data_3NTR # _model_server_result.job_id KRkdNDKQDZFNSA0YORFGtg _model_server_result.datetime_utc '2024-10-14 07:28:55' _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 3ntr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":400}' # _entry.id 3NTR # _exptl.entry_id 3NTR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 3NTR _cell.length_a 183.695 _cell.length_b 183.695 _cell.length_c 183.695 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NTR _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # 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 tetrameric 4 author_and_software_defined_assembly 1 PISA hexameric 6 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,G,H 1 1,2 A,B,C,D,E,F,G,H 2 1,3,4 # 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' 16_554 x,-y,-z-1/2 1 0 0 0 -1 0 0 0 -1 0 0 -91.8475 3 'crystal symmetry operation' 6_555 z+1/2,-x+1/2,-y 0 0 1 -1 0 0 0 -1 0 91.8475 91.8475 0 4 'crystal symmetry operation' 12_554 -y+1/2,-z,x-1/2 0 -1 0 0 0 -1 1 0 0 91.8475 0 -91.8475 # 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 H27 N7 O14 P2' _chem_comp.formula_weight 663.425 _chem_comp.id NAD _chem_comp.mon_nstd_flag . _chem_comp.name NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 NAD doub 261 n n PA O2A NAD sing 262 n n PA O5B NAD sing 263 n n PA O3 NAD sing 264 n n O2A HOA2 NAD sing 265 n n O5B C5B NAD sing 266 n n C5B C4B NAD sing 267 n n C5B H51A NAD sing 268 n n C5B H52A NAD sing 269 n n C4B O4B NAD sing 270 n n C4B C3B NAD sing 271 n n C4B H4B NAD sing 272 n n O4B C1B NAD sing 273 n n C3B O3B NAD sing 274 n n C3B C2B NAD sing 275 n n C3B H3B NAD sing 276 n n O3B HO3A NAD sing 277 n n C2B O2B NAD sing 278 n n C2B C1B NAD sing 279 n n C2B H2B NAD sing 280 n n O2B HO2A NAD sing 281 n n C1B N9A NAD sing 282 n n C1B H1B NAD sing 283 n n N9A C8A NAD sing 284 n y N9A C4A NAD sing 285 n y C8A N7A NAD doub 286 n y C8A H8A NAD sing 287 n n N7A C5A NAD sing 288 n y C5A C6A NAD sing 289 n y C5A C4A NAD doub 290 n y C6A N6A NAD sing 291 n n C6A N1A NAD doub 292 n y N6A H61A NAD sing 293 n n N6A H62A NAD sing 294 n n N1A C2A NAD sing 295 n y C2A N3A NAD doub 296 n y C2A H2A NAD sing 297 n n N3A C4A NAD sing 298 n y O3 PN NAD sing 299 n n PN O1N NAD doub 300 n n PN O2N NAD sing 301 n n PN O5D NAD sing 302 n n O5D C5D NAD sing 303 n n C5D C4D NAD sing 304 n n C5D H51N NAD sing 305 n n C5D H52N NAD sing 306 n n C4D O4D NAD sing 307 n n C4D C3D NAD sing 308 n n C4D H4D NAD sing 309 n n O4D C1D NAD sing 310 n n C3D O3D NAD sing 311 n n C3D C2D NAD sing 312 n n C3D H3D NAD sing 313 n n O3D HO3N NAD sing 314 n n C2D O2D NAD sing 315 n n C2D C1D NAD sing 316 n n C2D H2D NAD sing 317 n n O2D HO2N NAD sing 318 n n C1D N1N NAD sing 319 n n C1D H1D NAD sing 320 n n N1N C2N NAD sing 321 n y N1N C6N NAD doub 322 n y C2N C3N NAD doub 323 n y C2N H2N NAD sing 324 n n C3N C7N NAD sing 325 n n C3N C4N NAD sing 326 n y C7N