data_2YLT # _model_server_result.job_id Z17syO0jFOGi2ygnet99QA _model_server_result.datetime_utc '2025-07-08 05:49:36' _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 2ylt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 2YLT # _exptl.entry_id 2YLT _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 1 _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 120 _cell.entry_id 2YLT _cell.length_a 107.35 _cell.length_b 107.35 _cell.length_c 107.7 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YLT _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 353 n n PA O2A NAP sing 354 n n PA O5B NAP sing 355 n n PA O3 NAP sing 356 n n O2A HOA2 NAP sing 357 n n O5B C5B NAP sing 358 n n C5B C4B NAP sing 359 n n C5B H51A NAP sing 360 n n C5B H52A NAP sing 361 n n C4B O4B NAP sing 362 n n C4B C3B NAP sing 363 n n C4B H4B NAP sing 364 n n O4B C1B NAP sing 365 n n C3B O3B NAP sing 366 n n C3B C2B NAP sing 367 n n C3B H3B NAP sing 368 n n O3B HO3A NAP sing 369 n n C2B O2B NAP sing 370 n n C2B C1B NAP sing 371 n n C2B H2B NAP sing 372 n n O2B P2B NAP sing 373 n n C1B N9A NAP sing 374 n n C1B H1B NAP sing 375 n n N9A C8A NAP sing 376 n y N9A C4A NAP sing 377 n y C8A N7A NAP doub 378 n y C8A H8A NAP sing 379 n n N7A C5A NAP sing 380 n y C5A C6A NAP sing 381 n y C5A C4A NAP doub 382 n y C6A N6A NAP sing 383 n n C6A N1A NAP doub 384 n y N6A H61A NAP sing 385 n n N6A H62A NAP sing 386 n n N1A C2A NAP sing 387 n y C2A N3A NAP doub 388 n y C2A H2A NAP sing 389 n n N3A C4A NAP sing 390 n y O3 PN NAP sing 391 n n PN O1N NAP doub 392 n n PN O2N NAP sing 393 n n PN O5D NAP sing 394 n n O5D C5D NAP sing 395 n n C5D C4D NAP sing 396 n n C5D H51N NAP sing 397 n n C5D H52N NAP sing 398 n n C4D O4D NAP sing 399 n n C4D C3D NAP sing 400 n n C4D H4D NAP sing 401 n n O4D C1D NAP sing 402 n n C3D O3D NAP sing 403 n n C3D C2D NAP sing 404 n n C3D H3D NAP sing 405 n n O3D HO3N NAP sing 406 n n C2D O2D NAP sing 407 n n C2D C1D NAP sing 408 n n C2D H2D NAP sing 409 n n O2D HO2N NAP sing 410 n n C1D N1N NAP sing 411 n n C1D H1D NAP sing 412 n n N1N C2N NAP sing 413 n y N1N C6N NAP doub 414 n y C2N C3N NAP doub 415 n y C2N H2N NAP sing 416 n n C3N C7N NAP sing 417 n n C3N C4N NAP sing 418 n y C7N O7N NAP doub 419 n n C7N N7N NAP sing 420 n n N7N H71N NAP sing 421 n n N7N H72N NAP sing 422 n n C4N C5N NAP doub 423 n y C4N H4N NAP sing 424 n n C5N C6N NAP sing 425 n y C5N H5N NAP sing 426 n n C6N H6N NAP sing 427 n n P2B O1X NAP doub 428 n n P2B O2X NAP sing 429 n n P2B O3X NAP sing 430 n n O2X HOP2 NAP sing 431 n n O3X HOP3 NAP sing 432 n n # _atom_sites.entry_id 2YLT _atom_sites.fract_transf_matrix[1][1] 0.009315 _atom_sites.fract_transf_matrix[1][2] 0.005378 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010756 _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] 0.009285 _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 B 2 FAD A 1 700 700 FAD FAD . C 3 NAP A 1 701 701 NAP NAP . D 4 MES A 1 1543 1543 MES MES . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 HOH HOH . E 5 HOH A 25 2025 2025 HOH HOH . E 5 HOH A 26 2026 2026 HOH HOH . E 5 HOH A 27 2027 2027 HOH HOH . E 5 HOH A 28 2028 2028 HOH HOH . E 5 HOH A 29 2029 2029 HOH HOH . E 5 HOH A 30 2030 2030 HOH HOH . E 5 HOH A 31 2031 2031 HOH HOH . E 5 HOH A 32 2032 2032 HOH HOH . E 5 HOH A 33 2033 2033 HOH HOH . E 5 HOH A 34 2034 2034 HOH HOH . E 5 HOH A 35 2035 2035 HOH HOH . E 5 HOH A 36 2036 2036 HOH HOH . E 5 HOH A 37 2037 2037 HOH HOH . E 5 HOH A 38 2038 2038 HOH HOH . E 5 HOH A 39 2039 2039 HOH HOH . E 5 HOH A 40 2040 2040 HOH HOH . E 5 HOH A 41 2041 2041 HOH HOH . E 5 HOH A 42 2042 2042 HOH HOH . E 5 HOH A 43 2043 2043 HOH HOH . E 5 HOH A 44 2044 2044 HOH HOH . E 5 HOH A 45 2045 2045 HOH HOH . E 5 HOH A 46 2046 2046 HOH HOH . E 5 HOH A 47 2047 2047 HOH HOH . E 5 HOH A 48 2048 2048 HOH HOH . E 5 HOH A 49 2049 2049 HOH HOH . E 5 HOH A 50 2050 2050 HOH HOH . E 5 HOH A 51 2051 2051 HOH HOH . E 5 HOH A 52 2052 2052 HOH HOH . E 5 HOH A 53 2053 2053 HOH HOH . E 5 HOH A 54 2054 2054 HOH HOH . E 5 HOH A 55 2055 2055 HOH HOH . E 5 HOH A 56 2056 2056 HOH HOH . E 5 HOH A 57 2057 2057 HOH HOH . E 5 HOH A 58 2058 2058 HOH HOH . E 5 HOH A 59 2059 2059 HOH HOH . E 5 HOH A 60 2060 2060 HOH HOH . E 5 HOH A 61 2061 2061 HOH HOH . E 5 HOH A 62 2062 2062 HOH HOH . E 5 HOH A 63 2063 2063 HOH HOH . E 5 HOH A 64 2064 2064 HOH HOH . E 5 HOH A 65 2065 2065 HOH HOH . E 5 HOH A 66 2066 2066 HOH HOH . E 5 HOH A 67 2067 2067 HOH HOH . E 5 HOH A 68 2068 2068 HOH HOH . E 5 HOH A 69 2069 2069 HOH HOH . E 5 HOH A 70 2070 2070 HOH HOH . E 5 HOH A 71 2071 2071 HOH HOH . E 5 HOH A 72 2072 2072 HOH HOH . E 5 HOH A 73 2073 2073 HOH HOH . E 5 HOH A 74 2074 2074 HOH HOH . E 5 HOH A 75 2075 2075 HOH HOH . E 5 HOH A 76 2076 2076 HOH HOH . E 5 HOH A 77 2077 2077 HOH HOH . E 5 HOH A 78 2078 2078 HOH HOH . E 5 HOH A 79 2079 2079 HOH HOH . E 5 HOH A 80 2080 2080 HOH HOH . E 5 HOH A 81 2081 2081 HOH HOH . E 5 HOH A 82 2082 2082 HOH HOH . E 5 HOH A 83 2083 2083 HOH HOH . E 5 HOH A 84 2084 2084 HOH HOH . E 5 HOH A 85 2085 2085 HOH HOH . E 5 HOH A 86 2086 2086 HOH HOH . E 5 HOH A 87 2087 2087 HOH HOH . E 5 HOH A 88 2088 2088 HOH HOH . E 5 HOH A 89 