data_3GYF # _model_server_result.job_id HNHHmO3u7BspEksvt_1UuA _model_server_result.datetime_utc '2024-10-18 16:31:17' _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 3gyf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":188}' # _entry.id 3GYF # _exptl.entry_id 3GYF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 745.421 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 3GYF _cell.length_a 39.908 _cell.length_b 57.481 _cell.length_c 74.975 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GYF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,G _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 x,y,z _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 277 n n PA O2A NDP sing 278 n n PA O5B NDP sing 279 n n PA O3 NDP sing 280 n n O2A HOA2 NDP sing 281 n n O5B C5B NDP sing 282 n n C5B C4B NDP sing 283 n n C5B H51A NDP sing 284 n n C5B H52A NDP sing 285 n n C4B O4B NDP sing 286 n n C4B C3B NDP sing 287 n n C4B H4B NDP sing 288 n n O4B C1B NDP sing 289 n n C3B O3B NDP sing 290 n n C3B C2B NDP sing 291 n n C3B H3B NDP sing 292 n n O3B HO3A NDP sing 293 n n C2B O2B NDP sing 294 n n C2B C1B NDP sing 295 n n C2B H2B NDP sing 296 n n O2B P2B NDP sing 297 n n C1B N9A NDP sing 298 n n C1B H1B NDP sing 299 n n N9A C8A NDP sing 300 n y N9A C4A NDP sing 301 n y C8A N7A NDP doub 302 n y C8A H8A NDP sing 303 n n N7A C5A NDP sing 304 n y C5A C6A NDP sing 305 n y C5A C4A NDP doub 306 n y C6A N6A NDP sing 307 n n C6A N1A NDP doub 308 n y N6A H61A NDP sing 309 n n N6A H62A NDP sing 310 n n N1A C2A NDP sing 311 n y C2A N3A NDP doub 312 n y C2A H2A NDP sing 313 n n N3A C4A NDP sing 314 n y O3 PN NDP sing 315 n n PN O1N NDP doub 316 n n PN O2N NDP sing 317 n n PN O5D NDP sing 318 n n O2N H21N NDP sing 319 n n O5D C5D NDP sing 320 n n C5D C4D NDP sing 321 n n C5D H51N NDP sing 322 n n C5D H52N NDP sing 323 n n C4D O4D NDP sing 324 n n C4D C3D NDP sing 325 n n C4D H4D NDP sing 326 n n O4D C1D NDP sing 327 n n C3D O3D NDP sing 328 n n C3D C2D NDP sing 329 n n C3D H3D NDP sing 330 n n O3D HO3N NDP sing 331 n n C2D O2D NDP sing 332 n n C2D C1D NDP sing 333 n n C2D H2D NDP sing 334 n n O2D HO2N NDP sing 335 n n C1D N1N NDP sing 336 n n C1D H1D NDP sing 337 n n N1N C2N NDP sing 338 n n N1N C6N NDP sing 339 n n C2N C3N NDP doub 340 n n C2N H2N NDP sing 341 n n C3N C7N NDP sing 342 n n C3N C4N NDP sing 343 n n C7N O7N NDP doub 344 n n C7N N7N NDP sing 345 n n N7N H71N NDP sing 346 n n N7N H72N NDP sing 347 n n C4N C5N NDP sing 348 n n C4N H41N NDP sing 349 n n C4N H42N NDP sing 350 n n C5N C6N NDP doub 351 n n C5N H5N NDP sing 352 n n C6N H6N NDP sing 353 n n P2B O1X NDP doub 354 n n P2B O2X NDP sing 355 n n P2B O3X NDP