry_id 9F1U _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 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 9F1U _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 9F1U _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 hexamer _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.1615 0.9868 0.01063 -0.9869 0.1615 0.000808 -0.00092 -0.01062 0.9999 -18.59 211 -42.52 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 SG CYS 910 A CYS 907 1_555 F ZN ZN . A ZN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc2 A SG CYS 913 A CYS 910 1_555 F ZN ZN . A ZN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc3 A SG CYS 965 A CYS 962 1_555 F ZN ZN . A ZN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc4 A SG CYS 967 A CYS 964 1_555 F ZN ZN . A ZN 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? hydrog WATSON-CRICK hydrog1 B N3 C 1 X C 1 1_555 C N1 G 14 Z G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 C 1 X C 1 1_555 C O6 G 14 Z G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 C 1 X C 1 1_555 C N2 G 14 Z G 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 A 2 X A 2 1_555 C N3 U 13 Z U 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N6 A 2 X A 2 1_555 C O4 U 13 Z U 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 A 3 X A 3 1_555 C N3 U 12 Z U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 A 3 X A 3 1_555 C O4 U 12 Z U 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N1 G 4 X G 4 1_555 C N3 C 11 Z C 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N2 G 4 X G 4 1_555 C O2 C 11 Z C 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O6 G 4 X G 4 1_555 C N4 C 11 Z C 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N3 C 5 X C 5 1_555 C N1 G 10 Z G 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N4 C 5 X C 5 1_555 C O6 G 10 Z G 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O2 C 5 X C 5 1_555 C N2 G 10 Z G 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 C 6 X C 6 1_555 C N1 G 9 Z G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N4 C 6 X C 6 1_555 C O6 G 9 Z G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O2 C 6 X C 6 1_555 C N2 G 9 Z G 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N1 G 7 X G 7 1_555 C N3 C 8 Z C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N2 G 7 X G 7 1_555 C O2 C 8 Z C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B O6 G 7 X G 7 1_555 C N4 C 8 Z C 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 A 8 X A 8 1_555 C N3 U 7 Z U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N6 A 8 X A 8 1_555 C O4 U 7 Z U 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N1 G 9 X G 9 1_555 C N3 C 6 Z C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N2 G 9 X G 9 1_555 C O2 C 6 Z C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B O6 G 9 X G 9 1_555 C N4 C 6 Z C 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N1 G 10 X G 10 1_555 C N3 C 5 Z C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B N2 G 10 X G 10 1_555 C O2 C 5 Z C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B O6 G 10 X G 10 1_555 C N4 C 5 Z C 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N1 A 11 X A 11 1_555 C N3 U 4 Z U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N6 A 11 X A 11 1_555 C O4 U 4 Z U 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N1 G 12 X G 12 1_555 C N3 C 3 Z C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B N2 G 12 X G 12 1_555 C O2 C 3 Z C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 B O6 G 12 X G 12 1_555 C N4 C 3 Z C 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 B N1 A 13 X A 13 1_555 C N3 U 2 Z U 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 B N6 A 13 X A 13 1_555 C O4 U 2 Z U 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 B N3 U 14 X U 14 1_555 C N1 A 1 Z A 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 B O4 U 14 X U 14 1_555 C N6 A 1 Z A 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 40 n n PB O2B ADP sing 41 n n PB O3B ADP sing 42 n n PB O3A ADP sing 43 n n O2B HOB2 ADP sing 44 n n O3B HOB3 ADP sing 45 n n PA O1A ADP doub 46 n n PA O2A ADP sing 47 n n PA O3A ADP sing 48 n n PA O5' ADP sing 49 n n