2089 2089 HOH HOH . E 5 HOH A 90 2090 2090 HOH HOH . E 5 HOH A 91 2091 2091 HOH HOH . E 5 HOH A 92 2092 2092 HOH HOH . E 5 HOH A 93 2093 2093 HOH HOH . E 5 HOH A 94 2094 2094 HOH HOH . E 5 HOH A 95 2095 2095 HOH HOH . E 5 HOH A 96 2096 2096 HOH HOH . E 5 HOH A 97 2097 2097 HOH HOH . E 5 HOH A 98 2098 2098 HOH HOH . E 5 HOH A 99 2099 2099 HOH HOH . E 5 HOH A 100 2100 2100 HOH HOH . E 5 HOH A 101 2101 2101 HOH HOH . E 5 HOH A 102 2102 2102 HOH HOH . E 5 HOH A 103 2103 2103 HOH HOH . E 5 HOH A 104 2104 2104 HOH HOH . E 5 HOH A 105 2105 2105 HOH HOH . E 5 HOH A 106 2106 2106 HOH HOH . E 5 HOH A 107 2107 2107 HOH HOH . E 5 HOH A 108 2108 2108 HOH HOH . E 5 HOH A 109 2109 2109 HOH HOH . E 5 HOH A 110 2110 2110 HOH HOH . E 5 HOH A 111 2111 2111 HOH HOH . E 5 HOH A 112 2112 2112 HOH HOH . E 5 HOH A 113 2113 2113 HOH HOH . E 5 HOH A 114 2114 2114 HOH HOH . E 5 HOH A 115 2115 2115 HOH HOH . E 5 HOH A 116 2116 2116 HOH HOH . E 5 HOH A 117 2117 2117 HOH HOH . E 5 HOH A 118 2118 2118 HOH HOH . E 5 HOH A 119 2119 2119 HOH HOH . E 5 HOH A 120 2120 2120 HOH HOH . E 5 HOH A 121 2121 2121 HOH HOH . E 5 HOH A 122 2122 2122 HOH HOH . E 5 HOH A 123 2123 2123 HOH HOH . E 5 HOH A 124 2124 2124 HOH HOH . E 5 HOH A 125 2125 2125 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 3 49.812 -27.878 -11.787 1 32.3 ? PA NAP 701 A 1 HETATM 2 O O1A NAP . . . C 3 48.693 -28.833 -11.914 1 32.88 ? O1A NAP 701 A 1 HETATM 3 O O2A NAP . . . C 3 49.689 -26.923 -10.526 1 32.38 ? O2A NAP 701 A 1 HETATM 4 O O5B NAP . . . C 3 51.152 -28.7 -11.713 1 31.47 ? O5B NAP 701 A 1 HETATM 5 C C5B NAP . . . C 3 52.06 -28.212 -10.783 1 32.42 ? C5B NAP 701 A 1 HETATM 6 C C4B NAP . . . C 3 53.214 -29.191 -11.058 1 34.49 ? C4B NAP 701 A 1 HETATM 7 O O4B NAP . . . C 3 54.428 -28.479 -10.872 1 34.7 ? O4B NAP 701 A 1 HETATM 8 C C3B NAP . . . C 3 53.251 -30.385 -10.063 1 35.85 ? C3B NAP 701 A 1 HETATM 9 O O3B NAP . . . C 3 54.147 -31.45 -10.446 1 31.7 ? O3B NAP 701 A 1 HETATM 10 C C2B NAP . . . C 3 53.902 -29.703 -8.852 1 37.57 ? C2B NAP 701 A 1 HETATM 11 O O2B NAP . . . C 3 54.462 -30.688 -7.967 1 40.48 ? O2B NAP 701 A 1 HETATM 12 C C1B NAP . . . C 3 55.019 -29.001 -9.659 1 37.18 ? C1B NAP 701 A 1 HETATM 13 N N9A NAP . . . C 3 55.579 -27.934 -8.831 1 41.87 ? N9A NAP 701 A 1 HETATM 14 C C8A NAP . . . C 3 55.006 -26.715 -8.471 1 43.14 ? C8A NAP 701 A 1 HETATM 15 N N7A NAP . . . C 3 55.839 -26.031 -7.725 1 41.54 ? N7A NAP 701 A 1 HETATM 16 C C5A NAP . . . C 3 56.988 -26.775 -7.592 1 42.07 ? C5A NAP 701 A 1 HETATM 17 C C6A NAP . . . C 3 58.202 -26.561 -6.916 1 44.36 ? C6A NAP 701 A 1 