sing 356 n n O2X HOP2 NDP sing 357 n n O3X HOP3 NDP sing 358 n n # _atom_sites.entry_id 3GYF _atom_sites.fract_transf_matrix[1][1] 0.025058 _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] 0.017397 _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] 0.013338 _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 B 2 51P A 1 187 88 51P D09 . C 3 NDP A 1 188 187 NDP NDP . D 4 SO4 A 1 189 1 SO4 SO4 . E 4 SO4 A 1 190 2 SO4 SO4 . F 4 SO4 A 1 191 3 SO4 SO4 . G 5 HOH A 1 192 1 HOH HOH . G 5 HOH A 2 193 2 HOH HOH . G 5 HOH A 3 194 3 HOH HOH . G 5 HOH A 4 195 4 HOH HOH . G 5 HOH A 5 196 5 HOH HOH . G 5 HOH A 6 197 6 HOH HOH . G 5 HOH A 7 198 7 HOH HOH . G 5 HOH A 8 199 8 HOH HOH . G 5 HOH A 9 200 9 HOH HOH . G 5 HOH A 10 201 10 HOH HOH . G 5 HOH A 11 202 11 HOH HOH . G 5 HOH A 12 203 12 HOH HOH . G 5 HOH A 13 204 13 HOH HOH . G 5 HOH A 14 205 15 HOH HOH . G 5 HOH A 15 206 16 HOH HOH . G 5 HOH A 16 207 17 HOH HOH . G 5 HOH A 17 208 18 HOH HOH . G 5 HOH A 18 209 19 HOH HOH . G 5 HOH A 19 210 20 HOH HOH . G 5 HOH A 20 211 21 HOH HOH . G 5 HOH A 21 212 22 HOH HOH . G 5 HOH A 22 213 23 HOH HOH . G 5 HOH A 23 214 24 HOH HOH . G 5 HOH A 24 215 26 HOH HOH . G 5 HOH A 25 216 27 HOH HOH . G 5 HOH A 26 217 28 HOH HOH . G 5 HOH A 27 218 29 HOH HOH . G 5 HOH A 28 219 30 HOH HOH . G 5 HOH A 29 220 31 HOH HOH . G 5 HOH A 30 221 32 HOH HOH . G 5 HOH A 31 222 33 HOH HOH . G 5 HOH A 32 223 34 HOH HOH . G 5 HOH A 33 224 35 HOH HOH . G 5 HOH A 34 225 36 HOH HOH . G 5 HOH A 35 226 37 HOH HOH . G 5 HOH A 36 227 38 HOH HOH . G 5 HOH A 37 228 39 HOH HOH . G 5 HOH A 38 229 41 HOH HOH . G 5 HOH A 39 230 42 HOH HOH . G 5 HOH A 40 231 43 HOH HOH . G 5 HOH A 41 232 44 HOH HOH . G 5 HOH A 42 233 45 HOH HOH . G 5 HOH A 43 234 46 HOH HOH . G 5 HOH A 44 235 47 HOH HOH . G 5 HOH A 45 236 48 HOH HOH . G 5 HOH A 46 237 49 HOH HOH . G 5 HOH A 47 238 50 HOH HOH . G 5 HOH A 48 239 51 HOH HOH . G 5 HOH A 49 240 52 HOH HOH . G 5 HOH A 50 241 53 HOH HOH . G 5 HOH A 51 242 54 HOH HOH . G 5 HOH A 52 243 56 HOH HOH . G 5 HOH A 53 244 57 HOH HOH . G 5 HOH A 54 245 58 HOH HOH . G 5 HOH A 55 246 59 HOH HOH . G 5 HOH A 56 247 60 HOH HOH . G 5 HOH A 57 248 61 HOH HOH . G 5 HOH A 58 249 62 HOH HOH . G 5 HOH A 59 250 64 HOH HOH . G 5 HOH A 60 251 66 HOH HOH . G 5 HOH A 61 252 68 HOH HOH . G 5 HOH A 62 253 69 HOH HOH . G 5 HOH A 63 254 70 HOH HOH . G 5 HOH A 64 255 71 HOH HOH . G 5 HOH A 65 256 72 HOH HOH . G 5 HOH A 66 257 74 HOH HOH . G 5 HOH A 67 258 75 HOH HOH . G 5 HOH A 68 259 76 HOH HOH . G 5 HOH A 69 260 77 HOH HOH . G 5 HOH A 70 261 78 HOH HOH . G 5 HOH A 71 262 79 HOH HOH . G 5 HOH A 72 263 80 HOH HOH . G 5 HOH A 73 264 81 HOH HOH . G 5 HOH A 74 265 82 HOH HOH . G 5 HOH A 75 266 83 HOH HOH . G 5 HOH A 76 267 84 HOH HOH . G 5 HOH A 77 268 85 HOH HOH . G 5 HOH A 78 269 86 HOH HOH . G 5 HOH A 79 270 87 HOH HOH . G 5 HOH A 80 271 88 HOH HOH . G 5 HOH A 81 272 89 HOH HOH . G 5 HOH A 82 273 90 HOH HOH . G 5 HOH A 83 274 94 HOH HOH . G 5 HOH A 84 275 95 HOH HOH . G 5 HOH A 85 276 96 HOH HOH . G 5 HOH A 86 277 98 HOH HOH . G 5 HOH A 87 278 99 HOH HOH . G 5 HOH A 88 279 100 HOH HOH . G 5 HOH A 89 280 101 HOH HOH . G 5 HOH A 90 281 102 HOH HOH . G 5 HOH A 91 282 103 HOH HOH . G 5 HOH A 92 283 104 HOH HOH . G 5 HOH A 93 284 105 HOH HOH . G 5 HOH A 94 285 106 HOH HOH . G 5 HOH A 95 286 107 HOH HOH . G 5 HOH A 96 287 108 HOH HOH . G 5 HOH A 97 288 109 HOH HOH . G 5 HOH A 98 289 111 HOH HOH . G 5 HOH A 99 290 112 HOH HOH . G 5 HOH A 100 291 113 HOH HOH . G 5 HOH A 101 292 114 HOH HOH . G 5 HOH A 102 293 116 HOH HOH . G 5 HOH A 103 294 118 HOH HOH . G 5 HOH A 104 295 119 HOH HOH . G 5 HOH A 105 296 120 HOH HOH . G 5 HOH A 106 297 121 HOH HOH . G 5 HOH A 107 298 122 HOH HOH . G 5 HOH A 108 299 123 HOH HOH . G 5 HOH A 109 300 124 HOH HOH . G 5 HOH A 110 301 125 HOH HOH . G 5 HOH A 111 302 126 HOH HOH . G 5 HOH A 112 303 127 HOH HOH . G 5 HOH A 113 304 128 HOH HOH . G 5 HOH A 114 305 129 HOH HOH . G 5 HOH A 115 306 131 HOH HOH . G 5 HOH A 116 307 132 HOH HOH . G 5 HOH A 117 308 133 HOH HOH . G 5 HOH A 118 309 134 HOH HOH . G 5 HOH A 119 310 135 HOH HOH . G 5 HOH A 120 311 136 HOH HOH . G 5 HOH A 121 312 137 HOH HOH . G 5 HOH A 122 313 138 HOH HOH . G 5 HOH A 123 314 139 HOH HOH . G 5 HOH A 124 315 140 HOH HOH . G 5 HOH A 125 316 141 HOH HOH . G 5 HOH A 126 317 142 HOH HOH . G 5 HOH A 127 318 143 HOH HOH . G 5 HOH A 128 319 144 HOH HOH . # 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 3 1.02 7.988 1.8 1 18.96 ? PA NDP 188 A 1 HETATM 2 O O1A NDP . . . C 3 1.187 6.525 1.475 1 16.48 ? O1A NDP 188 A 1 HETATM 3 O O2A NDP . . . C 3 -0.167 8.448 2.547 1 21.98 ? O2A NDP 188 A 1 HETATM 4 O O5B NDP . . . C 3 1.213 8.789 0.427 1 24.71 ? O5B NDP 188 A 1 HETATM 5 C C5B NDP . . . C 3 0.958 10.233 0.379 1 25.88 ? C5B NDP 188 A 1 HETATM 6 C C4B NDP . . . C 3 0.674 10.614 -1.048 1 25.42 ? C4B NDP 188 A 1 HETATM 7 O O4B NDP . . . C 3 -0.355 9.668 -1.597 1 23.26 ? O4B NDP 188 A 1 HETATM 8 C C3B NDP . . . C 3 0.149 12.073 -1.297 1 21.87 ? C3B NDP 188 A 1 HETATM 9 O O3B NDP . . . C 3 1.378 12.781 -1.539 1 20.54 ? O3B NDP 188 A 1 HETATM 10 C C2B NDP . . . C 3 -0.486 11.525 -2.483 1 24.44 ? C2B NDP 188 A 1 HETATM 11 O O2B NDP . . . C 3 0.012 11.516 -3.718 1 26.74 ? O2B NDP 188 A 1 HETATM 12 C C1B NDP . . . C 3 -1.446 10.407 -2.107 1 24.04 ? C1B NDP 188 A 1 HETATM 13 N N9A NDP . . . C 3 -2.565 10.461 -1.115 1 28.32 ? N9A NDP 188 A 1 HETATM 14 C C8A NDP . . . C 3 -2.603 10.184 0.21 1 29.39 ? C8A NDP 188 A 1 HETATM 15 N N7A NDP . . . C 3 -3.877 10.341 0.633 1 30.15 ? N7A NDP 188 A 1 HETATM 16 C C5A NDP . . . C 3 -4.619 10.67 -0.425 1 30.29 ? C5A NDP 188 A 1 HETATM 17 C C6A NDP . . . C 3 -5.959 10.95 -0.634 1 28.89 ? C6A NDP 188 A 1 HETATM 18 N N6A NDP . . . C 3 -6.823 10.909 0.368 1 28.08 ? N6A NDP 188 A 1 HETATM 19 N N1A NDP . . . C 3 -6.356 11.276 -1.872 1 29.65 ? N1A NDP 188 A 1 HETATM 20 C C2A NDP . . . C 3 -5.511 11.335 -2.914 1 28.06 ? C2A NDP 188 A 1 HETATM 21 N N3A NDP . . . C 3 -4.214 11.09 -2.733 1 29.86 ? N3A NDP 188 A 1 HETATM 22 C C4A NDP . . . C 3 -3.778 10.768 -1.515 1 28.81 ? C4A NDP 188 A 1 HETATM 23 O O3 NDP . . . C 3 2.34 8.541 2.632 1 23.06 ? O3 NDP 188 A 1 HETATM 24 P PN NDP . . . C 3 2.995 8.518 4.135 1 23.41 ? PN NDP 188 A 1 HETATM 25 O O1N NDP . . . C 3 1.901 8.903 5.095 1 22.85 ? O1N NDP 188 A 1 HETATM 26 O O2N NDP . . . C 3 4.257 9.319 4.04 1 28.51 ? O2N NDP 188 A 1 HETATM 27 O O5D NDP . . . C 3 3.285 7.002 4.391 1 21.45 ? O5D NDP 188 A 1 HETATM 28 C C5D NDP . . . C 3 4.362 6.374 3.848 1 22.19 ? C5D NDP 188 A 1 HETATM 29 C C4D NDP . . . C 3 5.196 5.98 5.05 1 18.98 ? C4D NDP 188 A 1 HETATM 30 O O4D NDP . . . C 3 4.51 5.242 6.12 1 23.17 ? O4D NDP 188 A 1 HETATM 31 C C3D NDP . . . C 3 6.346 5.075 4.563 1 21.82 ? C3D NDP 188 A 1 HETATM 32 O O3D NDP . . . C 3 7.4 5.31 5.493 1 19.09 ? O3D NDP 188 A 1 HETATM 33 C C2D NDP . . . C 3 5.811 3.661 4.763 1 21.02 ? C2D NDP 188 A 1 HETATM 34 O O2D NDP . . . C 3 6.854 2.7 5.036 1 26.11 ? O2D NDP 188 A 1 HETATM 35 C C1D NDP . . . C 3 5.088 3.873 6.111 1 20.2 ? C1D NDP 188 A 1 HETATM 36 N N1N NDP . . . C 3 3.886 3.055 6.293 1 18.74 ? N1N NDP 188 A 1 HETATM 37 C C2N NDP . . . C 3 3.782 2.308 7.456 1 18.22 ? C2N NDP 188 A 1 HETATM 38 C C3N NDP . . . C 3 2.674 1.542 7.788 1 18.15 ? C3N NDP 188 A 1 HETATM 39 C C7N NDP . . . C 3 2.641 0.782 9.094 1 17.01 ? C7N NDP 188 A 1 HETATM 40 O O7N NDP . . . C 3 1.648 0.163 9.417 1 16.97 ? O7N NDP 188 A 1 HETATM 41 N N7N NDP . . . C 3 3.687 0.931 9.974 1 18.39 ? N7N NDP 188 A 1 HETATM 42 C C4N NDP . . . C 3 1.636 1.479 6.765 1 14.51 ? C4N NDP 188 A 1 HETATM 43 C C5N NDP . . . C 3 1.691 2.279 5.599 1 18.6 ? C5N NDP 188 A 1 HETATM 44 C C6N NDP . . . C 3 2.8 3.098 5.317 1 17.16 ? C6N NDP 188 A 1 HETATM 45 P P2B NDP . . . C 3 -0.094 12.658 -4.834 1 26.49 ? P2B NDP 188 A 1 HETATM 46 O O1X NDP . . . C 3 0.49 11.941 -6.067 1 26.38 ? O1X NDP 188 A 1 HETATM 47 O O2X NDP . . . C 3 0.992 13.699 -4.337 1 27.11 ? O2X NDP 188 A 1 HETATM 48 O O3X NDP . . . C 3 -1.425 13.31 -4.758 1 28.36 ? O3X NDP 188 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #