data_3KVO # _model_server_result.job_id 6wu_N5qKFixz9B0I7h3CcQ _model_server_result.datetime_utc '2024-12-26 18:52:12' _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 3kvo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":501}' # _entry.id 3KVO # _exptl.entry_id 3KVO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _entity.pdbx_number_of_molecules 4 _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 3KVO _cell.length_a 61.149 _cell.length_b 78.332 _cell.length_c 121.765 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KVO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 1 A,B,C,D,E,F,G,H 3 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 # 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 D N N ? 2 E N N ? 2 F N N # _chem_comp.formula 'C21 H28 N7 O17 P3' _chem_comp.formula_weight 743.405 _chem_comp.id NAP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" # 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 NAP doub 237 n n PA O2A NAP sing 238 n n PA O5B NAP sing 239 n n PA O3 NAP sing 240 n n O2A HOA2 NAP sing 241 n n O5B C5B NAP sing 242 n n C5B C4B NAP sing 243 n n C5B H51A NAP sing 244 n n C5B H52A NAP sing 245 n n C4B O4B NAP sing 246 n n C4B C3B NAP sing 247 n n C4B H4B NAP sing 248 n n O4B C1B NAP sing 249 n n C3B O3B NAP sing 250 n n C3B C2B NAP sing 251 n n C3B H3B NAP sing 252 n n O3B HO3A NAP sing 253 n n C2B O2B NAP sing 254 n n C2B C1B NAP sing 255 n n C2B H2B NAP sing 256 n n O2B P2B NAP sing 257 n n C1B N9A NAP sing 258 n n C1B H1B NAP sing 259 n n N9A C8A NAP sing 260 n y N9A C4A NAP sing 261 n y C8A N7A NAP doub 262 n y C8A H8A NAP sing 263 n n N7A C5A NAP sing 264 n y C5A C6A NAP sing 265 n y C5A C4A NAP doub 266 n y C6A N6A NAP sing 267 n n C6A N1A NAP doub 268 n y N6A H61A NAP sing 269 n n N6A H62A NAP sing 270 n n N1A C2A NAP sing 271 n y C2A N3A NAP doub 272 n y C2A H2A NAP sing 273 n n N3A C4A NAP sing 274 n y O3 PN NAP sing 275 n n PN O1N NAP doub 276 n n PN O2N NAP sing 277 n n PN O5D NAP sing 278 n n O5D C5D NAP sing 279 n n C5D C4D NAP sing 280 n n C5D H51N NAP sing 281 n n C5D H52N NAP sing 282 n n C4D O4D NAP sing 283 n n C4D C3D NAP sing 284 n n C4D H4D NAP sing 285 n n O4D C1D NAP sing 286 n n C3D O3D NAP sing 287 n n C3D C2D NAP sing 288 n n C3D H3D NAP sing 289 n n O3D HO3N NAP sing 290 n n C2D O2D NAP sing 291 n n C2D C1D NAP sing 292 n n C2D H2D NAP sing 293 n n O2D HO2N NAP sing 294 n n C1D N1N NAP sing 295 n n C1D H1D NAP sing 296 n n N1N C2N NAP sing 297 n y N1N C6N NAP doub 298 n y C2N C3N NAP doub 299 n y C2N