data_5B3U # _model_server_result.job_id zpvPVhggeJ1bcw6rkrJdKA _model_server_result.datetime_utc '2024-12-26 13:12:33' _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 5b3u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 5B3U # _exptl.entry_id 5B3U _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 90 _cell.entry_id 5B3U _cell.length_a 59.091 _cell.length_b 85.562 _cell.length_c 135.026 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B3U _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,H 1 1 B,E,F,G,I 2 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 E _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 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 5B3U _atom_sites.fract_transf_matrix[1][1] 0.016923 _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] 0.011687 _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] 0.007406 _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 PO4 A 1 401 1 PO4 PO4 . D 2 PO4 A 1 402 3 PO4 PO4 . E 3 NAP B 1 401 1 NAP NAP . F 2 PO4 B 1 402 2 PO4 PO4 . G 2 PO4 B 1 403 4 PO4 PO4 . H 4 HOH A 1 501 16 HOH HOH . H 4 HOH A 2 502 4 HOH HOH . H 4 HOH A 3 503 41 HOH HOH . H 4 HOH A 4 504 31 HOH HOH . H 4 HOH A 5 505 10 HOH HOH . H 4 HOH A 6 506 3 HOH HOH . H 4 HOH A 7 507 2 HOH HOH . H 4 HOH A 8 508 14 HOH HOH . H 4 HOH A 9 509 13 HOH HOH . H 4 HOH A 10 510 12 HOH HOH . H 4 HOH A 11 511 43 HOH HOH . H 4 HOH A 12 512 34 HOH HOH . H 4 HOH A 13 513 35 HOH HOH . H 4 HOH A 14 514 15 HOH HOH . H 4 HOH A 15 515 59 HOH HOH . H 4 HOH A 16 516 32 HOH HOH . H 4 HOH A 17 517 36 HOH HOH . H 4 HOH A 18 518 30 HOH HOH . H 4 HOH A 19 519 25 HOH HOH . H 4 HOH A 20 520 37 HOH HOH . H 4 HOH A 21 521 8 HOH HOH . H 4 HOH A 22 522 21 HOH HOH . H 4 HOH A 23 523 24 HOH HOH . H 4 HOH A 24 524 11 HOH HOH . H 4 HOH A 25 525 5 HOH HOH . H 4 HOH A 26 526 26 HOH HOH . H 4 HOH A 27 527 18 HOH HOH . H 4 HOH A 28 528 22 HOH HOH . H 4 HOH A 29 529 33 HOH HOH . H 4 HOH A 30 530 23 HOH HOH . H 4 HOH A 31 531 6 HOH HOH . I 4 HOH B 1 501 51 HOH HOH . I 4 HOH B 2 502 47 HOH HOH . I 4 HOH B 3 503 20 HOH HOH . I 4 HOH B 4 504 19 HOH HOH . I 4 HOH B 5 505 57 HOH HOH . I 4 HOH B 6 506 55 HOH HOH . I 4 HOH B 7 507 50 HOH HOH . I 4 HOH B 8 508 48 HOH HOH . I 4 HOH B 9 509 56 HOH HOH . I 4 HOH B 10 510 38 HOH HOH . I 4 HOH B 11 511 53 HOH HOH . I 4 HOH B 12 512 40 HOH HOH . I 4 HOH B 13 513 58 HOH HOH . I 4 HOH B 14 514 29 HOH HOH . I 4 HOH B 15 515 7 HOH HOH . I 4 HOH B 16 516 39 HOH HOH . I 4 HOH B 17 517 27 HOH HOH . I 4 HOH B 18 518 28 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 . . . E 3 25.267 63.95 