data_3NT5 # _model_server_result.job_id dBXdiGko84ijYvrnne6QmA _model_server_result.datetime_utc '2025-02-18 09:24:01' _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 3nt5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":400}' # _entry.id 3NT5 # _exptl.entry_id 3NT5 _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 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 3NT5 _cell.length_a 183.498 _cell.length_b 183.498 _cell.length_c 183.498 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NT5 _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 1 1,2 A,B,C,D,E,F 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' 15_455 -x-1/2,y,-z -1 0 0 0 1 0 0 0 -1 -91.749 0 0 3 'crystal symmetry operation' 8_555 -z,x+1/2,-y+1/2 0 0 -1 1 0 0 0 -1 0 0 91.749 91.749 4 'crystal symmetry operation' 11_455 y-1/2,-z+1/2,-x 0 1 0 0 0 -1 -1 0 0 -91.749 91.749 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 257 n n PA O2A NAD sing 258 n n PA O5B NAD sing 259 n n PA O3 NAD sing 260 n n O2A HOA2 NAD sing 261 n n O5B C5B NAD sing 262 n n C5B C4B NAD sing 263 n n C5B H51A NAD sing 264 n n C5B H52A NAD sing 265 n n C4B O4B NAD sing 266 n n C4B C3B NAD sing 267 n n C4B H4B NAD sing 268 n n O4B C1B NAD sing 269 n n C3B O3B NAD sing 270 n n C3B C2B NAD sing 271 n n C3B H3B NAD sing 272 n n O3B HO3A NAD sing 273 n n C2B O2B NAD sing 274 n n C2B C1B NAD sing 275 n n C2B H2B NAD sing 276 n n O2B HO2A NAD sing 277 n n C1B N9A NAD sing 278 n n C1B H1B NAD sing 279 n n N9A C8A NAD sing 280 n y N9A C4A NAD sing 281 n y C8A N7A NAD doub 282 n y C8A H8A NAD sing 283 n n N7A C5A NAD sing 284 n y C5A C6A NAD sing 285 n y C5A C4A NAD doub 286 n y C6A N6A NAD sing 287 n n C6A N1A NAD doub 288 n y N6A H61A NAD sing 289 n n N6A H62A NAD sing 290 n n N1A C2A NAD sing 291 n y C2A N3A NAD doub 292 n y C2A H2A NAD sing 293 n n N3A C4A NAD sing 294 n y O3 PN NAD sing 295 n n PN O1N NAD doub 296 n n PN O2N NAD sing 297 n n PN O5D NAD sing 298 n n O5D C5D NAD sing 299 n n C5D C4D NAD sing 300 n n C5D H51N NAD sing 301 n n C5D H52N NAD sing 302 n n C4D O4D NAD sing 303 n n C4D C3D NAD sing 304 n n C4D H4D NAD sing 305 n n O4D C1D NAD sing 306 n n C3D O3D NAD sing 307 n n C3D C2D NAD sing 308 n n C3D H3D NAD sing 309 n n O3D HO3N NAD sing 310 n n C2D O2D NAD sing 311 n n C2D C1D NAD sing 312 n n C2D H2D NAD sing 313 n n O2D HO2N NAD sing 314 n n C1D N1N NAD sing 315 n n C1D H1D NAD sing 316 n n N1N C2N NAD sing 317 n y N1N C6N NAD doub 318 n y C2N C3N NAD doub 319 n y C2N H2N NAD sing 320 n n C3N C7N NAD sing 321 n n C3N C4N NAD sing 322 n y C7N O7N NAD doub 323 n n C7N N7N NAD sing 324 n n N7N H71N NAD sing 325 n n N7N H72N NAD sing 326 n n C4N C5N NAD doub 327 n y C4N H4N NAD sing 328 n n C5N C6N NAD sing 329 n y C5N H5N NAD sing 330 n n C6N H6N NAD sing 331 n n # _atom_sites.entry_id 3NT5 _atom_sites.fract_transf_matrix[1][1] 0.00545 _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] 0.00545 _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] 0.00545 _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 ISE A 1 345 1 ISE ISE . E 4 NAI B 1 400 400 NAI NAI . F 3 ISE B 1 345 2 ISE ISE . # 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 . . . C 2 -62.409 -11.702 18.167 1 115.47 ? PA NAD 400 A 1 HETATM 2 O O1A NAD . . . C 2 -62.74 -11.695 16.705 1 115.47 ? O1A NAD 400 A 1 HETATM 3 O O2A NAD . . . C 