H2N NAP sing 300 n n C3N C7N NAP sing 301 n n C3N C4N NAP sing 302 n y C7N O7N NAP doub 303 n n C7N N7N NAP sing 304 n n N7N H71N NAP sing 305 n n N7N H72N NAP sing 306 n n C4N C5N NAP doub 307 n y C4N H4N NAP sing 308 n n C5N C6N NAP sing 309 n y C5N H5N NAP sing 310 n n C6N H6N NAP sing 311 n n P2B O1X NAP doub 312 n n P2B O2X NAP sing 313 n n P2B O3X NAP sing 314 n n O2X HOP2 NAP sing 315 n n O3X HOP3 NAP sing 316 n n # _atom_sites.entry_id 3KVO _atom_sites.fract_transf_matrix[1][1] 0.016353 _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] 0.012766 _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] 0.008213 _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 NAP A 1 501 501 NAP NAP . D 2 NAP A 1 502 502 NAP NAP . E 2 NAP B 1 501 501 NAP NAP . F 2 NAP B 1 502 502 NAP NAP . G 3 HOH A 1 312 1 HOH HOH . G 3 HOH A 2 313 2 HOH HOH . G 3 HOH A 3 314 3 HOH HOH . G 3 HOH A 4 315 7 HOH HOH . G 3 HOH A 5 316 8 HOH HOH . G 3 HOH A 6 317 9 HOH HOH . G 3 HOH A 7 318 10 HOH HOH . G 3 HOH A 8 319 11 HOH HOH . G 3 HOH A 9 320 12 HOH HOH . G 3 HOH A 10 321 14 HOH HOH . G 3 HOH A 11 322 18 HOH HOH . G 3 HOH A 12 323 36 HOH HOH . G 3 HOH A 13 324 40 HOH HOH . G 3 HOH A 14 325 45 HOH HOH . G 3 HOH A 15 326 47 HOH HOH . G 3 HOH A 16 327 48 HOH HOH . G 3 HOH A 17 328 49 HOH HOH . G 3 HOH A 18 329 51 HOH HOH . G 3 HOH A 19 330 52 HOH HOH . G 3 HOH A 20 331 53 HOH HOH . G 3 HOH A 21 332 54 HOH HOH . G 3 HOH A 22 333 55 HOH HOH . G 3 HOH A 23 334 56 HOH HOH . G 3 HOH A 24 335 57 HOH HOH . G 3 HOH A 25 336 58 HOH HOH . G 3 HOH A 26 337 59 HOH HOH . G 3 HOH A 27 338 60 HOH HOH . G 3 HOH A 28 339 61 HOH HOH . G 3 HOH A 29 340 63 HOH HOH . G 3 HOH A 30 341 64 HOH HOH . G 3 HOH A 31 342 65 HOH HOH . G 3 HOH A 32 343 66 HOH HOH . G 3 HOH A 33 344 67 HOH HOH . G 3 HOH A 34 345 68 HOH HOH . G 3 HOH A 35 346 69 HOH HOH . G 3 HOH A 36 347 70 HOH HOH . G 3 HOH A 37 348 71 HOH HOH . G 3 HOH A 38 349 76 HOH HOH . G 3 HOH A 39 350 77 HOH HOH . G 3 HOH A 40 351 78 HOH HOH . G 3 HOH A 41 352 79 HOH HOH . G 3 HOH A 42 353 80 HOH HOH . G 3 HOH A 43 354 81 HOH HOH . G 3 HOH A 44 355 89 HOH HOH . G 3 HOH A 45 356 90 HOH HOH . G 3 HOH A 46 357 91 HOH HOH . G 3 HOH A 47 358 94 HOH HOH . G 3 HOH A 48 359 95 HOH HOH . G 3 HOH A 49 360 96 HOH HOH . G 3 HOH A 50 361 99 HOH HOH . G 3 HOH A 51 362 101 HOH HOH . G 3 HOH A 52 363 106 HOH HOH . G 3 HOH A 53 364 107 HOH HOH . G 3 HOH A 54 365 108 HOH HOH . G 3 HOH A 55 366 112 HOH HOH . H 3 HOH B 1 312 6 HOH HOH . H 3 HOH B 2 313 15 HOH HOH . H 3 HOH B 3 314 16 HOH HOH . H 3 HOH B 4 315 17 HOH HOH . H 3 HOH B 5 316 23 HOH HOH . H 3 HOH B 6 317 24 HOH HOH . H 3 HOH B 7 318 25 HOH HOH . H 3 HOH B 8 319 26 HOH HOH . H 3 HOH B 9 320 27 HOH HOH . H 3 HOH B 10 321 28 HOH HOH . H 3 HOH B 11 322 29 HOH HOH . H 3 HOH B 12 323 30 HOH HOH . H 3 HOH B 13 324 31 HOH HOH . H 3 HOH B 14 325 32 HOH HOH . H 3 HOH B 15 326 33 HOH HOH . H 3 HOH B 16 327 35 HOH HOH . H 3 HOH B 17 328 37 HOH HOH . H 3 HOH B 18 329 38 HOH HOH . H 3 HOH B 19 330 39 HOH HOH . H 3 HOH B 20 331 41 HOH HOH . H 3 HOH B 21 332 42 HOH HOH . H 3 HOH B 22 333 43 HOH HOH . H 3 HOH B 23 334 44 HOH HOH . H 3 HOH B 24 335 50 HOH HOH . H 3 HOH B 25 336 62 HOH HOH . H 3 HOH B 26 337 72 HOH HOH . H 3 HOH B 27 338 73 HOH HOH . H 3 HOH B 28 339 74 HOH HOH . H 3 HOH B 29 340 75 HOH HOH . H 3 HOH B 30 341 82 HOH HOH . H 3 HOH B 31 342 83 HOH HOH . H 3 HOH B 32 343 84 HOH HOH . H 3 HOH B 33 344 85 HOH HOH . H 3 HOH B 34 345 86 HOH HOH . H 3 HOH B 35 346 87 HOH HOH . H 3 HOH B 36 347 88 HOH HOH . H 3 HOH B 37 348 93 HOH HOH . H 3 HOH B 38 349 97 HOH HOH . H 3 HOH B 39 350 98 HOH HOH . H 3 HOH B 40 351 100 HOH HOH . H 3 HOH B 41 352 102 HOH HOH . H 3 HOH B 42 353 103 HOH HOH . H 3 HOH B 43 354 104 HOH HOH . H 3 HOH B 44 355 105 HOH HOH . H 3 HOH B 45 356 109 HOH HOH . H 3 HOH B 46 357 110 HOH HOH . H 3 HOH B 47 358 111 HOH HOH . H 3 HOH B 48 359 113 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 NAP . . . E 2 46.685 -0.355 71.976 1 29.37 ? PA NAP 501 B 1 HETATM 2 O O1A NAP . . . E 2 47.955 -0.658 71.265 1 27.61 ? O1A NAP 501 B 1 HETATM 3 O O2A NAP . . . E 2 46.837 -0.105 73.422 1 29.14 ? O2A NAP 501 B 1 HETATM 4 O O5B NAP . . . E 2 45.887 0.83 71.236 1 28.04 ? O5B NAP 501 B 1 HETATM 5 C C5B NAP . . . E 2 45.368 1.886 72.002 1 25.69 ? C5B NAP 501 B 1 HETATM 6 C C4B NAP . . . E 2 45.647 3.203 71.303 1 21.7 ? C4B NAP 501 B 1 HETATM 7 O O4B NAP . . . E 2 44.903 4.178 71.986 1 20.35 ? O4B NAP 501 B 1 HETATM 8 C C3B NAP . . . E 2 47.096 3.614 71.364 1 19.61 ? C3B NAP 501 B 1 HETATM 9 O O3B NAP . . . E 2 47.48 4.101 70.074 1 19.11 ? O3B NAP 501 B 1 HETATM 10 C C2B NAP . . . E 2 47.123 4.708 72.416 1 18.33 ? C2B NAP 501 B 1 HETATM 11 O O2B NAP . . . E 2 48.076 5.646 72.004 1 16.58 ? O2B NAP 501 B 1 HETATM 12 C C1B NAP . . . E 2 45.696 5.251 72.371 1 18.43 ? C1B NAP 501 B 1 HETATM 13 N N9A NAP . . . E 2 45.213 5.821 73.629 1 18.39 ? N9A NAP 501 B 1 HETATM 14 C C8A NAP . . . E 2 45.192 5.26 74.865 1 17.47 ? C8A NAP 501 B 1 HETATM 15 N N7A NAP . . . E 2 44.69 6.172 75.732 1 17.88 ? N7A NAP 501 B 1 HETATM 16 C C5A NAP . . . E 2 44.392 7.314 75.076 1 18.93 ? C5A NAP 501 B 1 HETATM 17 C C6A NAP . . . E 2 43.865 8.56 75.454 1 19.15 ? C6A NAP 501 B 1 HETATM 18 N N6A NAP . . . E 2 43.508 8.867 76.698 1 17.43 ? N6A NAP 501 B 1 HETATM 19 N N1A NAP . . . E 2 43.669 9.513 74.491 1 17.95 ? N1A NAP 501 B 1 HETATM 20 C C2A NAP . . . E 2 43.991 9.259 73.179 1 17.09 ? C2A NAP 501 B 1 HETATM 21 N N3A NAP . . . E 2 44.525 8.049 72.824 1 18.59 ? N3A NAP 501 B 1 HETATM 22 C C4A NAP . . . E 2 44.712 7.087 73.747 1 18.7 ? C4A NAP 501 B 1 HETATM 23 O O3 NAP . . . E 2 45.631 -1.533 71.726 1 26.13 ? O3 NAP 501 B 1 HETATM 24 P PN NAP . . . E 2 45.036 -2.134 70.366 1 24.59 ? PN NAP 501 B 1 HETATM 25 O O1N NAP . . . E 2 45.599 -1.514 69.149 1 21.57 ? O1N NAP 501 B 1 HETATM 26 O O2N NAP . . . E 2 45.083 -3.624 70.509 1 23.44 ? O2N NAP 501 B 1 HETATM 27 O O5D NAP . . . E 2 43.478 -1.712 70.493 1 22.29 ? O5D NAP 501 B 1 HETATM 28 C C5D NAP . . . E 2 42.858 -0.555 69.965 1 19.78 ? C5D NAP 501 B 1 HETATM 29 C C4D NAP . . . E 2 41.336 -0.735 70.011 1 17.81 ? C4D NAP 501 B 1 HETATM 30 O O4D NAP . . . E 2 40.988 -2.047 69.546 1 19.06 ? O4D NAP 501 B 1 HETATM 31 C C3D NAP . . . E 2 40.753 -0.579 71.405 1 18.01 ? C3D NAP 501 B 1 HETATM 32 O O3D NAP . . . E 2 39.461 0.029 71.394 1 17.61 ? O3D NAP 501 B 1 HETATM 33 C C2D NAP . . . E 2 40.605 -2.002 71.849 1 18.14 ? C2D NAP 501 B 1 HETATM 34 O O2D NAP . . . E 2 39.62 -2.139 72.862 1 18.63 ? O2D NAP 501 B 1 HETATM 35 C C1D NAP . . . E 2 40.226 -2.683 70.536 1 17.65 ? C1D NAP 501 B 1 HETATM 36 N N1N NAP . . . E 2 40.408 -4.13 70.661 1 17.77 ? N1N NAP 501 B 1 HETATM 37 C C2N NAP . . . E 2 41.651 -4.761 70.694 1 17.25 ? C2N NAP 501 B 1 HETATM 38 C C3N NAP . . . E 2 41.74 -6.16 70.855 1 14.93 ? C3N NAP 501 B 1 HETATM 39 C C7N NAP . . . E 2 42.993 -6.957 70.579 1 16.54 ? C7N NAP 501 B 1 HETATM 40 O O7N NAP . . . E 2 42.891 -8.34 70.511 1 15.13 ? O7N NAP 501 B 1 HETATM 41 N N7N NAP . . . E 2 44.188 -6.394 70.361 1 15.53 ? N7N NAP 501 B 1 HETATM 42 C C4N NAP . . . E 2 40.584 -6.885 71.003 1 16.87 ? C4N NAP 501 B 1 HETATM 43 C C5N NAP . . . E 2 39.35 -6.228 70.986 1 17.71 ? C5N NAP 501 B 1 HETATM 44 C C6N NAP . . . E 2 39.259 -4.847 70.818 1 16.3 ? C6N NAP 501 B 1 HETATM 45 P P2B NAP . . . E 2 48.865 6.625 72.988 1 17.12 ? P2B NAP 501 B 1 HETATM 46 O O1X NAP . . . E 2 49.798 7.407 72.113 1 15.27 ? O1X NAP 501 B 1 HETATM 47 O O2X NAP . . . E 2 49.662 5.864 74.015 1 13.5 ? O2X NAP 501 B 1 HETATM 48 O O3X NAP . . . E 2 47.802 7.464 73.634 1 16.33 ? O3X NAP 501 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 48 #