data_1Y5R # _model_server_result.job_id XGiZTkfLSzq4PQgLyYQtvA _model_server_result.datetime_utc '2024-11-21 23:29:27' _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 1y5r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":2}' # _entry.id 1Y5R # _exptl.entry_id 1Y5R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 745.421 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _entity.pdbx_number_of_molecules 2 _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 1Y5R _cell.length_a 96.051 _cell.length_b 96.051 _cell.length_c 218.522 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Y5R _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 2 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 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,C,D,E,F 1 1 A,B,C,D,E,F 2 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 'crystal symmetry operation' 8_665 -y+1,-x+1,-z+1/4 0 -1 0 -1 0 0 0 0 -1 96.051 96.051 54.6305 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N N # _chem_comp.formula 'C21 H30 N7 O17 P3' _chem_comp.formula_weight 745.421 _chem_comp.id NDP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 PA O1A NDP doub 293 n n PA O2A NDP sing 294 n n PA O5B NDP sing 295 n n PA O3 NDP sing 296 n n O2A HOA2 NDP sing 297 n n O5B C5B NDP sing 298 n n C5B C4B NDP sing 299 n n C5B H51A NDP sing 300 n n C5B H52A NDP sing 301 n n C4B O4B NDP sing 302 n n C4B C3B NDP sing 303 n n C4B H4B NDP sing 304 n n O4B C1B NDP sing 305 n n C3B O3B NDP sing 306 n n C3B C2B NDP sing 307 n n C3B H3B NDP sing 308 n n O3B HO3A NDP sing 309 n n C2B O2B NDP sing 310 n n C2B C1B NDP sing 311 n n C2B H2B NDP sing 312 n n O2B P2B NDP sing 313 n n C1B N9A NDP sing 314 n n C1B H1B NDP sing 315 n n N9A C8A NDP sing 316 n y N9A C4A NDP sing 317 n y C8A N7A NDP doub 318 n y C8A H8A NDP sing 319 n n N7A C5A NDP sing 320 n y C5A C6A NDP sing 321 n y C5A C4A NDP doub 322 n y C6A N6A NDP sing 323 n n C6A N1A NDP doub 324 n y N6A H61A NDP sing 325 n n N6A H62A NDP sing 326 n n N1A C2A NDP sing 327 n y C2A N3A NDP doub 328 n y C2A H2A NDP sing 329 n n N3A C4A NDP sing 330 n y O3 PN NDP sing 331 n n PN O1N NDP doub 332 n n PN O2N NDP sing 333 n n PN O5D NDP sing 334 n n O2N H21N NDP sing 335 n n O5D C5D NDP sing 336 n n C5D C4D NDP sing 337 n n C5D H51N NDP sing 338 n n C5D H52N NDP sing 339 n n C4D O4D NDP sing 340 n n C4D C3D NDP sing 341 n n C4D H4D NDP sing 342 n n O4D C1D NDP sing 343 n n C3D O3D NDP sing 344 n n C3D C2D NDP sing 345 n n C3D H3D NDP sing 346 n n O3D HO3N NDP sing 347 n n C2D O2D NDP sing 348 n n C2D C1D NDP sing 349 n n C2D H2D NDP sing 350 n n O2D HO2N NDP sing 351 n n C1D N1N NDP sing 352 n n C1D H1D NDP sing 353 n n N1N C2N NDP sing 354 n n N1N C6N NDP sing 355 n n C2N C3N NDP doub 356 n n C2N H2N NDP sing 357 n n C3N C7N NDP sing 358 n n C3N C4N NDP sing 359 n n C7N O7N NDP doub 360 n n C7N N7N NDP sing 361 n n N7N H71N NDP sing 362 n n N7N H72N NDP sing 363 n n C4N C5N NDP sing 364 n n C4N H41N NDP sing 365 n n C4N H42N NDP sing 366 n n C5N C6N NDP doub 367 n n C5N H5N NDP sing 368 n n C6N