O7N NAD doub 327 n n C7N N7N NAD sing 328 n n N7N H71N NAD sing 329 n n N7N H72N NAD sing 330 n n C4N C5N NAD doub 331 n y C4N H4N NAD sing 332 n n C5N C6N NAD sing 333 n y C5N H5N NAD sing 334 n n C6N H6N NAD sing 335 n n # _atom_sites.entry_id 3NTR _atom_sites.fract_transf_matrix[1][1] 0.005444 _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] 0.005444 _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] 0.005444 _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 NAD A 1 400 400 NAD NAD . D 3 INS A 1 801 801 INS INS . E 2 NAD B 1 400 400 NAD NAD . F 3 INS B 1 802 802 INS INS . G 4 HOH A 1 345 3 HOH HOH . G 4 HOH A 2 346 5 HOH HOH . G 4 HOH A 3 347 7 HOH HOH . G 4 HOH A 4 348 9 HOH HOH . G 4 HOH A 5 349 10 HOH HOH . G 4 HOH A 6 350 11 HOH HOH . G 4 HOH A 7 351 12 HOH HOH . G 4 HOH A 8 352 13 HOH HOH . G 4 HOH A 9 353 18 HOH HOH . G 4 HOH A 10 354 19 HOH HOH . G 4 HOH A 11 355 20 HOH HOH . G 4 HOH A 12 356 21 HOH HOH . G 4 HOH A 13 357 23 HOH HOH . G 4 HOH A 14 358 25 HOH HOH . G 4 HOH A 15 359 26 HOH HOH . G 4 HOH A 16 360 27 HOH HOH . G 4 HOH A 17 361 29 HOH HOH . G 4 HOH A 18 362 31 HOH HOH . G 4 HOH A 19 363 33 HOH HOH . G 4 HOH A 20 364 35 HOH HOH . G 4 HOH A 21 365 36 HOH HOH . G 4 HOH A 22 366 38 HOH HOH . G 4 HOH A 23 367 39 HOH HOH . G 4 HOH A 24 368 42 HOH HOH . G 4 HOH A 25 369 43 HOH HOH . G 4 HOH A 26 370 44 HOH HOH . G 4 HOH A 27 371 46 HOH HOH . G 4 HOH A 28 372 47 HOH HOH . G 4 HOH A 29 373 48 HOH HOH . G 4 HOH A 30 374 56 HOH HOH . G 4 HOH A 31 375 57 HOH HOH . H 4 HOH B 1 345 1 HOH HOH . H 4 HOH B 2 346 2 HOH HOH . H 4 HOH B 3 347 4 HOH HOH . H 4 HOH B 4 348 6 HOH HOH . H 4 HOH B 5 349 8 HOH HOH . H 4 HOH B 6 350 14 HOH HOH . H 4 HOH B 7 351 15 HOH HOH . H 4 HOH B 8 352 16 HOH HOH . H 4 HOH B 9 353 17 HOH HOH . H 4 HOH B 10 354 24 HOH HOH . H 4 HOH B 11 355 28 HOH HOH . H 4 HOH B 12 356 30 HOH HOH . H 4 HOH B 13 357 32 HOH HOH . H 4 HOH B 14 358 34 HOH HOH . H 4 HOH B 15 359 37 HOH HOH . H 4 HOH B 16 360 40 HOH HOH . H 4 HOH B 17 361 41 HOH HOH . H 4 HOH B 18 362 45 HOH HOH . H 4 HOH B 19 363 49 HOH HOH . H 4 HOH B 20 364 50 HOH HOH . H 4 HOH B 21 365 51 HOH HOH . H 4 HOH B 22 366 52 HOH HOH . H 4 HOH B 23 367 53 HOH HOH . H 4 HOH B 24 368 54 HOH HOH . H 4 HOH B 25 369 55 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 NAD . . . E 2 47.104 19.253 -30.794 1 139.05 ? PA NAD 400 B 1 HETATM 2 O O1A NAD . . . E 2 47.043 17.831 -30.327 1 87.92 ? O1A NAD 400 B 1 HETATM 3 O O2A NAD . . . E 2 46.896 20.215 -29.689 1 136.23 ? O2A NAD 400 B 1 HETATM 4 O O5B NAD . . . E 2 48.52 19.526 -31.507 1 132.26 ? O5B NAD 400 B 1 HETATM 5 C C5B NAD . . . E 2 49.221 20.744 -31.394 1 124.47 ? C5B NAD 400 B 1 HETATM 6 C C4B NAD . . . E 2 50.677 20.426 -31.045 1 120.97 ? C4B NAD 400 B 1 HETATM 7 O O4B NAD . . . E 2 51.564 21.203 -31.819 1 136.18 ? O4B NAD 400 B 1 HETATM 8 C C3B NAD . . . E 2 51.049 20.686 -29.589 1 128.55 ? C3B NAD 400 B 1 HETATM 9 O O3B NAD . . . E 2 51.69 19.527 -29.106 1 106.85 ? O3B NAD 400 B 1 HETATM 10 C C2B NAD . . . E 2 51.973 21.902 -29.597 1 135.73 ? C2B NAD 400 B 1 HETATM 11 O O2B NAD . . . E 2 52.985 21.812 -28.615 1 126.53 ? O2B NAD 400 B 1 HETATM 12 C C1B NAD . . . E 2 52.548 21.841 -31.005 1 143.44 ? C1B NAD 400 B 1 HETATM 13 N N9A NAD . . . E 2 52.948 23.098 -31.685 1 151.38 ? N9A NAD 400 B 1 HETATM 14 C C8A NAD . . . E 2 52.256 24.284 -31.821 1 142.56 ? C8A NAD 400 B 1 HETATM 15 N N7A NAD . . . E 2 52.95 25.088 -32.671 1 145.77 ? N7A NAD 400 B 1 HETATM 16 C C5A NAD . . . E 2 54.073 24.434 -33.095 1 157.71 ? C5A NAD 400 B 1 HETATM 17 C C6A NAD . . . E 2 55.142 24.759 -33.958 1 150.04 ? C6A NAD 400 B 1 HETATM 18 N N6A NAD . . . E 2 55.215 25.928 -34.595 1 141.4 ? N6A NAD 400 B 1 HETATM 19 N N1A NAD . . . E 2 56.158 23.845 -34.182 1 137.84 ? N1A NAD 400 B 1 HETATM 20 C C2A NAD . . . E 2 56.127 22.607 -33.56 1 140.27 ? C2A NAD 400 B 1 HETATM 21 N N3A NAD . . . E 2 55.081 22.29 -32.712 1 141.15 ? N3A NAD 400 B 1 HETATM 22 C C4A NAD . . . E 2 54.073 23.179 -32.479 1 149.69 ? C4A NAD 400 B 1 HETATM 23 O O3 NAD . . . E 2 46.019 19.574 -31.958 1 139.58 ? O3 NAD 400 B 1 HETATM 24 P PN NAD . . . E 2 45.261 18.442 -32.832 1 142.24 ? PN NAD 400 B 1 HETATM 25 O O1N NAD . . . E 2 46.064 17.189 -32.785 1 107.54 ? O1N NAD 400 B 1 HETATM 26 O O2N NAD . . . E 2 43.817 18.442 -32.485 1 127.34 ? O2N NAD 400 B 1 HETATM 27 O O5D NAD . . . E 2 45.31 19.09 -34.304 1 131.68 ? O5D NAD 400 B 1 HETATM 28 C C5D NAD . . . E 2 46.434 19.737 -34.863 1 117.89 ? C5D NAD 400 B 1 HETATM 29 C C4D NAD . . . E 2 46.004 20.267 -36.234 1 125.3 ? C4D NAD 400 B 1 HETATM 30 O O4D NAD . . . E 2 45.343 19.232 -36.935 1 140.41 ? O4D NAD 400 B 1 HETATM 31 C C3D NAD . . . E 2 44.996 21.418 -36.165 1 141.56 ? C3D NAD 400 B 1 HETATM 32 O O3D NAD . . . E 2 45.267 22.364 -37.184 1 133.83 ? O3D NAD 400 B 1 HETATM 33 C C2D NAD . . . E 2 43.645 20.781 -36.424 1 127.64 ? C2D NAD 400 B 1 HETATM 34 O O2D NAD . . . E 2 42.775 21.667 -37.088 1 127.02 ? O2D NAD 400 B 1 HETATM 35 C C1D NAD . . . E 2 44.053 19.656 -37.355 1 137.13 ? C1D NAD 400 B 1 HETATM 36 N N1N NAD . . . E 2 43.093 18.539 -37.422 1 141.35 ? N1N NAD 400 B 1 HETATM 37 C C2N NAD . . . E 2 42.541 18.255 -38.648 1 127.44 ? C2N NAD 400 B 1 HETATM 38 C C3N NAD . . . E 2 41.639 17.2 -38.775 1 134.66 ? C3N NAD 400 B 1 HETATM 39 C C7N NAD . . . E 2 41.015 16.87 -40.104 1 129.89 ? C7N NAD 400 B 1 HETATM 40 O O7N NAD . . . E 2 39.769 16.217 -40.092 1 124.24 ? O7N NAD 400 B 1 HETATM 41 N N7N NAD . . . E 2 41.63 17.2 -41.248 1 123.77 ? N7N NAD 400 B 1 HETATM 42 C C4N NAD . . . E 2 41.305 16.444 -37.647 1 136.17 ? C4N NAD 400 B 1 HETATM 43 C C5N NAD . . . E 2 41.872 16.741 -36.402 1 130.47 ? C5N NAD 400 B 1 HETATM 44 C C6N NAD . . . E 2 42.771 17.798 -36.301 1 131.77 ? C6N NAD 400 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 44 #