data_6Y4D # _model_server_result.job_id OC-ZZca5p4k2TUOw1DlwFw _model_server_result.datetime_utc '2025-04-09 18:35:28' _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 6y4d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 6Y4D # _exptl.entry_id 6Y4D _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 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 6Y4D _cell.length_a 95.9 _cell.length_b 95.9 _cell.length_c 136.33 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y4D _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -95.9 0 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 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 250 n n PA O2A NAP sing 251 n n PA O5B NAP sing 252 n n PA O3 NAP sing 253 n n O2A HOA2 NAP sing 254 n n O5B C5B NAP sing 255 n n C5B C4B NAP sing 256 n n C5B H51A NAP sing 257 n n C5B H52A NAP sing 258 n n C4B O4B NAP sing 259 n n C4B C3B NAP sing 260 n n C4B H4B NAP sing 261 n n O4B C1B NAP sing 262 n n C3B O3B NAP sing 263 n n C3B C2B NAP sing 264 n n C3B H3B NAP sing 265 n n O3B HO3A NAP sing 266 n n C2B O2B NAP sing 267 n n C2B C1B NAP sing 268 n n C2B H2B NAP sing 269 n n O2B P2B NAP sing 270 n n C1B N9A NAP sing 271 n n C1B H1B NAP sing 272 n n N9A C8A NAP sing 273 n y N9A C4A NAP sing 274 n y C8A N7A NAP doub 275 n y C8A H8A NAP sing 276 n n N7A C5A NAP sing 277 n y C5A C6A NAP sing 278 n y C5A C4A NAP doub 279 n y C6A N6A NAP sing 280 n n C6A N1A NAP doub 281 n y N6A H61A NAP sing 282 n n N6A H62A NAP sing 283 n n N1A C2A NAP sing 284 n y C2A N3A NAP doub 285 n y C2A H2A NAP sing 286 n n N3A C4A NAP sing 287 n y O3 PN NAP sing 288 n n PN O1N NAP doub 289 n n PN O2N NAP sing 290 n n PN O5D NAP sing 291 n n O5D C5D NAP sing 292 n n C5D C4D NAP sing 293 n n C5D H51N NAP sing 294 n n C5D H52N NAP sing 295 n n C4D O4D NAP sing 296 n n C4D C3D NAP sing 297 n n C4D H4D NAP sing 298 n n O4D C1D NAP sing 299 n n C3D O3D NAP sing 300 n n C3D C2D NAP sing 301 n n C3D H3D NAP sing 302 n n O3D HO3N NAP sing 303 n n C2D O2D NAP sing 304 n n C2D C1D NAP sing 305 n n C2D H2D NAP sing 306 n n O2D HO2N NAP sing 307 n n C1D N1N NAP sing 308 n n C1D H1D NAP sing 309 n n N1N C2N NAP sing 310 n y N1N C6N NAP doub 311 n y C2N C3N NAP doub 312 n y C2N H2N NAP sing 313 n n C3N C7N NAP sing 314 n n C3N C4N NAP sing 315 n y C7N O7N NAP doub 316 n n C7N N7N NAP sing 317 n n N7N H71N NAP sing 318 n n N7N H72N NAP sing 319 n n C4N C5N NAP doub 320 n y C4N H4N NAP sing 321 n n C5N C6N NAP sing 322 n y C5N H5N NAP sing 323 n n C6N H6N NAP sing 324 n n P2B O1X NAP doub 325 n n P2B O2X NAP sing 326 n n P2B O3X NAP sing 327 n n O2X HOP2 NAP sing 328 n n O3X HOP3 NAP sing 329 n n # _atom_sites.entry_id 6Y4D _atom_sites.fract_transf_matrix[1][1] 0.010428 _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] 0.010428 _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] 0.007335 _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 1 301 2 NAP NAP . D 3 GOL A 1 302 2 GOL GOL . E 3 GOL A 1 303 3 GOL GOL . F 2 NAP B 1 301 3 NAP NAP . G 3 GOL B 1 302 1 GOL GOL . H 4 HOH A 1 401 1 HOH HOH . H 4 HOH A 2 402 50 HOH HOH . H 4 HOH A 3 403 130 HOH HOH . H 4 HOH A 4 404 132 HOH HOH . H 4 HOH A 5 405 13 HOH HOH . H 4 HOH A 6 406 152 HOH HOH . H 4 HOH A 7 407 131 HOH HOH . H 4 HOH A 8 408 4 HOH HOH . H 4 HOH A 9 409 26 HOH HOH . H 4 HOH A 10 410 3 HOH HOH . H 4 HOH A 11 411 2 HOH HOH . H 4 HOH A 12 412 44 HOH HOH . H 4 HOH A 13 413 34 HOH HOH . H 4 HOH A 14 414 7 HOH HOH . H 4 HOH A 15 415 38 HOH HOH . H 4 HOH A 16 416 9 HOH HOH . H 4 HOH A 17 417 125 HOH HOH . H 4 HOH A 18 418 15 HOH HOH . H 4 HOH A 19 419 68 HOH HOH . H 4 HOH A 20 420 35 HOH HOH . H 4 HOH A 21 421 33 HOH HOH . H 4 HOH A 22 422 115 HOH HOH . H 4 HOH A 23 423 91 HOH HOH . H 4 HOH A 24 424 19 HOH HOH . H 4 HOH A 25 425 103 HOH HOH . H 4 HOH A 26 426 98 HOH HOH . H 4 HOH A 27 427 143 HOH HOH . H 4 HOH A 28 428 88 HOH HOH . H 4 HOH A 29 429 14 HOH HOH . H 4 HOH A 30 430 67 HOH HOH . H 4 HOH A 31 431 23 HOH HOH . H 4 HOH A 32 432 93 HOH HOH . H 4 HOH A 33 433 42 HOH HOH . H 4 HOH A 34 434 20 HOH HOH . H 4 HOH A 35 435 111 HOH HOH . H 4 HOH A 36 436 48 HOH HOH . H 4 HOH A 37 437 84 HOH HOH . H 4 HOH A 38 438 21 HOH HOH . H 4 HOH A 39 439 41 HOH HOH . H 4 HOH A 40 440 37 HOH HOH . H 4 HOH A 41 441 28 HOH HOH . H 4 HOH A 42 442 107 HOH HOH . H 4 HOH A 43 443 96 HOH HOH . H 4 HOH A 44 444 61 HOH HOH . H 4 HOH A 45 445 153 HOH HOH . H 4 HOH A 46 446 17 HOH HOH . H 4 HOH A 47 447 104 HOH HOH . H 4 HOH A 48 448 89 HOH HOH . H 4 HOH A 49 449 112 HOH HOH . H 4 HOH A 50 450 51 HOH HOH . H 4 HOH A 51 451 82 HOH HOH . H 4 HOH A 52 452 141 HOH HOH . H 4 HOH A 53 453 60 HOH HOH . H 4 HOH A 54 454 102 HOH HOH . H 4 HOH A 55 455 154 HOH HOH . H 4 HOH A 56 456 155 HOH HOH . H 4 HOH A 57 457 95 HOH HOH . H 4 HOH A 58 458 133 HOH HOH . H 4 HOH A 59 459 80 HOH HOH . H 4 HOH A 60 460 57 HOH HOH . H 4 HOH A 61 461 134 HOH HOH . H 4 HOH A 62 462 128 HOH HOH . H 4 HOH A 63 463 119 HOH HOH . H 4 HOH A 64 464 64 HOH HOH . H 4 HOH A 65 465 101 HOH HOH . H 4 HOH A 66 466 114 HOH HOH . H 4 HOH A 67 467 117 HOH HOH . H 4 HOH A 68 468 58 HOH HOH . H 4 HOH A 69 469 79 HOH HOH . I 4 HOH B 1 401 120 HOH HOH . I 4 HOH B 2 402 5 HOH HOH . I 4 HOH B 3 403 126 HOH HOH . I 4 HOH B 4 404 16 HOH HOH . I 4 HOH B 5 405 31 HOH HOH . I 4 HOH B 6 406 11 HOH HOH . I 4 HOH B 7 407 70 HOH HOH . I 4 HOH B 8 408 6 HOH HOH . I 4 HOH B 9 409 32 HOH HOH . I 4 HOH B 10 410 122 HOH HOH . I 4 HOH B 11 411 27 HOH HOH . I 4 HOH B 12 412 24 HOH HOH . I 4 HOH B 13 413 10 HOH HOH . I 4 HOH B 14 414 39 HOH HOH . I 4 HOH B 15 415 90 HOH HOH . I 4 HOH B 16 416 140 HOH HOH . I 4 HOH B 17 417 8 HOH HOH . I 4 HOH B 18 418 22 HOH HOH . I 4 HOH B 19 419 45 HOH HOH . I 4 HOH B 20 420 86 HOH HOH . I 4 HOH B 21 421 30 HOH HOH . I 4 