2 -63.63 -11.281 18.921 1 115.47 ? O2A NAD 400 A 1 HETATM 4 O O5B NAD . . . C 2 -61.999 -13.187 18.646 1 115.47 ? O5B NAD 400 A 1 HETATM 5 C C5B NAD . . . C 2 -61.155 -13.499 19.759 1 115.47 ? C5B NAD 400 A 1 HETATM 6 C C4B NAD . . . C 2 -61.038 -15.029 19.709 1 115.47 ? C4B NAD 400 A 1 HETATM 7 O O4B NAD . . . C 2 -60.175 -15.585 20.692 1 115.47 ? O4B NAD 400 A 1 HETATM 8 C C3B NAD . . . C 2 -62.429 -15.677 19.867 1 115.47 ? C3B NAD 400 A 1 HETATM 9 O O3B NAD . . . C 2 -62.799 -16.478 18.743 1 115.47 ? O3B NAD 400 A 1 HETATM 10 C C2B NAD . . . C 2 -62.339 -16.466 21.172 1 115.47 ? C2B NAD 400 A 1 HETATM 11 O O2B NAD . . . C 2 -63.153 -17.637 21.159 1 115.47 ? O2B NAD 400 A 1 HETATM 12 C C1B NAD . . . C 2 -60.829 -16.747 21.229 1 115.47 ? C1B NAD 400 A 1 HETATM 13 N N9A NAD . . . C 2 -60.265 -17.16 22.541 1 115.47 ? N9A NAD 400 A 1 HETATM 14 C C8A NAD . . . C 2 -60.305 -16.474 23.737 1 115.47 ? C8A NAD 400 A 1 HETATM 15 N N7A NAD . . . C 2 -59.555 -17.145 24.654 1 115.47 ? N7A NAD 400 A 1 HETATM 16 C C5A NAD . . . C 2 -59.036 -18.262 24.068 1 115.47 ? C5A NAD 400 A 1 HETATM 17 C C6A NAD . . . C 2 -58.195 -19.299 24.532 1 115.47 ? C6A NAD 400 A 1 HETATM 18 N N6A NAD . . . C 2 -57.723 -19.303 25.789 1 115.47 ? N6A NAD 400 A 1 HETATM 19 N N1A NAD . . . C 2 -57.83 -20.323 23.648 1 115.47 ? N1A NAD 400 A 1 HETATM 20 C C2A NAD . . . C 2 -58.288 -20.323 22.33 1 115.47 ? C2A NAD 400 A 1 HETATM 21 N N3A NAD . . . C 2 -59.113 -19.299 21.882 1 115.47 ? N3A NAD 400 A 1 HETATM 22 C C4A NAD . . . C 2 -59.481 -18.285 22.728 1 115.47 ? C4A NAD 400 A 1 HETATM 23 O O3 NAD . . . C 2 -61.035 -10.89 18.609 1 115.47 ? O3 NAD 400 A 1 HETATM 24 P PN NAD . . . C 2 -59.565 -10.893 17.87 1 115.47 ? PN NAD 400 A 1 HETATM 25 O O1N NAD . . . C 2 -59.21 -12.276 17.392 1 115.47 ? O1N NAD 400 A 1 HETATM 26 O O2N NAD . . . C 2 -59.619 -9.774 16.897 1 115.47 ? O2N NAD 400 A 1 HETATM 27 O O5D NAD . . . C 2 -58.429 -10.387 18.943 1 115.47 ? O5D NAD 400 A 1 HETATM 28 C C5D NAD . . . C 2 -57.736 -11.213 19.88 1 115.47 ? C5D NAD 400 A 1 HETATM 29 C C4D NAD . . . C 2 -56.798 -10.465 20.871 1 115.47 ? C4D NAD 400 A 1 HETATM 30 O O4D NAD . . . C 2 -55.456 -10.25 20.389 1 115.47 ? O4D NAD 400 A 1 HETATM 31 C C3D NAD . . . C 2 -57.329 -9.144 21.486 1 115.47 ? C3D NAD 400 A 1 HETATM 32 O O3D NAD . . . C 2 -57.578 -9.227 22.892 1 115.47 ? O3D NAD 400 A 1 HETATM 33 C C2D NAD . . . C 2 -56.258 -8.101 21.134 1 115.47 ? C2D NAD 400 A 1 HETATM 34 O O2D NAD . . . C 2 -55.929 -7.172 22.153 1 115.47 ? O2D NAD 400 A 1 HETATM 35 C C1D NAD . . . C 2 -55.07 -8.867 20.502 1 115.47 ? C1D NAD 400 A 1 HETATM 36 N N1N NAD . . . C 2 -54.749 -8.281 19.163 1 115.47 ? N1N NAD 400 A 1 HETATM 37 C C2N NAD . . . C 2 -53.459 -7.88 18.848 1 115.47 ? C2N NAD 400 A 1 HETATM 38 C C3N NAD . . . C 2 -53.172 -7.307 17.584 1 115.47 ? C3N NAD 400 A 1 HETATM 39 C C7N NAD . . . C 2 -51.774 -6.871 17.198 1 115.47 ? C7N NAD 400 A 1 HETATM 40 O O7N NAD . . . C 2 -51.604 -6.141 15.985 1 115.47 ? O7N NAD 400 A 1 HETATM 41 N N7N NAD . . . C 2 -50.737 -7.222 17.985 1 115.47 ? N7N NAD 400 A 1 HETATM 42 C C4N NAD . . . C 2 -54.203 -7.135 16.642 1 115.47 ? C4N NAD 400 A 1 HETATM 43 C C5N NAD . . . C 2 -55.508 -7.532 16.964 1 115.47 ? C5N NAD 400 A 1 HETATM 44 C C6N NAD . . . C 2 -55.761 -8.102 18.223 1 115.47 ? C6N NAD 400 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #