data_4PZD # _model_server_result.job_id JeJMRrE7Qkh4RAUkWPZDLg _model_server_result.datetime_utc '2025-02-05 04:07:57' _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 4pzd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":301}' # _entry.id 4PZD # _exptl.entry_id 4PZD _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 9 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.09 _cell.angle_gamma 90 _cell.entry_id 4PZD _cell.length_a 235.076 _cell.length_b 135.586 _cell.length_c 97.445 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PZD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 PISA dimeric 2 author_and_software_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,J,S 1 1,2 B,C,K,L,T,U 2 1 D,G,M,P,V,Y 3 1 E,F,N,O,W,X 4 1 H,I,Q,R,Z,AA 5 1 # 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' 2_554 -x,y,-z-1 -1 0 0 0 1 0 0 0 -1 0.153066 0 -97.44488 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 J N N ? 2 K N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 O N N ? 2 P N N ? 2 Q N N ? 2 R 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 237 n n PA O2A NAD sing 238 n n PA O5B NAD sing 239 n n PA O3 NAD sing 240 n n O2A HOA2 NAD sing 241 n n O5B C5B NAD sing 242 n n C5B C4B NAD sing 243 n n C5B H51A NAD sing 244 n n C5B H52A NAD sing 245 n n C4B O4B NAD sing 246 n n C4B C3B NAD sing 247 n n C4B H4B NAD sing 248 n n O4B C1B NAD sing 249 n n C3B O3B NAD sing 250 n n C3B C2B NAD sing 251 n n C3B H3B NAD sing 252 n n O3B HO3A NAD sing 253 n n C2B O2B NAD sing 254 n n C2B C1B NAD sing 255 n n C2B H2B NAD sing 256 n n O2B HO2A NAD sing 257 n n C1B N9A NAD sing 258 n n C1B H1B NAD sing 259 n n N9A C8A NAD sing 260 n y N9A C4A NAD sing 261 n y C8A N7A NAD doub 262 n y C8A H8A NAD sing 263 n n N7A C5A NAD sing 264 n y C5A C6A NAD sing 265 n y C5A C4A NAD doub 266 n y C6A N6A NAD sing 267 n n C6A N1A NAD doub 268 n y N6A H61A NAD sing 269 n n N6A H62A NAD sing 270 n n N1A C2A NAD sing 271 n y C2A N3A NAD doub 272 n y C2A H2A NAD sing 273 n n N3A C4A NAD sing 274 n y O3 PN NAD sing 275 n n PN O1N NAD doub 276 n n PN O2N NAD sing 277 n n PN O5D NAD sing 278 n n O5D C5D NAD sing 279 n n C5D C4D NAD sing 280 n n C5D H51N NAD sing 281 n n C5D H52N NAD sing 282 n n C4D O4D NAD sing 283 n n C4D C3D NAD sing 284 n n C4D H4D NAD sing 285 n n O4D C1D NAD sing 286 n n C3D O3D NAD sing 287 n n C3D C2D NAD sing 288 n n C3D H3D NAD sing 289 n n O3D HO3N NAD sing 290 n n C2D O2D NAD sing 291 n n C2D C1D NAD sing 292 n n C2D H2D NAD sing 293 n n O2D HO2N NAD sing 294 n n C1D N1N NAD sing 295 n n C1D H1D NAD sing 296 n n N1N C2N NAD sing 297 n y N1N C6N NAD doub 298 n y C2N C3N NAD doub 299 n y C2N H2N NAD sing 300 n n C3N C7N NAD sing 301 n n C3N C4N NAD sing 302 n y C7N O7N NAD doub 303 n n C7N N7N NAD sing 304 n n N7N H71N NAD sing 305 n n N7N H72N NAD sing 306 n n C4N C5N NAD doub 307 n y C4N H4N NAD sing 308 n n C5N C6N NAD sing 309 n y C5N H5N NAD sing 310 n n C6N H6N NAD sing 311 n n # _atom_sites.entry_id 4PZD _atom_sites.fract_transf_matrix[1][1] 0.004254 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000006 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007375 _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] 0.010262 _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 J 2 NAD A 1 301 1 NAD NAD . K 2 NAD B 1 301 2 NAD NAD . L 2 NAD C 1 301 3 NAD NAD . M 2 NAD D 1 301 4 NAD NAD . N 2 NAD E 1 301 5 NAD NAD . O 2 NAD F 1 301 6 NAD NAD . P 2 NAD G 1 301 7 NAD NAD . Q 2 NAD H 1 301 8 NAD NAD . R 2 NAD I 1 301 9 NAD NAD . S 3 HOH A 1 401 9 HOH HOH . S 3 HOH A 2 402 10 HOH HOH . S 3 HOH A 3 403 17 HOH HOH . S 3 HOH A 4 404 18 HOH HOH . S 3 HOH A 5 405 46 HOH HOH . S 3 HOH A 6 406 70 HOH HOH . S 3 HOH A 7 407 86 HOH HOH . S 3 HOH A 8 408 95 HOH HOH . S 3 HOH A 9 409 96 HOH HOH . S 3 HOH A 10 410 98 HOH HOH . T 3 HOH B 1 401 11 HOH HOH . T 3 HOH B 2 402 15 HOH HOH . T 3 HOH B 3 403 19 HOH HOH . T 3 HOH B 4 404 32 HOH HOH . T 3 HOH B 5 405 38 HOH HOH . T 3 HOH B 6 406 42 HOH HOH . T 3 HOH B 7 407 54 HOH HOH . T 3 HOH B 8 408 62 HOH HOH . T 3 HOH B 9 409 92 HOH HOH . T 3 HOH B 10 410 93 HOH HOH . U 3 HOH C 1 401 5 HOH HOH . U 3 HOH C 2 402 22 HOH HOH . U 3 HOH C 3 403 24 HOH HOH . U 3 HOH C 4 404 25 HOH HOH . U 3 HOH C 5 405 26 HOH HOH . U 3 HOH C 6 406 34 HOH HOH . U 3 HOH C 7 407 35 HOH HOH . U 3 HOH C 8 408 45 HOH HOH . U 3 HOH C 9 409 51 HOH HOH . U 3 HOH C 10 410 57 HOH HOH . U 3 HOH C 11 411 60 HOH HOH . U 3 HOH C 12 412 75 HOH HOH . U 3 HOH C 13 413 77 HOH HOH . U 3 HOH C 14 414 80 HOH HOH . U 3 HOH C 15 415 85 HOH HOH . U 3 HOH C 16 416 88 HOH HOH . U 3 HOH C 17 417 97 HOH HOH . V 3 HOH D 1 401 3 HOH HOH . V 3 HOH D 2 402 16 HOH HOH . V 3 HOH D 3 403 21 HOH HOH . V 3 HOH D 4 404 67 HOH HOH . V 3 HOH D 5 405 83 HOH HOH . V 3 HOH D 6 406 94 HOH HOH . W 3 HOH E 1 401 14 HOH HOH . W 3 HOH E 2 402 27 HOH HOH . W 3 HOH E 3 403 31 HOH HOH . W 3 HOH E 4 404 43 HOH HOH . W 3 HOH E 5 405 50 HOH HOH . W 3 HOH E 6 406 52 HOH HOH . W 3 HOH E 7 407 65 HOH HOH . W 3 HOH E 8 408 66 HOH HOH . W 3 HOH E 9 409 69 HOH HOH . W 3 HOH E 10 410 73 HOH HOH . W 3 HOH E 11 411 82 HOH HOH . W 3 HOH E 12 412 90 HOH HOH . W 3 HOH E 13 413 99 HOH HOH . W 3 HOH E 14 414 100 HOH HOH . X 3 HOH F 1 401 8 HOH HOH . X 3 HOH F 2 402 12 HOH HOH . X 3 HOH F 3 403 13 HOH HOH . X 3 HOH F 4 404 20 HOH HOH . X 3 HOH F 5 405 28 HOH HOH . X 3 HOH F 6 406 33 HOH HOH . X 3 HOH F 7 407 47 HOH HOH . X 3 HOH F 8 408 56 HOH HOH . X 3 HOH F 9 409 63 HOH HOH . X 3 HOH F 10 410 64 HOH HOH . X 3 HOH F 11 411 68 HOH HOH . X 3 HOH F 12 412 71 HOH HOH . X 3 HOH F 13 413 74 HOH HOH . X 3 HOH F 14 414 78 HOH HOH . X 3 HOH F 15 415 79 HOH HOH . X 3 HOH F 16 416 87 HOH HOH . X 3 HOH F 17 417 89 HOH HOH . Y 3 HOH G 1 401 2 HOH HOH . Y 3 HOH G 2 402 7 HOH HOH . Y 3 HOH G 3 403 30 HOH HOH . Y 3 HOH G 4 404 41 HOH HOH . Y 3 HOH G 5 405 48 HOH HOH . Y 3 HOH G 6 406 76 HOH HOH . Y 3 HOH G 7 407 81 HOH HOH . Z 3 HOH H 1 401 4 HOH HOH . Z 3 HOH H 2 402 36 HOH HOH . Z 3 HOH H 3 403 37 HOH HOH . Z 3 HOH H 4 404 40 HOH HOH . Z 3 HOH H 5 405 44 HOH HOH . Z 3 HOH H 6 406 59 HOH HOH . Z 3 HOH H 7 407 61 HOH HOH . Z 3 HOH H 8 408 72 HOH HOH . Z 3 HOH H 9 409 91 HOH HOH . AA 3 HOH I 1 401 1 HOH HOH . AA 3 HOH I 2 402 6 HOH HOH . AA 3 HOH I 3 403 23 HOH HOH . AA 3 HOH I 4 404 29 HOH HOH . AA 3 HOH I 5 405 39 HOH HOH . AA 3 HOH I 6 406 49 HOH HOH . AA 3 HOH I 7 407 53 HOH HOH . AA 3 HOH I 8 408 55 HOH HOH . AA 3 HOH I 9 409 58 HOH HOH . AA 3 HOH I 10 410 84 HOH HOH . AA 3 HOH I 11 411 101 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 . . . J 2 -17.988 -32.102 -28.303 1 120.36 ? PA NAD 301 A 1 HETATM 2 O O1A NAD . . . J 2 -19.162 -31.328 -28.853 1 114.06 ? O1A NAD 301 A 1 HETATM 3 O O2A NAD . . . J 2 -17.736 -33.501 -28.821 1 115.02 ? O2A NAD 301 A 1 HETATM 4 O O5B NAD . . . J 2 -18.18 -32.17 -26.702 1 121.5 ? O5B NAD 301 A 1 HETATM 5 C C5B NAD . . . J 2 -17.876 -31.07 -25.837 1 120.32 ? C5B NAD 301 A 1 HETATM 6 C C4B NAD . . . J 2 -17.951 -31.538 -24.386 1 117.79 ? C4B NAD 301 A 1 HETATM 7 O O4B NAD . . . J 2 -17.465 -30.511 -23.503 1 111.84 ? O4B NAD 301 A 1 HETATM 8 C C3B NAD . . . J 2 -19.393 -31.886 -23.979 1 117.04 ? C3B NAD 301 A 1 HETATM 9 O O3B NAD . . . J 2 -19.52 -33.238 -23.481 1 101.36 ? O3B NAD 301 A 1 HETATM 10 C C2B NAD . . . J 2 -19.737 -30.829 -22.935 1 115.94 ? C2B NAD 301 A 1 HETATM 11 O O2B NAD . . . J 2 -20.662 -31.281 -21.928 1 112.62 ? O2B NAD 301 A 1 HETATM 12 C C1B NAD . . . J 2 -18.362 -30.439 -22.376 1 109.94 ? C1B NAD 301 A 1 HETATM 13 N N9A NAD . . . J 2 -18.436 -29.135 -21.629 1 92.76 ? N9A NAD 301 A 1 HETATM 