data_3D84 # _model_server_result.job_id ekd0lSOvUOCZHJZUFxqneQ _model_server_result.datetime_utc '2024-11-20 06:33:20' _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 3d84 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":187}' # _entry.id 3D84 # _exptl.entry_id 3D84 _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 118.26 _cell.angle_gamma 90 _cell.entry_id 3D84 _cell.length_a 41.226 _cell.length_b 61.172 _cell.length_c 43.15 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D84 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 2 _struct_asym.id B _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 250 n n PA O2A NDP sing 251 n n PA O5B NDP sing 252 n n PA O3 NDP sing 253 n n O2A HOA2 NDP sing 254 n n O5B C5B NDP sing 255 n n C5B C4B NDP sing 256 n n C5B H51A NDP sing 257 n n C5B H52A NDP sing 258 n n C4B O4B NDP sing 259 n n C4B C3B NDP sing 260 n n C4B H4B NDP sing 261 n n O4B C1B NDP sing 262 n n C3B O3B NDP sing 263 n n C3B C2B NDP sing 264 n n C3B H3B NDP sing 265 n n O3B HO3A NDP sing 266 n n C2B O2B NDP sing 267 n n C2B C1B NDP sing 268 n n C2B H2B NDP sing 269 n n O2B P2B NDP sing 270 n n C1B N9A NDP sing 271 n n C1B H1B NDP sing 272 n n N9A C8A NDP sing 273 n y N9A C4A NDP sing 274 n y C8A N7A NDP doub 275 n y C8A H8A NDP sing 276 n n N7A C5A NDP sing 277 n y C5A C6A NDP sing 278 n y C5A C4A NDP doub 279 n y C6A N6A NDP sing 280 n n C6A N1A NDP doub 281 n y N6A H61A NDP sing 282 n n N6A H62A NDP sing 283 n n N1A C2A NDP sing 284 n y C2A N3A NDP doub 285 n y C2A H2A NDP sing 286 n n N3A C4A NDP sing 287 n y O3 PN NDP sing 288 n n PN O1N NDP doub 289 n n PN O2N NDP sing 290 n n PN O5D NDP sing 291 n n O2N H21N NDP sing 292 n n O5D C5D NDP sing 293 n n C5D C4D NDP sing 294 n n C5D H51N NDP sing 295 n n C5D H52N NDP sing 296 n n C4D O4D NDP sing 297 n n C4D C3D NDP sing 298 n n C4D H4D NDP sing 299 n n O4D C1D NDP sing 300 n n C3D O3D NDP sing 301 n n C3D C2D NDP sing 302 n n C3D H3D NDP sing 303 n n O3D HO3N NDP sing 304 n n C2D O2D NDP sing 305 n n C2D C1D NDP sing 306 n n C2D H2D NDP sing 307 n n O2D HO2N NDP sing 308 n n C1D N1N NDP sing 309 n n C1D H1D NDP sing 310 n n N1N C2N NDP sing 311 n n N1N C6N NDP sing 312 n n C2N C3N NDP doub 313 n n C2N H2N NDP sing 314 n n C3N C7N NDP sing 315 n n C3N C4N NDP sing 316 n n C7N O7N NDP doub 317 n n C7N N7N NDP sing 318 n n N7N H71N NDP sing 319 n n N7N H72N NDP sing 320 n n C4N C5N NDP sing 321 n n C4N H41N NDP sing 322 n n C4N H42N NDP sing 323 n n C5N C6N NDP doub 324 n n C5N H5N NDP sing 325 n n C6N H6N NDP sing 326 n n P2B O1X NDP doub 327 n n P2B O2X NDP sing 328 n n P2B O3X NDP sing 329 n n O2X HOP2 NDP sing 330 n n O3X HOP3 NDP sing 331 n n # _atom_sites.entry_id 3D84 _atom_sites.fract_transf_matrix[1][1] 0.024257 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.013041 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016347 _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] 0.026312 _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 NDP X 1 187 1 NDP NDP . C 3 GOL X 1 188 1 GOL GOL . D 3 GOL X 1 189 1 GOL GOL . E 4 HOH X 1 190 1 HOH HOH . E 4 HOH X 2 191 2 HOH HOH . E 4 HOH X 3 192 3 HOH HOH . E 4 HOH X 4 193 4 HOH HOH . E 4 HOH X 5 194 5 HOH HOH . E 4 HOH X 6 195 7 HOH HOH . E 4 HOH X 7 196 8 HOH HOH . E 4 HOH X 8 197 9 HOH HOH . E 4 HOH X 9 198 10 HOH HOH . E 4 HOH X 10 199 11 HOH HOH . E 4 HOH X 11 200 12 HOH HOH . E 4 HOH X 12 201 13 HOH HOH . E 4 HOH X 13 202 14 HOH HOH . E 4 HOH X 14 203 15 HOH HOH . E 4 HOH X 15 204 16 HOH HOH . E 4 HOH X 16 205 17 HOH HOH . E 4 HOH X 17 206 18 HOH HOH . E 4 HOH X 18 207 19 HOH HOH . E 4 HOH X 19 208 20 HOH HOH . E 4 HOH X 20 209 21 HOH HOH . E 4 HOH X 21 210 22 HOH HOH . E 4 HOH X 22 211 23 HOH HOH . E 4 HOH X 23 212 24 HOH HOH . E 4 HOH X 24 213 25 HOH HOH . E 4 HOH X 25 214 26 HOH HOH . E 4 HOH X 26 215 27 HOH HOH . E 4 HOH X 27 216 28 HOH HOH . E 4 HOH X 28 217 29 HOH HOH . E 4 HOH X 29 218 30 HOH HOH . E 4 HOH X 30 219 31 HOH HOH . E 4 HOH X 31 220 32 HOH HOH . E 4 HOH X 32 221 33 HOH HOH . E 4 HOH X 33 222 34 HOH HOH . E 4 HOH X 34 223 35 HOH HOH . E 4 HOH X 35 224 36 HOH HOH . E 4 HOH X 36 225 37 HOH HOH . E 4 HOH X 37 226 38 HOH HOH . E 4 HOH X 38 227 39 HOH HOH . E 4 HOH X 39 228 40 HOH HOH . E 4 HOH X 40 229 41 HOH HOH . E 4 HOH X 41 230 42 HOH HOH . E 4 HOH X 42 231 43 HOH HOH . E 4 HOH X 43 232 44 HOH HOH . E 4 HOH X 44 233 45 HOH HOH . E 4 HOH X 45 234 46 HOH HOH . E 4 HOH X 46 235 47 HOH HOH . E 4 HOH X 47 236 48 HOH HOH . E 4 HOH X 48 237 50 HOH HOH . E 4 HOH X 49 238 51 HOH HOH . E 4 HOH X 50 239 53 HOH HOH . E 4 HOH X 51 240 54 HOH HOH . E 4 HOH X 52 241 55 HOH HOH . E 4 HOH X 53 242 57 HOH HOH . E 4 HOH X 54 243 58 HOH HOH . E 4 HOH X 55 244 59 HOH HOH . E 4 HOH X 56 245 60 HOH HOH . E 4 HOH X 57 246 61 HOH HOH . E 4 HOH X 58 247 62 HOH HOH . E 4 HOH X 59 248 63 HOH HOH . E 4 HOH X 60 249 64 HOH HOH . E 4 HOH X 61 250 65 HOH HOH . E 4 HOH X 62 251 66 HOH HOH . E 4 HOH X 63 252 67 HOH HOH . E 4 HOH X 64 253 68 HOH HOH . E 4 HOH X 65 254 69 HOH HOH . E 4 HOH X 66 255 70 HOH HOH . E 4 HOH X 67 256 71 HOH HOH . E 4 HOH X 68 257 72 HOH HOH . E 4 HOH X 69 258 73 HOH HOH . E 4 HOH X 70 259 74 HOH HOH . E 4 HOH X 71 260 75 HOH HOH . E 4 HOH X 72 261 76 HOH HOH . E 4 HOH X 73 262 77 HOH HOH . E 4 HOH X 74 263 78 HOH HOH . E 4 HOH X 75 264 79 HOH HOH . E 4 HOH X 76 265 80 HOH HOH . E 4 HOH X 77 266 81 HOH HOH . E 4 HOH X 78 267 82 HOH HOH . E 4 HOH X 79 268 83 HOH HOH . E 4 HOH X 80 269 84 HOH HOH . E 4 HOH X 81 270 85 HOH HOH . E 4 HOH X 82 271 86 HOH HOH . E 4 HOH X 83 272 87 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 . . . B 2 2.231 8.946 16.79 1 14.42 ? PA NDP 187 X 1 HETATM 2 O O1A NDP . . . B 2 3.001 7.954 16.014 1 15.83 ? O1A NDP 187 X 1 HETATM 3 O O2A NDP . . . B 2 0.757 9.097 16.526 1 11.64 ? O2A NDP 187 X 1 HETATM 4 O O5B NDP . . . B 2 2.991 10.305 16.68 1 15.52 ? O5B NDP 187 X 1 HETATM 5 C C5B NDP . . . B 2 2.488 11.45 17.331 1 12.24 ? C5B NDP 187 X 1 HETATM 6 C C4B NDP . . . B 2 3.015 12.568 16.514 1 12.54 ? C4B NDP 187 X 1 HETATM 7 O O4B NDP . . . B 2 2.715 12.372 15.056 1 10.58 ? O4B NDP 187 X 1 HETATM 8 C C3B NDP . . . B 2 2.491 13.983 16.813 1 15.7 ? C3B NDP 187 X 1 HETATM 9 O O3B NDP . . . B 2 3.188 14.507 17.914 1 14.38 ? O3B NDP 187 X 1 HETATM 10 C C2B NDP . . . B 2 3.25 14.271 15.546 1 16.04 ? C2B NDP 187 X 1 HETATM 11 O O2B NDP . . . B 2 3.68 15.49 15.167 1 16.7 ? O2B NDP 187 X 1 HETATM 12 C C1B NDP . . . B 2 2.364 13.624 14.481 1 14.07 ? C1B NDP 187 X 1 HETATM 13 N N9A NDP . . . B 2 0.864 13.641 14.192 1 14.6 ? N9A NDP 187 X 1 HETATM 14 C C8A NDP . . . B 2 -0.072 12.78 14.657 1 17.28 ? C8A NDP 187 X 1 HETATM 15 N N7A NDP . . . B 2 -1.273 13.054 14.15 1 15.55 ? N7A NDP 187 X 1 HETATM 16 C C5A NDP . . . B 2 -1.115 14.089 13.314 1 16.13 ? C5A NDP 187 X 1 HETATM 17 C C6A NDP . . . B 2 -1.985 14.846 12.516 1 17.78 ? C6A NDP 187 X 1 HETATM 18 N N6A NDP . . . B 2 -3.291 14.568 12.445 1 17.19 ? N6A NDP 187 X 1 HETATM 19 N N1A NDP . . . B 2 -1.494 15.866 11.782 1 14.34 ? N1A NDP 187 X 1 HETATM 20 C C2A NDP . . . B 2 -0.205 16.151 11.843 1 15.24 ? C2A NDP 187 X 1 HETATM 21 N N3A NDP . . . B 2 0.635 15.468 12.601 1 11.78 ? N3A NDP 187 X 1 HETATM 22 C C4A NDP . . . B 2 0.224 14.448 13.343 1 12.64 ? C4A NDP 187 X 1 HETATM 23 O O3 NDP . . . B 2 2.43 8.794 18.392 1 16.07 ? O3 NDP 187 X 1 HETATM 24 P PN NDP . . . B 2 1.965 7.702 19.474 1 23.25 ? PN NDP 187 X 1 HETATM 25 O O1N NDP . . . B 2 0.495 7.637 19.547 1 22.78 ? O1N NDP 187 X 1 HETATM 26 O O2N NDP . . . B 2 2.753 8.057 20.666 1 23.7 ? O2N NDP 187 X 1 HETATM 27 O O5D NDP . . . B 2 2.478 6.284 18.887 1 22.32 ? O5D NDP 187 X 1 HETATM 28 C C5D NDP . . . B 2 3.846 5.857 19.137 1 22.48 ? C5D NDP 187 X 1 HETATM 29 C C4D NDP . . . B 2 3.749 4.682 20.137 1 22.03 ? C4D NDP 187 X 1 HETATM 30 O O4D NDP . . . B 2 2.801 3.665 19.635 1 19.67 ? O4D NDP 187 X 1 HETATM 31 C C3D NDP . . . B 2 5.101 3.988 20.304 1 22.14 ? C3D NDP 187 X 1 HETATM 32 O O3D NDP . . . B 2 5.097 3.433 21.625 1 20.89 ? O3D NDP 187 X 1 HETATM 33 C C2D NDP . . . B 2 5.024 2.884 19.241 1 23.24 ? C2D NDP 187 X 1 HETATM 34 O O2D NDP . . . B 2 5.901 1.778 19.563 1 26.44 ? O2D NDP 187 X 1 HETATM 35 C C1D NDP . . . B 2 3.546 2.459 19.38 1 20.98 ? C1D NDP 187 X 1 HETATM 36 N N1N NDP . . . B 2 2.88 1.911 18.167 1 19.59 ? N1N NDP 187 X 1 HETATM 37 C C2N NDP . . . B 2 2.21 0.672 18.324 1 19.74 ? C2N NDP 187 X 1 HETATM 38 C C3N NDP . . . B 2 1.543 0.108 17.238 1 17.8 ? C3N NDP 187 X 1 HETATM 39 C C7N NDP . . . B 2 0.809 -1.22 17.402 1 16.69 ? C7N NDP 187 X 1 HETATM 40 O O7N NDP . . . B 2 0.13 -1.629 16.481 1 15.86 ? O7N NDP 187 X 1 HETATM 41 N N7N NDP . . . B 2 0.955 -1.892 18.55 1 18.8 ? N7N NDP 187 X 1 HETATM 42 C C4N NDP . . . B 2 1.54 0.788 15.99 1 18.54 ? C4N NDP 187 X 1 HETATM 43 C C5N NDP . . . B 2 2.196 2.027 15.83 1 14.63 ? C5N NDP 187 X 1 HETATM 44 C C6N NDP . . . B 2 2.851 2.611 16.921 1 16.65 ? C6N NDP 187 X 1 HETATM 45 P P2B NDP . . . B 2 4.85 16.412 15.678 1 15.31 ? P2B NDP 187 X 1 HETATM 46 O O1X NDP . . . B 2 4.047 17.608 15.085 1 11.83 ? O1X NDP 187 X 1 HETATM 47 O O2X NDP . . . B 2 6.135 16.222 14.878 1 13.58 ? O2X NDP 187 X 1 HETATM 48 O O3X NDP . . . B 2 4.939 16.456 17.171 1 14.8 ? O3X NDP 187 X 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 48 #