HOH B 22 422 52 HOH HOH . I 4 HOH B 23 423 109 HOH HOH . I 4 HOH B 24 424 12 HOH HOH . I 4 HOH B 25 425 53 HOH HOH . I 4 HOH B 26 426 116 HOH HOH . I 4 HOH B 27 427 65 HOH HOH . I 4 HOH B 28 428 29 HOH HOH . I 4 HOH B 29 429 110 HOH HOH . I 4 HOH B 30 430 129 HOH HOH . I 4 HOH B 31 431 54 HOH HOH . I 4 HOH B 32 432 87 HOH HOH . I 4 HOH B 33 433 18 HOH HOH . I 4 HOH B 34 434 149 HOH HOH . I 4 HOH B 35 435 83 HOH HOH . I 4 HOH B 36 436 25 HOH HOH . I 4 HOH B 37 437 36 HOH HOH . I 4 HOH B 38 438 40 HOH HOH . I 4 HOH B 39 439 62 HOH HOH . I 4 HOH B 40 440 55 HOH HOH . I 4 HOH B 41 441 139 HOH HOH . I 4 HOH B 42 442 148 HOH HOH . I 4 HOH B 43 443 63 HOH HOH . I 4 HOH B 44 444 56 HOH HOH . I 4 HOH B 45 445 75 HOH HOH . I 4 HOH B 46 446 47 HOH HOH . I 4 HOH B 47 447 99 HOH HOH . I 4 HOH B 48 448 59 HOH HOH . I 4 HOH B 49 449 73 HOH HOH . I 4 HOH B 50 450 151 HOH HOH . I 4 HOH B 51 451 135 HOH HOH . I 4 HOH B 52 452 142 HOH HOH . I 4 HOH B 53 453 136 HOH HOH . I 4 HOH B 54 454 69 HOH HOH . I 4 HOH B 55 455 137 HOH HOH . I 4 HOH B 56 456 100 HOH HOH . I 4 HOH B 57 457 81 HOH HOH . I 4 HOH B 58 458 43 HOH HOH . I 4 HOH B 59 459 66 HOH HOH . I 4 HOH B 60 460 138 HOH HOH . I 4 HOH B 61 461 113 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 . A . C 2 -56.033 16.462 -3.261 0.52 43.21 ? PA NAP 301 A 1 HETATM 2 P PA NAP . B . C 2 -57.277 18.307 -2.848 0.48 41.84 ? PA NAP 301 A 1 HETATM 3 O O1A NAP . A . C 2 -56.918 16.319 -4.476 0.52 41.36 ? O1A NAP 301 A 1 HETATM 4 O O1A NAP . B . C 2 -57.982 19.342 -2.004 0.48 41.74 ? O1A NAP 301 A 1 HETATM 5 O O2A NAP . A . C 2 -55.165 15.293 -2.863 0.52 41.66 ? O2A NAP 301 A 1 HETATM 6 O O2A NAP . B . C 2 -57.954 17.719 -4.062 0.48 36.35 ? O2A NAP 301 A 1 HETATM 7 O O5B NAP . A . C 2 -55.108 17.758 -3.495 0.52 43.21 ? O5B NAP 301 A 1 HETATM 8 O O5B NAP . B . C 2 -55.864 18.897 -3.323 0.48 42.37 ? O5B NAP 301 A 1 HETATM 9 C C5B NAP . . . C 2 -55.388 18.581 -4.622 1 42.58 ? C5B NAP 301 A 1 HETATM 10 C C4B NAP . . . C 2 -54.253 19.523 -4.96 1 45.62 ? C4B NAP 301 A 1 HETATM 11 O O4B NAP . . . C 2 -53.243 18.777 -5.634 1 45.03 ? O4B NAP 301 A 1 HETATM 12 C C3B NAP . . . C 2 -54.825 20.483 -5.978 1 46.11 ? C3B NAP 301 A 1 HETATM 13 O O3B NAP . . . C 2 -54.047 21.682 -5.982 1 46.13 ? O3B NAP 301 A 1 HETATM 14 C C2B NAP . . . C 2 -54.631 19.728 -7.272 1 44.83 ? C2B NAP 301 A 1 HETATM 15 O O2B NAP . . . C 2 -54.624 20.607 -8.391 1 49.35 ? O2B NAP 301 A 1 HETATM 16 C C1B NAP . . . C 2 -53.298 19.041 -7.04 1 42.49 ? C1B NAP 301 A 1 HETATM 17 N N9A NAP . . . C 2 -53.179 17.766 -7.785 1 40.28 ? N9A NAP 301 A 1 HETATM 18 C C8A NAP . . . C 2 -54.042 16.732 -7.749 1 40.04 ? C8A NAP 301 A 1 HETATM 19 N N7A NAP . . . C 2 -53.623 15.72 -8.552 1 38.44 ? N7A NAP 301 A 1 HETATM 20 C C5A NAP . . . C 2 -52.466 16.111 -9.118 1 38.65 ? C5A NAP 301 A 1 HETATM 21 C C6A NAP . . . C 2 -51.494 15.525 -10.067 1 38.28 ? C6A