14 C C8A NAD . . . J 2 -18.952 -27.946 -22.043 1 85.74 ? C8A NAD 301 A 1 HETATM 15 N N7A NAD . . . J 2 -18.86 -27.018 -21.044 1 77.63 ? N7A NAD 301 A 1 HETATM 16 C C5A NAD . . . J 2 -18.29 -27.605 -19.972 1 73.94 ? C5A NAD 301 A 1 HETATM 17 C C6A NAD . . . J 2 -17.893 -27.202 -18.584 1 82.63 ? C6A NAD 301 A 1 HETATM 18 N N6A NAD . . . J 2 -18.104 -25.925 -18.142 1 78.41 ? N6A NAD 301 A 1 HETATM 19 N N1A NAD . . . J 2 -17.315 -28.147 -17.775 1 78.93 ? N1A NAD 301 A 1 HETATM 20 C C2A NAD . . . J 2 -17.106 -29.416 -18.207 1 80.4 ? C2A NAD 301 A 1 HETATM 21 N N3A NAD . . . J 2 -17.44 -29.834 -19.457 1 73.95 ? N3A NAD 301 A 1 HETATM 22 C C4A NAD . . . J 2 -18.02 -28.999 -20.362 1 76.84 ? C4A NAD 301 A 1 HETATM 23 O O3 NAD . . . J 2 -16.663 -31.184 -28.462 1 121.18 ? O3 NAD 301 A 1 HETATM 24 P PN NAD . . . J 2 -15.138 -31.694 -28.657 1 114.15 ? PN NAD 301 A 1 HETATM 25 O O1N NAD . . . J 2 -14.97 -32.162 -30.087 1 114.14 ? O1N NAD 301 A 1 HETATM 26 O O2N NAD . . . J 2 -14.757 -32.613 -27.513 1 108.97 ? O2N NAD 301 A 1 HETATM 27 O O5D NAD . . . J 2 -14.336 -30.29 -28.531 1 115.36 ? O5D NAD 301 A 1 HETATM 28 C C5D NAD . . . J 2 -13.695 -29.881 -27.328 1 127.4 ? C5D NAD 301 A 1 HETATM 29 C C4D NAD . . . J 2 -12.655 -28.792 -27.59 1 140.18 ? C4D NAD 301 A 1 HETATM 30 O O4D NAD . . . J 2 -11.424 -29.325 -28.101 1 151.75 ? O4D NAD 301 A 1 HETATM 31 C C3D NAD . . . J 2 -13.065 -27.764 -28.622 1 148.05 ? C3D NAD 301 A 1 HETATM 32 O O3D NAD . . . J 2 -13.915 -26.769 -28.072 1 160.98 ? O3D NAD 301 A 1 HETATM 33 C C2D NAD . . . J 2 -11.719 -27.228 -29.043 1 149.87 ? C2D NAD 301 A 1 HETATM 34 O O2D NAD . . . J 2 -11.236 -26.316 -28.053 1 151.56 ? O2D NAD 301 A 1 HETATM 35 C C1D NAD . . . J 2 -10.808 -28.424 -29.044 1 158.13 ? C1D NAD 301 A 1 HETATM 36 N N1N NAD . . . J 2 -10.642 -28.971 -30.421 1 161.75 ? N1N NAD 301 A 1 HETATM 37 C C2N NAD . . . J 2 -11.702 -29.456 -31.109 1 162.16 ? C2N NAD 301 A 1 HETATM 38 C C3N NAD . . . J 2 -11.579 -29.981 -32.4 1 154.12 ? C3N NAD 301 A 1 HETATM 39 C C7N NAD . . . J 2 -12.815 -30.516 -33.094 1 136.05 ? C7N NAD 301 A 1 HETATM 40 O O7N NAD . . . J 2 -13.088 -30.154 -34.223 1 126.88 ? O7N NAD 301 A 1 HETATM 41 N N7N NAD . . . J 2 -13.606 -31.389 -32.463 1 123.64 ? N7N NAD 301 A 1 HETATM 42 C C4N NAD . . . J 2 -10.311 -30 -32.997 1 150.67 ? C4N NAD 301 A 1 HETATM 43 C C5N NAD . . . J 2 -9.227 -29.503 -32.284 1 146 ? C5N NAD 301 A 1 HETATM 44 C C6N NAD . . . J 2 -9.417 -28.987 -30.998 1 152.79 ? C6N NAD 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #