data_1YQX # _model_server_result.job_id SytnojTG9zzBcR3M5aVivA _model_server_result.datetime_utc '2025-08-30 13:05:56' _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 1yqx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":500}' # _entry.id 1YQX # _exptl.entry_id 1YQX _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 1YQX _cell.length_a 76.362 _cell.length_b 138.165 _cell.length_c 67.629 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1YQX _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 H N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A SG CYS 54 A CYS 50 1_555 C ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc2 A NE2 HIS 76 A HIS 72 1_555 C ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc3 A SG CYS 107 A CYS 103 1_555 D ZN ZN . A ZN 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc4 A SG CYS 110 A CYS 106 1_555 D ZN ZN . A ZN 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc5 A SG CYS 113 A CYS 109 1_555 D ZN ZN . A ZN 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc6 A SG CYS 121 A CYS 117 1_555 D ZN ZN . A ZN 2000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc7 A SG CYS 170 A CYS 166 1_555 C ZN ZN . A ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc8 C ZN ZN . A ZN 1000 1_555 I O HOH . A HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc9 B SG CYS 54 B CYS 50 1_555 G ZN ZN . B ZN 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc10 B NE2 HIS 76 B HIS 72 1_555 G ZN ZN . B ZN 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc11 B SG CYS 107 B CYS 103 1_555 F ZN ZN . B ZN 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc12 B SG CYS 110 B CYS 106 1_555 F ZN ZN . B ZN 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc13 B SG CYS 113 B CYS 109 1_555 F ZN ZN . B ZN 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc14 B SG CYS 121 B CYS 117 1_555 F ZN ZN . B ZN 3000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? metalc ? metalc15 B SG CYS 170 B CYS 166 1_555 G ZN ZN . B ZN 4000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc16 G ZN ZN . B ZN 4000 1_555 J O HOH . B HOH 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? # _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 1YQX _atom_sites.fract_transf_matrix[1][1] 0.013096 _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] 0.007238 _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] 0.014787 _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 ZN A 1 1000 1000 ZN ZN . D 2 ZN A 1 2000 2000 ZN ZN . E 3 NAP A 1 500 500 NAP NAP . F 2 ZN B 1 3000 3000 ZN ZN . G 2 ZN B 1 4000 4000 ZN ZN . H 3 NAP B 1 600 600 NAP NAP . I 4 HOH A 1 2001 2 HOH TIP . I 4 HOH A 2 2002 9 HOH TIP . I 4 HOH A 3 2003 13 HOH TIP . I 4 HOH A 4 2004 15 HOH TIP . I 4 HOH A 5 2005 16 HOH TIP . I 4 HOH A 6 2006 18 HOH TIP . I 4 HOH A 7 2007 21 HOH TIP . I 4 HOH A 8 2008 22 HOH TIP . I 4 HOH A 9 2009 23 HOH TIP . I 4 HOH A 10 2010 26 HOH TIP . I 4 HOH A 11 2011 27 HOH TIP . I 4 HOH A 12 2012 29 HOH TIP . I 4 HOH A 13 2013 31 HOH TIP . I 4 HOH A 14 2014 35 HOH TIP . I 4 HOH A 15 2015 36 HOH TIP . I 4 HOH A 16 2016 37 HOH TIP . I 4 HOH A 17 2017 40 HOH TIP . I 4 HOH A 18 2018 41 HOH TIP . I 4 HOH A 19 2019 43 HOH TIP . J 4 HOH B 1 4001 3 HOH TIP . J 4 HOH B 2 4002 5 HOH TIP . J 4 HOH B 3 4003 6 HOH TIP . J 4 HOH B 4 4004 7 HOH TIP . J 4 HOH B 5 4005 8 HOH TIP . J 4 HOH B 6 4006 10 HOH TIP . J 4 HOH B 7 4007 11 HOH TIP . J 4 HOH B 8 4008 12 HOH TIP . J 4 HOH B 9 4009 14 HOH TIP . J 4 HOH B 10 4010 17 HOH TIP . J 4 HOH B 11 4011 19 HOH TIP . J 4 HOH B 12 4012 20 HOH TIP . J 4 HOH B 13 4013 24 HOH TIP . J 4 HOH B 14 4014 28 HOH TIP . J 4 HOH B 15 4015 30 HOH TIP . J 4 HOH B 16 4016 32 HOH TIP . J 4 HOH B 17 4017 33 HOH TIP . J 4 HOH B 18 4018 34 HOH TIP . J 4 HOH B 19 4019 38 HOH TIP . J 4 HOH B 20 4020 39 HOH TIP . J 4 HOH B 21 4021 42 HOH TIP . # 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 3 48.994 129.37 23.273 1 10.68 ? PA NAP 500 A 1 HETATM 2 O O1A NAP . . . E 3 47.632 129.242 23.448 1 9.96 ? O1A NAP 500 A 1 HETATM 3 O O2A NAP . . . E 3 49.811 130.537 23.707 1 10.86 ? O2A NAP 500 A 1 HETATM 4 O O5B NAP . . . E 3 49.413 129.19 21.738 1 15.09 ? O5B NAP 500 A 1 HETATM 5 C C5B NAP . . . E 3 48.77 128.134 21.009 1 16.05 ? C5B NAP 500 A 1 HETATM 6 C C4B NAP . . . E 3 48.901 128.761 19.615 1 16.83 ? C4B NAP 500 A 1 HETATM 7 O O4B NAP . . . E 3 48.152 127.756 18.547 1 16.79 ? O4B NAP 500 A 1 HETATM 8 C C3B NAP . . . E 3 47.566 129.769 19.325 1 16.85 ? C3B NAP 500 A 1 HETATM 9 O O3B NAP . . . E 3 48.329 131.083 19.273 1 16.54 ? O3B NAP 500 A 1 HETATM 10 C C2B NAP . . . E 3 47.114 129.674 17.938 1 17.02 ? C2B NAP 500 A 1 HETATM 11 O O2B NAP . . . E 3 48.079 130.068 16.993 1 16.72 ? O2B NAP 500 A 1 HETATM 12 C C1B NAP . . . E 3 47.186 128.074 17.824 1 16.55 ? C1B NAP 500 A 1 HETATM 13 N N9A NAP . . . E 3 45.855 127.492 18.072 1 16.38 ? N9A NAP 500 A 1 HETATM 14 C C8A NAP . . . E 3 45.031 127.53 19.192 1 17.9 ? C8A NAP 500 A 1 HETATM 15 N N7A NAP . . . E 3 43.883 126.865 19.02 1 19.28 ? N7A NAP 500 A 1 HETATM 16 C C5A NAP . . . E 3 43.978 126.369 17.711 1 19.54 ? C5A NAP 500 A 1 HETATM 17 C C6A NAP . . . E 3 43.044 125.557 16.92 1 21 ? C6A NAP 500 A 1 HETATM 18 N N6A NAP . . . E 3 41.826 125.092 17.304 1 20.05 ? N6A NAP 500 A 1 HETATM 19 N N1A NAP . . . E 3 43.443 125.202 15.585 1 19.87 ? N1A NAP 500 A 1 HETATM 20 C C2A NAP . . . E 3 44.706 125.637 15.069 1 18.05 ? C2A NAP 500 A 1 HETATM 21 N N3A NAP . . . E 3 45.619 126.425 15.818 1 17.78 ? N3A NAP 500 A 1 HETATM 22 C C4A NAP . . . E 3 45.215 126.765 17.131 1 16.82 ? C4A NAP 500 A 1 HETATM 23 O O3 NAP . . . E 3 49.723 128.131 23.94 1 12.74 ? O3 NAP 500 A 1 HETATM 24 P PN NAP . . . E 3 51.24 128.018 24.352 1 6.14 ? PN NAP 500 A 1 HETATM 25 O O1N NAP . . . E 3 52.272 127.812 23.362 1 12.25 ? O1N NAP 500 A 1 HETATM 26 O O2N NAP . . . E 3 51.467 128.064 25.778 1 8.56 ? O2N NAP 500 A 1 HETATM 27 O O5D NAP . . . E 3 51.063 126.392 24.465 1 10.15 ? O5D NAP 500 A 1 HETATM 28 C C5D NAP . . . E 3 50.764 125.528 23.279 1 15.95 ? C5D NAP 500 A 1 HETATM 29 C C4D NAP . . . E 3 50.659 124.017 23.569 1 18.02 ? C4D NAP 500 A 1 HETATM 30 O O4D NAP . . . E 3 51.949 123.39 23.862 1 18.84 ? O4D NAP 500 A 1 HETATM 31 C C3D NAP . . . E 3 49.739 123.492 24.767 1 19.87 ? C3D NAP 500 A 1 HETATM 32 O O3D NAP . . . E 3 48.978 122.309 24.351 1 21.06 ? O3D NAP 500 A 1 HETATM 33 C C2D NAP . . . E 3 50.729 123.154 25.845 1 19.14 ? C2D NAP 500 A 1 HETATM 34 O O2D NAP . . . E 3 50.171 122.278 26.82 1 16.77 ? O2D NAP 500 A 1 HETATM 35 C C1D NAP . . . E 3 51.795 122.55 25.057 1 19.31 ? C1D NAP 500 A 1 HETATM 36 N N1N NAP . . . E 3 53.151 122.48 25.623 1 22.05 ? N1N NAP 500 A 1 HETATM 37 C C2N NAP . . . E 3 53.926 121.29 25.499 1 22.31 ? C2N NAP 500 A 1 HETATM 38 C C3N NAP . . . E 3 55.222 121.261 26.046 1 24.79 ? C3N NAP 500 A 1 HETATM 39 C C7N NAP . . . E 3 56.032 119.978 25.901 1 25.34 ? C7N NAP 500 A 1 HETATM 40 O O7N NAP . . . E 3 57.144 119.966 26.384 1 23.43 ? O7N NAP 500 A 1 HETATM 41 N N7N NAP . . . E 3 55.528 118.951 25.281 1 28.72 ? N7N NAP 500 A 1 HETATM 42 C C4N NAP . . . E 3 55.799 122.427 26.745 1 22.53 ? C4N NAP 500 A 1 HETATM 43 C C5N NAP . . . E 3 54.981 123.602 26.842 1 24.78 ? C5N NAP 500 A 1 HETATM 44 C C6N NAP . . . E 3 53.64 123.658 26.285 1 23.07 ? C6N NAP 500 A 1 HETATM 45 P P2B NAP . . . E 3 47.592 130.845 15.557 1 19.22 ? P2B NAP 500 A 1 HETATM 46 O O1X NAP . . . E 3 48.909 131.13 14.833 1 18.71 ? O1X NAP 500 A 1 HETATM 47 O O2X NAP . . . E 3 46.733 129.811 14.877 1 22.26 ? O2X NAP 500 A 1 HETATM 48 O O3X NAP . . . E 3 46.907 132.117 15.976 1 21.77 ? O3X NAP 500 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 48 #