HETATM 18 N N6A NAP . . . C 3 58.35 -25.365 -6.192 1 42.12 ? N6A NAP 701 A 1 HETATM 19 N N1A NAP . . . C 3 59.157 -27.534 -7.002 1 43.32 ? N1A NAP 701 A 1 HETATM 20 C C2A NAP . . . C 3 58.934 -28.656 -7.706 1 41.8 ? C2A NAP 701 A 1 HETATM 21 N N3A NAP . . . C 3 57.802 -28.901 -8.356 1 40.2 ? N3A NAP 701 A 1 HETATM 22 C C4A NAP . . . C 3 56.845 -27.991 -8.308 1 40.35 ? C4A NAP 701 A 1 HETATM 23 O O3 NAP . . . C 3 49.895 -26.946 -13.137 1 32.67 ? O3 NAP 701 A 1 HETATM 24 P PN NAP . . . C 3 49.586 -27.68 -14.54 1 27.54 ? PN NAP 701 A 1 HETATM 25 O O1N NAP . . . C 3 50.37 -28.986 -14.741 1 27.42 ? O1N NAP 701 A 1 HETATM 26 O O2N NAP . . . C 3 49.97 -26.583 -15.542 1 24.71 ? O2N NAP 701 A 1 HETATM 27 O O5D NAP . . . C 3 48.011 -27.919 -14.658 1 30.99 ? O5D NAP 701 A 1 HETATM 28 C C5D NAP . . . C 3 47.347 -26.698 -14.315 1 33.28 ? C5D NAP 701 A 1 HETATM 29 C C4D NAP . . . C 3 45.846 -26.972 -14.297 1 31.68 ? C4D NAP 701 A 1 HETATM 30 O O4D NAP . . . C 3 45.332 -26.264 -15.452 1 32.47 ? O4D NAP 701 A 1 HETATM 31 C C3D NAP . . . C 3 45.516 -28.462 -14.574 1 30.04 ? C3D NAP 701 A 1 HETATM 32 O O3D NAP . . . C 3 45.191 -29.217 -13.44 1 26.15 ? O3D NAP 701 A 1 HETATM 33 C C2D NAP . . . C 3 44.164 -28.333 -15.258 1 30.94 ? C2D NAP 701 A 1 HETATM 34 O O2D NAP . . . C 3 43.199 -27.831 -14.348 1 27.93 ? O2D NAP 701 A 1 HETATM 35 C C1D NAP . . . C 3 44.542 -27.191 -16.247 1 33.78 ? C1D NAP 701 A 1 HETATM 36 N N1N NAP . . . C 3 45.279 -27.832 -17.373 1 37.72 ? N1N NAP 701 A 1 HETATM 37 C C2N NAP . . . C 3 44.606 -28.766 -18.099 1 40.02 ? C2N NAP 701 A 1 HETATM 38 C C3N NAP . . . C 3 45.219 -29.449 -19.189 1 42.36 ? C3N NAP 701 A 1 HETATM 39 C C7N NAP . . . C 3 44.499 -30.503 -19.988 1 42.18 ? C7N NAP 701 A 1 HETATM 40 O O7N NAP . . . C 3 43.3 -30.534 -20.097 1 42.93 ? O7N NAP 701 A 1 HETATM 41 N N7N NAP . . . C 3 45.12 -31.534 -20.594 1 43.63 ? N7N NAP 701 A 1 HETATM 42 C C4N NAP . . . C 3 46.574 -29.127 -19.466 1 38.94 ? C4N NAP 701 A 1 HETATM 43 C C5N NAP . . . C 3 47.23 -28.176 -18.669 1 38.23 ? C5N NAP 701 A 1 HETATM 44 C C6N NAP . . . C 3 46.565 -27.531 -17.631 1 37.12 ? C6N NAP 701 A 1 HETATM 45 P P2B NAP . . . C 3 53.57 -30.854 -6.618 1 39.31 ? P2B NAP 701 A 1 HETATM 46 O O1X NAP . . . C 3 52.935 -29.41 -6.236 1 38.98 ? O1X NAP 701 A 1 HETATM 47 O O2X NAP . . . C 3 54.306 -31.675 -5.594 1 38.65 ? O2X NAP 701 A 1 HETATM 48 O O3X NAP . . . C 3 52.224 -31.677 -6.924 1 39.9 ? O3X NAP 701 A 1 # _model_server_stats.io_time_ms 79 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 564 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 48 #