H6N NDP sing 369 n n P2B O1X NDP doub 370 n n P2B O2X NDP sing 371 n n P2B O3X NDP sing 372 n n O2X HOP2 NDP sing 373 n n O3X HOP3 NDP sing 374 n n # _atom_sites.entry_id 1Y5R _atom_sites.fract_transf_matrix[1][1] 0.010411 _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] 0.010411 _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] 0.004576 _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 C 2 NDP A 1 1 1 NDP NDP . D 3 C0R A 1 11 11 C0R C0R . E 2 NDP B 1 2 2 NDP NDP . F 3 C0R B 1 12 12 C0R C0R . # 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 PA NDP . . . E 2 63.643 67.353 13.46 1 36.34 ? PA NDP 2 B 1 HETATM 2 O O1A NDP . . . E 2 62.695 67.566 12.305 1 34.62 ? O1A NDP 2 B 1 HETATM 3 O O2A NDP . . . E 2 65.091 67.22 12.97 1 35.22 ? O2A NDP 2 B 1 HETATM 4 O O5B NDP . . . E 2 63.513 68.454 14.531 1 35.36 ? O5B NDP 2 B 1 HETATM 5 C C5B NDP . . . E 2 64.653 68.654 15.348 1 36.53 ? C5B NDP 2 B 1 HETATM 6 C C4B NDP . . . E 2 64.534 70.024 15.99 1 37.03 ? C4B NDP 2 B 1 HETATM 7 O O4B NDP . . . E 2 65.642 70.276 16.808 1 35.57 ? O4B NDP 2 B 1 HETATM 8 C C3B NDP . . . E 2 64.451 71.191 14.984 1 37.79 ? C3B NDP 2 B 1 HETATM 9 O O3B NDP . . . E 2 63.814 72.42 15.453 1 39.03 ? O3B NDP 2 B 1 HETATM 10 C C2B NDP . . . E 2 65.905 71.617 14.99 1 37.62 ? C2B NDP 2 B 1 HETATM 11 O O2B NDP . . . E 2 66.035 73.018 14.73 1 41.53 ? O2B NDP 2 B 1 HETATM 12 C C1B NDP . . . E 2 66.288 71.43 16.436 1 35.39 ? C1B NDP 2 B 1 HETATM 13 N N9A NDP . . . E 2 67.724 71.256 16.605 1 32.85 ? N9A NDP 2 B 1 HETATM 14 C C8A NDP . . . E 2 68.562 70.565 15.833 1 32.68 ? C8A NDP 2 B 1 HETATM 15 N N7A NDP . . . E 2 69.839 70.64 16.235 1 33.42 ? N7A NDP 2 B 1 HETATM 16 C C5A NDP . . . E 2 69.839 71.422 17.362 1 31 ? C5A NDP 2 B 1 HETATM 17 C C6A NDP . . . E 2 70.804 71.898 18.252 1 31.57 ? C6A NDP 2 B 1 HETATM 18 N N6A NDP . . . E 2 72.1 71.596 18.037 1 32.31 ? N6A NDP 2 B 1 HETATM 19 N N1A NDP . . . E 2 70.505 72.724 19.324 1 30.7 ? N1A NDP 2 B 1 HETATM 20 C C2A NDP . . . E 2 69.175 73.083 19.503 1 31.88 ? C2A NDP 2 B 1 HETATM 21 N N3A NDP . . . E 2 68.175 72.635 18.654 1 31.53 ? N3A NDP 2 B 1 HETATM 22 C C4A NDP . . . E 2 68.498 71.817 17.596 1 30.87 ? C4A NDP 2 B 1 HETATM 23 O O3 NDP . . . E 2 63.206 66.096 14.265 1 36.06 ? O3 NDP 2 B 1 HETATM 24 P PN NDP . . . E 2 61.837 65.491 14.684 1 35.52 ? PN NDP 2 B 1 HETATM 25 O O1N NDP . . . E 2 61.405 64.452 13.719 1 34.23 ? O1N NDP 2 B 1 HETATM 26 O O2N NDP . . . E 2 60.798 66.549 14.847 1 35.76 ? O2N NDP 2 B 1 HETATM 27 O O5D NDP . . . E 2 62.194 64.858 16.049 1 37.45 ? O5D NDP 2 B 1 HETATM 28 C C5D NDP . . . E 2 61.722 65.44 17.267 1 37.98 ? C5D NDP 2 B 1 HETATM 29 C C4D NDP . . . E 2 61.908 64.422 18.41 1 37.69 ? C4D NDP 2 B 1 HETATM 30 O O4D NDP . . . E 2 61.189 63.25 18.077 1 37.82 ? O4D NDP 2 B 1 HETATM 31 C C3D NDP . . . E 2 63.381 64.033 18.635 1 37.13 ? C3D NDP 2 B 1 HETATM 32 O O3D NDP . . . E 2 63.559 64.105 20.064 1 38.4 ? O3D NDP 2 B 1 HETATM 33 C C2D NDP . . . E 2 63.466 62.626 18.008 1 36.96 ? C2D NDP 2 B 1 HETATM 34 O O2D NDP . . . E 2 64.332 61.624 18.572 1 36.41 ? O2D NDP 2 B 1 HETATM 35 C C1D NDP . . . E 2 62.034 62.125 18.157 1 37.69 ? C1D NDP 2 B 1 HETATM 36 N N1N NDP . . . E 2 61.631 61.103 17.188 1 38 ? N1N NDP 2 B 1 HETATM 37 C C2N NDP . . . E 2 61.396 61.391 15.877 1 38.35 ? C2N NDP 2 B 1 HETATM 38 C C3N NDP . . . E 2 60.842 60.427 15.015 1 38.91 ? C3N NDP 2 B 1 HETATM 39 C C7N NDP . . . E 2 60.488 60.684 13.645 1 38.23 ? C7N NDP 2 B 1 HETATM 40 O O7N NDP . . . E 2 60.288 59.793 12.862 1 39.29 ? O7N NDP 2 B 1 HETATM 41 N N7N NDP . . . E 2 60.318 61.944 13.292 1 39.27 ? N7N NDP 2 B 1 HETATM 42 C C4N NDP . . . E 2 60.555 59.149 15.52 1 39.76 ? C4N NDP 2 B 1 HETATM 43 C C5N NDP . . . E 2 60.826 58.836 16.861 1 39.29 ? C5N NDP 2 B 1 HETATM 44 C C6N NDP . . . E 2 61.369 59.849 17.654 1 38.82 ? C6N NDP 2 B 1 HETATM 45 P P2B NDP . . . E 2 67.332 73.64 14.088 1 43.3 ? P2B NDP 2 B 1 HETATM 46 O O1X NDP . . . E 2 68.264 74.15 15.222 1 38.94 ? O1X NDP 2 B 1 HETATM 47 O O2X NDP . . . E 2 66.791 74.769 13.173 1 42.88 ? O2X NDP 2 B 1 HETATM 48 O O3X NDP . . . E 2 68.024 72.54 13.23 1 44.14 ? O3X NDP 2 B 1 HETATM 49 H H51A NDP . . . E 2 65.559 68.565 14.772 0 36.21 ? H51A NDP 2 B 1 HETATM 50 H H52A NDP . . . E 2 64.657 67.887 16.107 0 36.21 ? H52A NDP 2 B 1 HETATM 51 H H4B NDP . . . E 2 63.687 69.874 16.644 0 36.62 ? H4B NDP 2 B 1 HETATM 52 H H3B NDP . . . E 2 64.213 70.855 13.946 0 37.73 ? H3B NDP 2 B 1 HETATM 53 H HO3A NDP . . . E 2 62.895 72.443 15.768 0 38.49 ? HO3A NDP 2 B 1 HETATM 54 H H2B NDP . . . E 2 66.484 71.039 14.279 0 37.92 ? H2B NDP 2 B 1 HETATM 55 H H1B NDP . . . E 2 65.897 72.241 17.036 0 35.27 ? H1B NDP 2 B 1 HETATM 56 H H8A NDP . . . E 2 68.246 70.007 14.966 0 32.95 ? H8A NDP 2 B 1 HETATM 57 H H61A NDP . . . E 2 72.804 71.968 18.637 0 31.92 ? H61A NDP 2 B 1 HETATM 58 H H62A NDP . . . E 2 72.364 70.992 17.282 0 31.92 ? H62A NDP 2 B 1 HETATM 59 H H2A NDP . . . E 2 68.908 73.752 20.317 0 31.53 ? H2A NDP 2 B 1 HETATM 60 H H51N NDP . . . E 2 60.679 65.705 17.148 0 37.64 ? H51N NDP 2 B 1 HETATM 61 H H52N NDP . . . E 2 62.285 66.345 17.457 0 37.64 ? H52N NDP 2 B 1 HETATM 62 H H4D NDP . . . E 2 61.485 64.829 19.313 0 37.56 ? H4D NDP 2 B 1 HETATM 63 H H3D NDP . . . E 2 64.005 64.766 18.082 0 37.4 ? H3D NDP 2 B 1 HETATM 64 H HO3N NDP . . . E 2 63.982 63.363 20.525 0 37.84 ? HO3N NDP 2 B 1 HETATM 65 H H2D NDP . . . E 2 63.645 62.77 16.927 0 36.99 ? H2D NDP 2 B 1 HETATM 66 H HO2N NDP . . . E 2 64.827 61.867 19.368 0 36.51 ? HO2N NDP 2 B 1 HETATM 67 H H1D NDP . . . E 2 61.843 61.695 19.129 0 37.56 ? H1D NDP 2 B 1 HETATM 68 H H2N NDP . . . E 2 61.618 62.384 15.491 0 38.4 ? H2N NDP 2 B 1 HETATM 69 H H71N NDP . . . E 2 60.092 62.149 12.342 0 38.86 ? H71N NDP 2 B 1 HETATM 70 H H72N NDP . . . E 2 60.374 62.705 13.936 0 38.86 ? H72N NDP 2 B 1 HETATM 71 H H42N NDP . . . E 2 60.119 58.409 14.867 0 39.35 ? H42N NDP 2 B 1 HETATM 72 H H5N NDP . . . E 2 60.61 57.854 17.25 0 39.24 ? H5N NDP 2 B 1 HETATM 73 H H6N NDP . . . E 2 61.574 59.616 18.684 0 38.69 ? H6N NDP 2 B 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 358 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 73 #