data_5O8R # _model_server_result.job_id IhS7cIZbrrZZDHNWjoz-XA _model_server_result.datetime_utc '2024-12-12 11:13:49' _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 5o8r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 5O8R # _exptl.entry_id 5O8R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 3 _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 5O8R _cell.length_a 163.937 _cell.length_b 163.937 _cell.length_c 166.73 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5O8R _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 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 # 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 1,4 B,E,F,H 1 2,3 # 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' 4_554 y+1/2,-x+1/2,z-1/4 0 1 0 -1 0 0 0 0 1 81.9685 81.9685 -41.6825 3 'crystal symmetry operation' 6_555 x+1/2,-y+1/2,-z+3/4 1 0 0 0 -1 0 0 0 -1 81.9685 81.9685 125.0475 4 'crystal symmetry operation' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 163.937 163.937 83.365 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 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 328 n n PA O2A NAP sing 329 n n PA O5B NAP sing 330 n n PA O3 NAP sing 331 n n O2A HOA2 NAP sing 332 n n O5B C5B NAP sing 333 n n C5B C4B NAP sing 334 n n C5B H51A NAP sing 335 n n C5B H52A NAP sing 336 n n C4B O4B NAP sing 337 n n C4B C3B NAP sing 338 n n C4B H4B NAP sing 339 n n O4B C1B NAP sing 340 n n C3B O3B NAP sing 341 n n C3B C2B NAP sing 342 n n C3B H3B NAP sing 343 n n O3B HO3A NAP sing 344 n n C2B O2B NAP sing 345 n n C2B C1B NAP sing 346 n n C2B H2B NAP sing 347 n n O2B P2B NAP sing 348 n n C1B N9A NAP sing 349 n n C1B H1B NAP sing 350 n n N9A C8A NAP sing 351 n y N9A C4A NAP sing 352 n y C8A N7A NAP doub 353 n y C8A H8A NAP sing 354 n n N7A C5A NAP sing 355 n y C5A C6A NAP sing 356 n y C5A C4A NAP doub 357 n y C6A N6A NAP sing 358 n n C6A N1A NAP doub 359 n y N6A H61A NAP sing 360 n n N6A H62A NAP sing 361 n n N1A C2A NAP sing 362 n y C2A N3A NAP doub 363 n y C2A H2A NAP sing 364 n n N3A C4A NAP sing 365 n y O3 PN NAP sing 366 n n PN O1N NAP doub 367 n n PN O2N NAP sing 368 n n PN O5D NAP sing 369 n n O5D C5D NAP sing 370 n n C5D C4D NAP sing 371 n n C5D H51N NAP sing 372 n n C5D H52N NAP sing 373 n n C4D O4D NAP sing 374 n n C4D C3D NAP sing 375 n n C4D H4D NAP sing 376 n n O4D C1D NAP sing 377 n n C3D O3D NAP sing 378 n n C3D C2D NAP sing 379 n n C3D H3D NAP sing 380 n n O3D HO3N NAP sing 381 n n C2D O2D NAP sing 382 n n C2D C1D NAP sing 383 n n C2D H2D NAP sing 384 n n O2D HO2N NAP sing 385 n n C1D N1N NAP sing 386 n n C1D H1D NAP sing 387 n n N1N C2N NAP sing 388 n y N1N C6N NAP doub 389 n y C2N C3N NAP doub 390 n y C2N H2N NAP sing 391 n n C3N C7N NAP sing 392 n n C3N C4N NAP sing 393 n y C7N O7N NAP doub 394 n n C7N N7N NAP sing 395 n n N7N H71N NAP sing 396 n n N7N H72N NAP sing 397 n n C4N C5N NAP doub 398 n y C4N H4N NAP sing 399 n n C5N C6N NAP sing 400 n y C5N H5N NAP sing 401 n n C6N H6N NAP sing 402 n n P2B O1X NAP doub 403 n n P2B O2X NAP sing 404 n n P2B O3X NAP sing 405 n n O2X HOP2 NAP sing 406 n n O3X HOP3 NAP sing 407 n n # _atom_sites.entry_id 5O8R _atom_sites.fract_transf_matrix[1][1] 0.0061 _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] 0.0061 _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] 0.005998 _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 FAD A 1 501 1 FAD FAD . D 3 NAP A 1 502 2 NAP NAP . E 2 FAD B 1 501 1 FAD FAD . F 3 NAP B 1 502 2 NAP NAP . G 4 HOH A 1 601 71 HOH HOH . G 4 HOH A 2 602 50 HOH HOH . G 4 HOH A 3 603 29 HOH HOH . G 4 HOH A 4 604 20 HOH HOH . G 4 HOH A 5 605 57 HOH HOH . G 4 HOH A 6 606 15 HOH HOH . G 4 HOH A 7 607 52 HOH HOH . G 4 HOH A 8 608 59 HOH HOH . G 4 HOH A 9 609 10 HOH HOH . G 4 HOH A 10 610 40 HOH HOH . G 4 HOH A 11 611 55 HOH HOH . G 4 HOH A 12 612 33 HOH HOH . G 4 HOH A 13 613 14 HOH HOH . G 4 HOH A 14 614 68 HOH HOH . G 4 HOH A 15 615 22 HOH HOH . G 4 HOH A 16 616 53 HOH HOH . G 4 HOH A 17 617 4 HOH HOH . G 4 HOH A 18 618 58 HOH HOH . G 4 HOH A 19 619 9 HOH HOH . G 4 HOH A 20 620 69 HOH HOH . G 4 HOH A 21 621 77 HOH HOH . G 4 HOH A 22 622 45 HOH HOH . G 4 HOH A 23 623 17 HOH HOH . G 4 HOH A 24 624 27 HOH HOH . G 4 HOH A 25 625 90 HOH HOH . G 4 HOH A 26 626 25 HOH HOH . G 4 HOH A 27 627 46 HOH HOH . G 4 HOH A 28 628 26 HOH HOH . G 4 HOH A 29 629 8 HOH HOH . G 4 HOH A 30 630 78 HOH HOH . G 4 HOH A 31 631 18 HOH HOH . G 4 HOH A 32 632 79 HOH HOH . G 4 HOH A 33 633 5 HOH HOH . G 4 HOH A 34 634 80 HOH HOH . G 4 HOH A 35 635 24 HOH HOH . G 4 HOH A 36 636 94 HOH HOH . G 4 HOH A 37 637 87 HOH HOH . G 4 HOH A 38 638 6 HOH HOH . G 4 HOH A 39 639 11 HOH HOH . G 4 HOH A 40 640 31 HOH HOH . G 4 HOH A 41 641 44 HOH HOH . G 4 HOH A 42 642 89 HOH HOH . G 4 HOH A 43 643 43 HOH HOH . H 4 HOH B 1 601 60 HOH HOH . H 4 HOH B 2 602 92 HOH HOH . H 4 HOH B 3 603 37 HOH HOH . H 4 HOH B 4 604 39 HOH HOH . H 4 HOH B 5 605 81 HOH HOH . H 4 HOH B 6 606 38 HOH HOH . H 4 HOH B 7 607 97 HOH HOH . H 4 HOH B 8 608 47 HOH HOH . H 4 HOH B 9 609 56 HOH HOH . H 4 HOH B 10 610 48 HOH HOH . H 4 HOH B 11 611 54 HOH HOH . H 4 HOH B 12 612 35 HOH HOH . H 4 HOH B 13 613 34 HOH HOH . H 4 HOH B 14 614 36 HOH HOH . H 4 HOH B 15 615 96 HOH HOH . H 4 HOH B 16 616 49 HOH HOH . H 4 HOH B 17 617 91 HOH HOH . H 4 HOH B 18 618 19 HOH HOH . H 4 HOH B 19 619 12 HOH HOH . H 4 HOH B 20 620 21 HOH HOH . H 4 HOH B 21 621 93 HOH HOH . H 4 HOH B 22 622 85 HOH HOH . H 4 HOH B 23 623 41 HOH HOH . H 4 HOH B 24 624 51 HOH HOH . H 4 HOH B 25 625 72 HOH HOH . H 4 HOH B 26 626 16 HOH HOH . H 4 HOH B 27 627 95 HOH HOH . H 4 HOH B 28 628 23 HOH HOH . H 4 HOH B 29 629 7 HOH HOH . H 4 HOH B 30 630 66 HOH HOH . H 4 HOH B 31 631 30 HOH HOH . H 4 HOH B 32 632 13 HOH HOH . H 4 HOH B 33 633 84 HOH HOH . H 4 HOH B 34 634 32 HOH HOH . H 4 HOH B 35 635 42 HOH HOH . H 4 HOH B 36 636 2 HOH HOH . H 4 HOH B 37 637 3 HOH HOH . H 4 HOH B 38 638 1 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 . . . D 3 120.586 31.114 63.618 1 79.98 ? PA NAP 502 A 1 HETATM 2 O O1A NAP . . . D 3 119.91 30.326 64.762 1 73.93 ? O1A NAP 502 A 1 HETATM 3 O O2A NAP . . . D 3 122.006 30.768 63.133 1 73.03 ? O2A NAP 502 A 1 HETATM 4 O O5B NAP . . . D 3 120.528 32.709 63.855 1 73.61 ? O5B NAP 502 A 1 HETATM 5 C C5B NAP . . . D 3 120.755 33.165 65.179 1 72.79 ? C5B NAP 502 A 1 HETATM 6 C C4B NAP . . . D 3 121.756 34.287 65.195 1 68.6 ? C4B NAP 502 A 1 HETATM 7 O O4B NAP . . . D 3 121.128 35.169 66.098 1 67.91 ? O4B NAP 502 A 1 HETATM 8 C C3B NAP . . . D 3 123.145 33.857 65.72 1 70.17 ? C3B NAP 502 A 1 HETATM 9 O O3B NAP . . . D 3 124.286 34.543 65.11 1 55.7 ? O3B NAP 502 A 1 HETATM 10 C C2B NAP . . . D 3 122.918 34.122 67.205 1 74.98 ? C2B NAP 502 A 1 HETATM 11 O O2B NAP . . . D 3 124.129 34.231 67.986 1 78.38 ? O2B NAP 502 A 1 HETATM 12 C C1B NAP . . . D 3 122.071 35.391 67.118 1 73.7 ? C1B NAP 502 A 1 HETATM 13 N N9A NAP . . . D 3 121.445 35.805 68.401 1 72.04 ? N9A NAP 502 A 1 HETATM 14 C C8A NAP . . . D 3 120.579 35.162 69.238 1 69.56 ? C8A NAP 502 A 1 HETATM 15 N N7A NAP . . . D 3 120.323 35.953 70.337 1 62.64 ? N7A NAP 502 A 1 HETATM 16 C C5A NAP . . . D 3 121.025 37.082 70.166 1 61.54 ? C5A NAP 502 A 1 HETATM 17 C C6A NAP . . . D 3 121.244 38.319 70.901 1 59.18 ? C6A NAP 502 A 1 HETATM 18 N N6A NAP . . . D 3 120.591 38.45 72.039 1 63.48 ? N6A NAP 502 A 1 HETATM 19 N N1A NAP . . . D 3 122.08 39.276 70.417 1 63.59 ? N1A NAP 502 A 1 HETATM 20 C C2A NAP . . . D 3 122.725 39.14 69.225 1 67.97 ? C2A NAP 502 A 1 HETATM 21 N N3A NAP . . . D 3 122.591 38.022 68.462 1 68.31 ? N3A NAP 502 A 1 HETATM 22 C C4A NAP . . . D 3 121.77 36.993 68.896 1 71.24 ? C4A NAP 502 A 1 HETATM 23 O O3 NAP . . . D 3 119.485 30.893 62.453 1 81.61 ? O3 NAP 502 A 1 HETATM 24 P PN NAP . . . D 3 119.108 31.724 61.125 1 70.52 ? PN NAP 502 A 1 HETATM 25 O O1N NAP . . . D 3 117.614 31.839 61.173 1 60.28 ? O1N NAP 502 A 1 HETATM 26 O O2N NAP . . . D 3 119.975 33.026 60.966 1 79.18 ? O2N NAP 502 A 1 HETATM 27 O O5D NAP . . . D 3 119.367 30.559 60.007 1 106.87 ? O5D NAP 502 A 1 HETATM 28 C C5D NAP . . . D 3 120.161 29.369 60.233 1 135.63 ? C5D NAP 502 A 1 HETATM 29 C C4D NAP . . . D 3 119.359 28.23 60.891 1 145.26 ? C4D NAP 502 A 1 HETATM 30 O O4D NAP . . . D 3 118.415 27.859 59.903 1 139.47 ? O4D NAP 502 A 1 HETATM 31 C C3D NAP . . . D 3 120.203 26.992 61.292 1 151.21 ? C3D NAP 502 A 1 HETATM 32 O O3D NAP . . . D 3 119.975 26.429 62.615 1 125.03 ? O3D NAP 502 A 1 HETATM 33 C C2D NAP . . . D 3 119.916 25.977 60.205 1 149.79 ? C2D NAP 502 A 1 HETATM 34 O O2D NAP . . . D 3 119.413 24.732 60.722 1 142.4 ? O2D NAP 502 A 1 HETATM 35 C C1D NAP . . . D 3 118.885 26.664 59.28 1 157.52 ? C1D NAP 502 A 1 HETATM 36 N N1N NAP . . . D 3 119.313 26.967 57.895 1 159.9 ? N1N NAP 502 A 1 HETATM 37 C C2N NAP . . . D 3 118.656 27.952 57.211 1 136.39 ? C2N NAP 502 A 1 HETATM 38 C C3N NAP . . . D 3 119.006 28.213 55.878 1 146.43 ? C3N NAP 502 A 1 HETATM 39 C C7N NAP . . . D 3 118.355 29.276 55.062 1 124.35 ? C7N NAP 502 A 1 HETATM 40 O O7N NAP . . . D 3 118.164 29.049 53.85 1 109.28 ? O7N NAP 502 A 1 HETATM 41 N N7N NAP . . . D 3 118.058 30.411 55.704 1 104.96 ? N7N NAP 502 A 1 HETATM 42 C C4N NAP . . . D 3 120.014 27.474 55.257 1 167.19 ? C4N NAP 502 A 1 HETATM 43 C C5N NAP . . . D 3 120.669 26.479 55.974 1 168.24 ? C5N NAP 502 A 1 HETATM 44 C C6N NAP . . . D 3 120.292 26.233 57.289 1 165.98 ? C6N NAP 502 A 1 HETATM 45 P P2B NAP . . . D 3 124.966 32.922 68.44 1 84.35 ? P2B NAP 502 A 1 HETATM 46 O O1X NAP . . . D 3 125.761 33.395 69.66 1 78.06 ? O1X NAP 502 A 1 HETATM 47 O O2X NAP . . . D 3 125.801 32.525 67.226 1 83.34 ? O2X NAP 502 A 1 HETATM 48 O O3X NAP . . . D 3 123.893 31.89 68.733 1 82.28 ? O3X NAP 502 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 48 #