data_1YBV # _model_server_result.job_id lWGmFr2k48OffN4QqQdgiA _model_server_result.datetime_utc '2024-11-26 17:52:01' _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 1ybv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":284}' # _entry.id 1YBV # _exptl.entry_id 1YBV _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 120 _cell.entry_id 1YBV _cell.length_a 142.6 _cell.length_b 142.6 _cell.length_c 72.9 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YBV _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_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 'crystal symmetry operation' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 48.6 # 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 258 n n PA O2A NDP sing 259 n n PA O5B NDP sing 260 n n PA O3 NDP sing 261 n n O2A HOA2 NDP sing 262 n n O5B C5B NDP sing 263 n n C5B C4B NDP sing 264 n n C5B H51A NDP sing 265 n n C5B H52A NDP sing 266 n n C4B O4B NDP sing 267 n n C4B C3B NDP sing 268 n n C4B H4B NDP sing 269 n n O4B C1B NDP sing 270 n n C3B O3B NDP sing 271 n n C3B C2B NDP sing 272 n n C3B H3B NDP sing 273 n n O3B HO3A NDP sing 274 n n C2B O2B NDP sing 275 n n C2B C1B NDP sing 276 n n C2B H2B NDP sing 277 n n O2B P2B NDP sing 278 n n C1B N9A NDP sing 279 n n C1B H1B NDP sing 280 n n N9A C8A NDP sing 281 n y N9A C4A NDP sing 282 n y C8A N7A NDP doub 283 n y C8A H8A NDP sing 284 n n N7A C5A NDP sing 285 n y C5A C6A NDP sing 286 n y C5A C4A NDP doub 287 n y C6A N6A NDP sing 288 n n C6A N1A NDP doub 289 n y N6A H61A NDP sing 290 n n N6A H62A NDP sing 291 n n N1A C2A NDP sing 292 n y C2A N3A NDP doub 293 n y C2A H2A NDP sing 294 n n N3A C4A NDP sing 295 n y O3 PN NDP sing 296 n n PN O1N NDP doub 297 n n PN O2N NDP sing 298 n n PN O5D NDP sing 299 n n O2N H21N NDP sing 300 n n O5D C5D NDP sing 301 n n C5D C4D NDP sing 302 n n C5D H51N NDP sing 303 n n C5D H52N NDP sing 304 n n C4D O4D NDP sing 305 n n C4D C3D NDP sing 306 n n C4D H4D NDP sing 307 n n O4D C1D NDP sing 308 n n C3D O3D NDP sing 309 n n C3D C2D NDP sing 310 n n C3D H3D NDP sing 311 n n O3D HO3N NDP sing 312 n n C2D O2D NDP sing 313 n n C2D C1D NDP sing 314 n n C2D H2D NDP sing 315 n n O2D HO2N NDP sing 316 n n C1D N1N NDP sing 317 n n C1D H1D NDP sing 318 n n N1N C2N NDP sing 319 n n N1N C6N NDP sing 320 n n C2N C3N NDP doub 321 n n C2N H2N NDP sing 322 n n C3N C7N NDP sing 323 n n C3N C4N NDP sing 324 n n C7N O7N NDP doub 325 n n C7N N7N NDP sing 326 n n N7N H71N NDP sing 327 n n N7N H72N NDP sing 328 n n C4N C5N NDP sing 329 n n C4N H41N NDP sing 330 n n C4N H42N NDP sing 331 n n C5N C6N NDP doub 332 n n C5N H5N NDP sing 333 n n C6N H6N NDP sing 334 n n P2B O1X NDP doub 335 n n P2B O2X NDP sing 336 n n P2B O3X NDP sing 337 n n O2X HOP2 NDP sing 338 n n O3X HOP3 NDP sing 339 n n # _atom_sites.entry_id 1YBV _atom_sites.fract_transf_matrix[1][1] 0.007013 _atom_sites.fract_transf_matrix[1][2] 0.004049 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008097 _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] 0.013717 _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 1 284 1 NDP NDP . D 3 BEA A 1 285 2 BEA BEA . E 2 NDP B 1 284 1 NDP NDP . F 3 BEA B 1 285 2 BEA BEA . # 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 . . . C 2 90.58 19.763 19.953 1 21.23 ? PA NDP 284 A 1 HETATM 2 O O1A NDP . . . C 2 91.101 19.107 18.721 1 21.23 ? O1A NDP 284 A 1 HETATM 3 O O2A NDP . . . C 2 90.104 21.169 19.877 1 21.23 ? O2A NDP 284 A 1 HETATM 4 O O5B NDP . . . C 2 91.717 19.556 21.094 1 21.23 ? O5B NDP 284 A 1 HETATM 5 C C5B NDP . . . C 2 91.305 19.539 22.477 1 21.23 ? C5B NDP 284 A 1 HETATM 6 C C4B NDP . . . C 2 92.371 19.227 23.459 1 21.23 ? C4B NDP 284 A 1 HETATM 7 O O4B NDP . . . C 2 92.811 17.895 23.707 1 21.23 ? O4B NDP 284 A 1 HETATM 8 C C3B NDP . . . C 2 93.544 20.138 23.664 1 21.23 ? C3B NDP 284 A 1 HETATM 9 O O3B NDP . . . C 2 93.736 20.844 24.723 1 21.23 ? O3B NDP 284 A 1 HETATM 10 C C2B NDP . . . C 2 94.726 19.211 23.505 1 21.23 ? C2B NDP 284 A 1 HETATM 11 O O2B NDP . . . C 2 95.849 19.701 24.292 1 21.23 ? O2B NDP 284 A 1 HETATM 12 C C1B NDP . . . C 2 94.186 17.921 24.08 1 21.23 ? C1B NDP 284 A 1 HETATM 13 N N9A NDP . . . C 2 95.071 16.886 24.118 1 21.23 ? N9A NDP 284 A 1 HETATM 14 C C8A NDP . . . C 2 95.496 16.152 23.09 1 21.23 ? C8A NDP 284 A 1 HETATM 15 N N7A NDP . . . C 2 96.506 15.371 23.487 1 21.23 ? N7A NDP 284 A 1 HETATM 16 C C5A NDP . . . C 2 96.679 15.665 24.765 1 21.23 ? C5A NDP 284 A 1 HETATM 17 C C6A NDP . . . C 2 97.569 15.047 25.631 1 21.23 ? C6A NDP 284 A 1 HETATM 18 N N6A NDP . . . C 2 98.495 14.189 25.215 1 21.23 ? N6A NDP 284 A 1 HETATM 19 N N1A NDP . . . C 2 97.503 15.446 26.92 1 21.23 ? N1A NDP 284 A 1 HETATM 20 C C2A NDP . . . C 2 96.653 16.39 27.334 1 21.23 ? C2A NDP 284 A 1 HETATM 21 N N3A NDP . . . C 2 95.809 16.984 26.483 1 21.23 ? N3A NDP 284 A 1 HETATM 22 C C4A NDP . . . C 2 95.796 16.616 25.189 1 21.23 ? C4A NDP 284 A 1 HETATM 23 O O3 NDP . . . C 2 89.39 18.85 20.539 1 21.23 ? O3 NDP 284 A 1 HETATM 24 P PN NDP . . . C 2 87.861 19.06 21.013 1 21.23 ? PN NDP 284 A 1 HETATM 25 O O1N NDP . . . C 2 87.937 20.162 22.007 1 21.23 ? O1N NDP 284 A 1 HETATM 26 O O2N NDP . . . C 2 87.012 19.152 19.802 1 21.23 ? O2N NDP 284 A 1 HETATM 27 O O5D NDP . . . C 2 87.542 17.64 21.7 1 21.23 ? O5D NDP 284 A 1 HETATM 28 C C5D NDP . . . C 2 87.759 17.469 23.1 1 21.23 ? C5D NDP 284 A 1 HETATM 29 C C4D NDP . . . C 2 87.252 16.109 23.523 1 21.23 ? C4D NDP 284 A 1 HETATM 30 O O4D NDP . . . C 2 85.868 15.908 23.182 1 21.23 ? O4D NDP 284 A 1 HETATM 31 C C3D NDP . . . C 2 88.019 15.006 22.83 1 21.23 ? C3D NDP 284 A 1 HETATM 32 O O3D NDP . . . C 2 88.213 13.917 23.741 1 21.23 ? O3D NDP 284 A 1 HETATM 33 C C2D NDP . . . C 2 87.134 14.629 21.658 1 21.23 ? C2D NDP 284 A 1 HETATM 34 O O2D NDP . . . C 2 87.391 13.311 21.194 1 21.23 ? O2D NDP 284 A 1 HETATM 35 C C1D NDP . . . C 2 85.795 14.763 22.319 1 21.23 ? C1D NDP 284 A 1 HETATM 36 N N1N NDP . . . C 2 84.774 14.99 21.302 1 21.23 ? N1N NDP 284 A 1 HETATM 37 C C2N NDP . . . C 2 84.819 16.088 20.42 1 21.23 ? C2N NDP 284 A 1 HETATM 38 C C3N NDP . . . C 2 83.781 16.296 19.512 1 21.23 ? C3N NDP 284 A 1 HETATM 39 C C7N NDP . . . C 2 83.812 17.364 18.402 1 21.23 ? C7N NDP 284 A 1 HETATM 40 O O7N NDP . . . C 2 83.019 17.3 17.468 1 21.23 ? O7N NDP 284 A 1 HETATM 41 N N7N NDP . . . C 2 84.757 18.3 18.457 1 21.23 ? N7N NDP 284 A 1 HETATM 42 C C4N NDP . . . C 2 82.709 15.412 19.527 1 21.23 ? C4N NDP 284 A 1 HETATM 43 C C5N NDP . . . C 2 82.668 14.325 20.401 1 21.23 ? C5N NDP 284 A 1 HETATM 44 C C6N NDP . . . C 2 83.707 14.101 21.297 1 21.23 ? C6N NDP 284 A 1 HETATM 45 P P2B NDP . . . C 2 97 20.617 23.636 1 21.23 ? P2B NDP 284 A 1 HETATM 46 O O1X NDP . . . C 2 97.414 21.418 24.8 1 21.23 ? O1X NDP 284 A 1 HETATM 47 O O2X NDP . . . C 2 96.284 21.377 22.582 1 21.23 ? O2X NDP 284 A 1 HETATM 48 O O3X NDP . . . C 2 97.975 19.585 23.201 1 21.23 ? O3X NDP 284 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 48 #