NAP 301 A 1 HETATM 22 N N6A NAP . . . C 2 -51.687 14.287 -10.581 1 37.25 ? N6A NAP 301 A 1 HETATM 23 N N1A NAP . . . C 2 -50.412 16.266 -10.399 1 38.56 ? N1A NAP 301 A 1 HETATM 24 C C2A NAP . . . C 2 -50.215 17.496 -9.889 1 38.65 ? C2A NAP 301 A 1 HETATM 25 N N3A NAP . . . C 2 -51.054 18.09 -9.024 1 40.12 ? N3A NAP 301 A 1 HETATM 26 C C4A NAP . . . C 2 -52.179 17.459 -8.611 1 39.9 ? C4A NAP 301 A 1 HETATM 27 O O3 NAP . A . C 2 -56.983 16.898 -2.031 0.52 43.14 ? O3 NAP 301 A 1 HETATM 28 O O3 NAP . B . C 2 -56.788 17.097 -1.908 0.48 43.16 ? O3 NAP 301 A 1 HETATM 29 P PN NAP . A . C 2 -56.48 17.167 -0.521 0.52 42.74 ? PN NAP 301 A 1 HETATM 30 P PN NAP . B . C 2 -56.491 17.301 -0.341 0.48 42.31 ? PN NAP 301 A 1 HETATM 31 O O1N NAP . A . C 2 -55.877 18.548 -0.429 0.52 41.99 ? O1N NAP 301 A 1 HETATM 32 O O1N NAP . B . C 2 -55.816 18.637 -0.14 0.48 41.94 ? O1N NAP 301 A 1 HETATM 33 O O2N NAP . A . C 2 -57.623 16.783 0.386 0.52 41.4 ? O2N NAP 301 A 1 HETATM 34 O O2N NAP . B . C 2 -57.751 16.951 0.408 0.48 41.76 ? O2N NAP 301 A 1 HETATM 35 O O5D NAP . A . C 2 -55.323 16.074 -0.319 0.52 42.29 ? O5D NAP 301 A 1 HETATM 36 O O5D NAP . B . C 2 -55.422 16.127 -0.09 0.48 41.71 ? O5D NAP 301 A 1 HETATM 37 C C5D NAP . . . C 2 -54.076 16.411 0.281 1 42.68 ? C5D NAP 301 A 1 HETATM 38 C C4D NAP . . . C 2 -53.397 15.111 0.678 1 43.62 ? C4D NAP 301 A 1 HETATM 39 O O4D NAP . . . C 2 -53.931 14.688 1.932 1 44.02 ? O4D NAP 301 A 1 HETATM 40 C C3D NAP . . . C 2 -53.681 14.006 -0.325 1 43.25 ? C3D NAP 301 A 1 HETATM 41 O O3D NAP . . . C 2 -52.469 13.306 -0.619 1 43.49 ? O3D NAP 301 A 1 HETATM 42 C C2D NAP . . . C 2 -54.639 13.069 0.379 1 43.33 ? C2D NAP 301 A 1 HETATM 43 O O2D NAP . . . C 2 -54.358 11.715 0.022 1 43.71 ? O2D NAP 301 A 1 HETATM 44 C C1D NAP . . . C 2 -54.375 13.335 1.853 1 42.54 ? C1D NAP 301 A 1 HETATM 45 N N1N NAP . . . C 2 -55.559 13.156 2.698 1 41.72 ? N1N NAP 301 A 1 HETATM 46 C C2N NAP . . . C 2 -56.598 14.007 2.639 1 37.57 ? C2N NAP 301 A 1 HETATM 47 C C3N NAP . . . C 2 -57.703 13.813 3.469 1 42.05 ? C3N NAP 301 A 1 HETATM 48 C C7N NAP . . . C 2 -58.889 14.733 3.431 1 42.22 ? C7N NAP 301 A 1 HETATM 49 O O7N NAP . . . C 2 -58.843 15.764 2.78 1 42.23 ? O7N NAP 301 A 1 HETATM 50 N N7N NAP . . . C 2 -59.973 14.393 4.127 1 42.74 ? N7N NAP 301 A 1 HETATM 51 C C4N NAP . . . C 2 -57.716 12.743 4.353 1 41.88 ? C4N NAP 301 A 1 HETATM 52 C C5N NAP . . . C 2 -56.627 11.887 4.399 1 39.94 ? C5N NAP 301 A 1 HETATM 53 C C6N NAP . . . C 2 -55.553 12.127 3.555 1 43.6 ? C6N NAP 301 A 1 HETATM 54 P P2B NAP . . . C 2 -55.247 20.108 -9.792 1 46.08 ? P2B NAP 301 A 1 HETATM 55 O O1X NAP . . . C 2 -56.431 19.253 -9.408 1 45.3 ? O1X NAP 301 A 1 HETATM 56 O O2X NAP . . . C 2 -55.613 21.391 -10.499 1 46.95 ? O2X NAP 301 A 1 HETATM 57 O O3X NAP . . . C 2 -54.108 19.33 -10.403 1 45.19 ? O3X NAP 301 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 57 #