O2A HOA2 ADP sing 50 n n O5' C5' ADP sing 51 n n C5' C4' ADP sing 52 n n C5' "H5'1" ADP sing 53 n n C5' "H5'2" ADP sing 54 n n C4' O4' ADP sing 55 n n C4' C3' ADP sing 56 n n C4' H4' ADP sing 57 n n O4' C1' ADP sing 58 n n C3' O3' ADP sing 59 n n C3' C2' ADP sing 60 n n C3' H3' ADP sing 61 n n O3' HO3' ADP sing 62 n n C2' O2' ADP sing 63 n n C2' C1' ADP sing 64 n n C2' H2' ADP sing 65 n n O2' HO2' ADP sing 66 n n C1' N9 ADP sing 67 n n C1' H1' ADP sing 68 n n N9 C8 ADP sing 69 n y N9 C4 ADP sing 70 n y C8 N7 ADP doub 71 n y C8 H8 ADP sing 72 n n N7 C5 ADP sing 73 n y C5 C6 ADP sing 74 n y C5 C4 ADP doub 75 n y C6 N6 ADP sing 76 n n C6 N1 ADP doub 77 n y N6 HN61 ADP sing 78 n n N6 HN62 ADP sing 79 n n N1 C2 ADP sing 80 n y C2 N3 ADP doub 81 n y C2 H2 ADP sing 82 n n N3 C4 ADP sing 83 n y # _atom_sites.entry_id 9F1U _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 D 4 ADP A 1 1101 1101 ADP ADP . E 5 ALF A 1 1102 1102 ALF ALF . F 6 ZN A 1 1103 1103 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 . . . D 4 89.598 128.287 112.783 1 146.63 ? PB ADP 1101 A 1 HETATM 2 O O1B ADP . . . D 4 88.672 127.291 112.13 1 146.63 ? O1B ADP 1101 A 1 HETATM 3 O O2B ADP . . . D 4 90.573 128.94 111.832 1 146.63 ? O2B ADP 1101 A 1 HETATM 4 O O3B ADP . . . D 4 90.21 127.815 114.08 1 146.63 ? O3B ADP 1101 A 1 HETATM 5 P PA ADP . . . D 4 87.293 129.168 114.076 1 146.63 ? PA ADP 1101 A 1 HETATM 6 O O1A ADP . . . D 4 86.462 128.185 113.286 1 146.63 ? O1A ADP 1101 A 1 HETATM 7 O O2A ADP . . . D 4 87.691 128.831 115.494 1 146.63 ? O2A ADP 1101 A 1 HETATM 8 O O3A ADP . . . D 4 88.621 129.486 113.225 1 146.63 ? O3A ADP 1101 A 1 HETATM 9 O O5' ADP . . . D 4 86.516 130.577 114.074 1 146.63 ? O5' ADP 1101 A 1 HETATM 10 C C5' ADP . . . D 4 85.098 130.595 114.201 1 146.63 ? C5' ADP 1101 A 1 HETATM 11 C C4' ADP . . . D 4 84.579 132.029 114.216 1 146.63 ? C4' ADP 1101 A 1 HETATM 12 O O4' ADP . . . D 4 83.318 132.068 113.545 1 146.63 ? O4' ADP 1101 A 1 HETATM 13 C C3' ADP . . . D 4 84.378 132.586 115.619 1 146.63 ? C3' ADP 1101 A 1 HETATM 14 O O3' ADP . . . D 4 85.209 133.738 115.812 1 146.63 ? O3' ADP 1101 A 1 HETATM 15 C C2' ADP . . . D 4 82.884 132.862 115.76 1 146.63 ? C2' ADP 1101 A 1 HETATM 16 O O2' ADP . . . D 4 82.555 134.211 116.121 1 146.63 ? O2' ADP 1101 A 1 HETATM 17 C C1' ADP . . . D 4 82.279 132.548 114.399 1 146.63 ? C1' ADP 1101 A 1 HETATM 18 N N9 ADP . . . D 4 81.249 131.487 114.524 1 146.63 ? N9 ADP 1101 A 1 HETATM 19 C C8 ADP . . . D 4 81.439 130.191 114.208 1 146.63 ? C8 ADP 1101 A 1 HETATM 20 N N7 ADP . . . D 4 80.308 129.474 114.427 1 146.63 ? N7 ADP 1101 A 1 HETATM 21 C C5 ADP . . . D 4 79.371 130.319 114.89 1 146.63 ? C5 ADP 1101 A 1 HETATM 22 C C6 ADP . . . D 4 77.958 130.213 115.319 1 146.63 ? C6 ADP 1101 A 1 HETATM 23 N N6 ADP . . . D 4 77.31 129.024 115.292 1 146.63 ? N6 ADP 1101 A 1 HETATM 24 N N1 ADP . . . D 4 77.342 131.342 115.735 1 146.63 ? N1 ADP 1101 A 1 HETATM 25 C C2 ADP . . . D 4 77.972 132.533 115.768 1 146.63 ? C2 ADP 1101 A 1 HETATM 26 N N3 ADP . . . D 4 79.254 132.693 115.391 1 146.63 ? N3 ADP 1101 A 1 HETATM 27 C C4 ADP . . . D 4 79.995 131.647 114.951 1 146.63 ? C4 ADP 1101 A 1 HETATM 28 H "H5'1" ADP . . . D 4 84.805 130.075 115.115 1 146.63 ? "H5'1" ADP 1101 A 1 HETATM 29 H "H5'2" ADP . . . D 4 84.652 130.06 113.358 1 146.63 ? "H5'2" ADP 1101 A 1 HETATM 30 H H4' ADP . . . D 4 85.301 132.667 113.686 1 146.63 ? H4' ADP 1101 A 1 HETATM 31 H H3' ADP . . . D 4 84.658 131.818 116.352 1 146.63 ? H3' ADP 1101 A 1 HETATM 32 H HO3' ADP . . . D 4 85.006 134.416 115.155 1 146.63 ? HO3' ADP 1101 A 1 HETATM 33 H H2' ADP . . . D 4 82.459 132.171 116.5 1 146.63 ? H2' ADP 1101 A 1 HETATM 34 H HO2' ADP . . . D 4 83.088 134.844 115.626 1 146.63 ? HO2' ADP 1101 A 1 HETATM 35 H H1' ADP . . . D 4 81.836 133.463 113.983 1 146.63 ? H1' ADP 1101 A 1 HETATM 36 H H8 ADP . . . D 4 82.367 129.777 113.832 1 146.63 ? H8 ADP 1101 A 1 HETATM 37 H HN61 ADP . . . D 4 77.793 128.195 114.976 1 146.63 ? HN61 ADP 1101 A 1 HETATM 38 H HN62 ADP . . . D 4 76.346 128.966 115.587 1 146.63 ? HN62 ADP 1101 A 1 HETATM 39 H H2 ADP . . . D 4 77.421 133.399 116.112 1 146.63 ? H2 ADP 1101 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #