data_1NY3 # _model_server_result.job_id 9OAj0nCluN20RWeB44R9_Q _model_server_result.datetime_utc '2024-10-25 20:19:09' _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 1ny3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 1NY3 # _exptl.entry_id 1NY3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 1NY3 _cell.length_a 253.049 _cell.length_b 253.049 _cell.length_c 253.049 _cell.Z_PDB 96 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NY3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 210 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'F 41 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA,PQS dodecameric 12 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B 1 1 A,B 2 1,2,3,4,5,6,7,8,9,10,11,12 # 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 'crystal symmetry operation' 8_646 -z+3/2,x-1/2,-y+1 0 0 -1 1 0 0 0 -1 0 379.5735 -126.5245 253.049 3 'crystal symmetry operation' 11_566 y+1/2,-z+1,-x+3/2 0 1 0 0 0 -1 -1 0 0 126.5245 253.049 379.5735 4 'crystal symmetry operation' 27_656 -x+3/2,y,-z+3/2 -1 0 0 0 1 0 0 0 -1 379.5735 0 379.5735 5 'crystal symmetry operation' 29_545 z,x-1/2,y+1/2 0 0 1 1 0 0 0 1 0 0 -126.5245 126.5245 6 'crystal symmetry operation' 36_665 -y+1,-z+1,x 0 -1 0 0 0 -1 1 0 0 253.049 253.049 0 7 'crystal symmetry operation' 50_655 -x+3/2,-y+1/2,z -1 0 0 0 -1 0 0 0 1 379.5735 126.5245 0 8 'crystal symmetry operation' 54_566 z,-x+1,-y+1 0 0 1 -1 0 0 0 -1 0 0 253.049 253.049 9 'crystal symmetry operation' 58_646 -y+1,z-1/2,-x+3/2 0 -1 0 0 0 1 -1 0 0 253.049 -126.5245 379.5735 10 'crystal symmetry operation' 76_556 x,-y+1/2,-z+3/2 1 0 0 0 -1 0 0 0 -1 0 126.5245 379.5735 11 'crystal symmetry operation' 79_665 -z+3/2,-x+1,y+1/2 0 0 -1 -1 0 0 0 1 0 379.5735 253.049 126.5245 12 'crystal symmetry operation' 81_545 y+1/2,z-1/2,x 0 1 0 0 0 1 1 0 0 126.5245 -126.5245 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 1NY3 _atom_sites.fract_transf_matrix[1][1] 0.003952 _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] 0.003952 _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] 0.003952 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id ADP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 401 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id ADP _pdbx_nonpoly_scheme.auth_mon_id ADP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . B 2 229.414 75.93 184.638 1 144.05 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 228.095 75.638 184.02 1 142.49 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 229.282 76.005 186.238 1 122.65 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 230.444 74.946 184.218 1 144.86 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 230.706 78.491 184.989 1 102.14 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 230.276 79.816 184.543 1 174.47 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 230.524 78.38 186.435 1 153.66 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 229.878 77.381 184.234 1 60.21 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 232.245 78.264 184.682 1 117.31 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 232.874 77.159 184.03 1 53.55 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 234.396 77.4 184.26 1 67.72 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 234.874 78.078 183.094 1 74.41 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 234.701 78.366 185.418 1 57.09 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 234.973 77.677 186.65 1 113.37 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 235.912 79.155 184.952 1 75.95 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 237.163 78.609 185.403 1 92.7 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 235.708 79.212 183.442 1 75.9 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 234.976 80.439 182.996 1 81.65 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 233.649 80.489 182.77 1 67.8 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 233.314 81.705 182.387 1 84.52 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 234.401 82.426 182.294 1 77.01 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 234.688 83.726 181.905 1 74.49 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 233.702 84.538 181.513 1 67.62 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 235.979 84.183 181.928 1 58.39 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 237.002 83.396 182.326 1 72.98 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 236.742 82.122 182.681 1 88.25 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 235.482 81.611 182.69 1 72.84 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #