data_3KVO # _model_server_result.job_id 1MCAYF-WtxebLttrgMKLeQ _model_server_result.datetime_utc '2024-12-26 18:46:07' _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":"C","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 . . . C 2 14.729 13.755 92.909 1 34.33 ? PA NAP 501 A 1 HETATM 2 O O1A NAP . . . C 2 15.687 14.589 92.121 1 33.2 ? O1A NAP 501 A 1 HETATM 3 O O2A NAP . . . C 2 13.697 14.499 93.689 1 32.2 ? O2A NAP 501 A 1 HETATM 4 O O5B NAP . . . C 2 15.621 12.747 93.793 1 27.74 ? O5B NAP 501 A 1 HETATM 5 C C5B NAP . . . C 2 17.004 12.71 93.594 1 23.11 ? C5B NAP 501 A 1 HETATM 6 C C4B NAP . . . C 2 17.563 12.451 94.963 1 21.08 ? C4B NAP 501 A 1 HETATM 7 O O4B NAP . . . C 2 18.933 12.17 94.859 1 19.85 ? O4B NAP 501 A 1 HETATM 8 C C3B NAP . . . C 2 17.396 13.662 95.852 1 19.96 ? C3B NAP 501 A 1 HETATM 9 O O3B NAP . . . C 2 17.097 13.2 97.15 1 19.56 ? O3B NAP 501 A 1 HETATM 10 C C2B NAP . . . C 2 18.747 14.342 95.789 1 19.16 ? C2B NAP 501 A 1 HETATM 11 O O2B NAP . . . C 2 18.962 14.999 97.025 1 18.4 ? O2B NAP 501 A 1 HETATM 12 C C1B NAP . . . C 2 19.682 13.148 95.542 1 18.85 ? C1B NAP 501 A 1 HETATM 13 N N9A NAP . . . C 2 20.911 13.478 94.814 1 17.32 ? N9A NAP 501 A 1 HETATM 14 C C8A NAP . . . C 2 21.035 14.127 93.615 1 17.24 ? C8A NAP 501 A 1 HETATM 15 N N7A NAP . . . C 2 22.356 14.229 93.342 1 17.3 ? N7A NAP 501 A 1 HETATM 16 C C5A NAP . . . C 2 23.063 13.659 94.33 1 15.35 ? C5A NAP 501 A 1 HETATM 17 C C6A NAP . . . C 2 24.417 13.52 94.54 1 16.37 ? C6A NAP 501 A 1 HETATM 18 N N6A NAP . . . C 2 25.288 13.986 93.645 1 17.01 ? N6A NAP 501 A 1 HETATM 19 N N1A NAP . . . C 2 24.857 12.893 95.683 1 16.24 ? N1A NAP 501 A 1 HETATM 20 C C2A NAP . . . C 2 23.953 12.405 96.603 1 17.04 ? C2A NAP 501 A 1 HETATM 21 N N3A NAP . . . C 2 22.604 12.555 96.399 1 15.6 ? N3A NAP 501 A 1 HETATM 22 C C4A NAP . . . C 2 22.17 13.178 95.268 1 17.22 ? C4A NAP 501 A 1 HETATM 23 O O3 NAP . . . C 2 13.969 12.727 91.922 1 33.28 ? O3 NAP 501 A 1 HETATM 24 P PN NAP . . . C 2 13.096 11.414 92.256 1 31.24 ? PN NAP 501 A 1 HETATM 25 O O1N NAP . . . C 2 13.108 11.209 93.728 1 30.71 ? O1N NAP 501 A 1 HETATM 26 O O2N NAP . . . C 2 11.756 11.521 91.594 1 31.1 ? O2N NAP 501 A 1 HETATM 27 O O5D NAP . . . C 2 14.027 10.325 91.547 1 28.79 ? O5D NAP 501 A 1 HETATM 28 C C5D NAP . . . C 2 14.794 9.433 92.343 1 27.34 ? C5D NAP 501 A 1 HETATM 29 C C4D NAP . . . C 2 15.213 8.213 91.535 1 25.9 ? C4D NAP 501 A 1 HETATM 30 O O4D NAP . . . C 2 14.085 7.667 90.904 1 27.04 ? O4D NAP 501 A 1 HETATM 31 C C3D NAP . . . C 2 16.189 8.516 90.418 1 26.61 ? C3D NAP 501 A 1 HETATM 32 O O3D NAP . . . C 2 17.09 7.43 90.35 1 26.32 ? O3D NAP 501 A 1 HETATM 33 C C2D NAP . . . C 2 15.349 8.596 89.161 1 25.61 ? C2D NAP 501 A 1 HETATM 34 O O2D NAP . . . C 2 16.055 8.326 87.949 1 25.07 ? O2D NAP 501 A 1 HETATM 35 C C1D NAP . . . C 2 14.312 7.554 89.503 1 26.22 ? C1D NAP 501 A 1 HETATM 36 N N1N NAP . . . C 2 13.078 7.724 88.699 1 27.34 ? N1N NAP 501 A 1 HETATM 37 C C2N NAP . . . C 2 12.052 8.55 89.086 1 25.65 ? C2N NAP 501 A 1 HETATM 38 C C3N NAP . . . C 2 10.928 8.649 88.271 1 25.74 ? C3N NAP 501 A 1 HETATM 39 C C7N NAP . . . C 2 9.808 9.579 88.622 1 24.77 ? C7N NAP 501 A 1 HETATM 40 O O7N NAP . . . C 2 8.674 9.571 87.791 1 23.37 ? O7N NAP 501 A 1 HETATM 41 N N7N NAP . . . C 2 9.907 10.384 89.68 1 24.4 ? N7N NAP 501 A 1 HETATM 42 C C4N NAP . . . C 2 10.848 7.922 87.083 1 25.61 ? C4N NAP 501 A 1 HETATM 43 C C5N NAP . . . C 2 11.894 7.1 86.713 1 26.15 ? C5N NAP 501 A 1 HETATM 44 C C6N NAP . . . C 2 13.012 7.017 87.529 1 27.34 ? C6N NAP 501 A 1 HETATM 45 P P2B NAP . . . C 2 19.986 16.215 97.199 1 16.43 ? P2B NAP 501 A 1 HETATM 46 O O1X NAP . . . C 2 19.891 16.637 98.632 1 17.67 ? O1X NAP 501 A 1 HETATM 47 O O2X NAP . . . C 2 19.577 17.326 96.29 1 16.85 ? O2X NAP 501 A 1 HETATM 48 O O3X NAP . . . C 2 21.404 15.798 96.891 1 15.68 ? O3X NAP 501 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 48 #