29.264 1 39.58 ? PA NAP 401 B 1 HETATM 2 O O1A NAP . . . E 3 26.028 65.207 29.327 1 41.99 ? O1A NAP 401 B 1 HETATM 3 O O2A NAP . . . E 3 24.765 63.569 30.692 1 40.66 ? O2A NAP 401 B 1 HETATM 4 O O5B NAP . . . E 3 26.228 62.754 28.667 1 41.53 ? O5B NAP 401 B 1 HETATM 5 C C5B NAP . . . E 3 27.386 63.138 27.915 1 41.2 ? C5B NAP 401 B 1 HETATM 6 C C4B NAP . . . E 3 28.325 61.913 27.765 1 42.95 ? C4B NAP 401 B 1 HETATM 7 O O4B NAP . . . E 3 29.388 62.178 26.658 1 41.65 ? O4B NAP 401 B 1 HETATM 8 C C3B NAP . . . E 3 28.994 61.76 28.843 1 43.66 ? C3B NAP 401 B 1 HETATM 9 O O3B NAP . . . E 3 29.349 60.361 29.021 1 42.3 ? O3B NAP 401 B 1 HETATM 10 C C2B NAP . . . E 3 30.366 62.667 28.648 1 42.76 ? C2B NAP 401 B 1 HETATM 11 O O2B NAP . . . E 3 31.41 62.095 29.507 1 43.02 ? O2B NAP 401 B 1 HETATM 12 C C1B NAP . . . E 3 30.702 62.525 27.421 1 42.54 ? C1B NAP 401 B 1 HETATM 13 N N9A NAP . . . E 3 31.292 63.783 26.866 1 43.44 ? N9A NAP 401 B 1 HETATM 14 C C8A NAP . . . E 3 31.207 65.114 26.965 1 43.69 ? C8A NAP 401 B 1 HETATM 15 N N7A NAP . . . E 3 32.103 65.608 26.092 1 43.67 ? N7A NAP 401 B 1 HETATM 16 C C5A NAP . . . E 3 32.725 64.562 25.47 1 44.13 ? C5A NAP 401 B 1 HETATM 17 C C6A NAP . . . E 3 33.715 64.516 24.5 1 43.75 ? C6A NAP 401 B 1 HETATM 18 N N6A NAP . . . E 3 34.548 65.403 23.695 1 43.04 ? N6A NAP 401 B 1 HETATM 19 N N1A NAP . . . E 3 34.154 63.331 24.054 1 43.89 ? N1A NAP 401 B 1 HETATM 20 C C2A NAP . . . E 3 33.632 62.174 24.55 1 43.5 ? C2A NAP 401 B 1 HETATM 21 N N3A NAP . . . E 3 32.668 62.216 25.494 1 44.4 ? N3A NAP 401 B 1 HETATM 22 C C4A NAP . . . E 3 32.221 63.426 25.948 1 43.91 ? C4A NAP 401 B 1 HETATM 23 O O3 NAP . . . E 3 23.945 64.165 28.26 1 41.36 ? O3 NAP 401 B 1 HETATM 24 P PN NAP . . . E 3 23.017 62.975 27.695 1 38.38 ? PN NAP 401 B 1 HETATM 25 O O1N NAP . . . E 3 23.362 61.692 28.34 1 43.68 ? O1N NAP 401 B 1 HETATM 26 O O2N NAP . . . E 3 21.553 63.317 27.971 1 41.55 ? O2N NAP 401 B 1 HETATM 27 O O5D NAP . . . E 3 23.266 62.879 26.048 1 41.48 ? O5D NAP 401 B 1 HETATM 28 C C5D NAP . . . E 3 23.605 61.606 25.426 1 42.68 ? C5D NAP 401 B 1 HETATM 29 C C4D NAP . . . E 3 22.879 61.519 24.076 1 43.18 ? C4D NAP 401 B 1 HETATM 30 O O4D NAP . . . E 3 21.361 61.055 24.322 1 45.98 ? O4D NAP 401 B 1 HETATM 31 C C3D NAP . . . E 3 22.839 62.697 23.493 1 43.2 ? C3D NAP 401 B 1 HETATM 32 O O3D NAP . . . E 3 23.201 62.551 22.03 1 41.72 ? O3D NAP 401 B 1 HETATM 33 C C2D NAP . . . E 3 21.393 63.205 23.636 1 42.87 ? C2D NAP 401 B 1 HETATM 34 O O2D NAP . . . E 3 21.037 63.929 22.554 1 42.28 ? O2D NAP 401 B 1 HETATM 35 C C1D NAP . . . E 3 20.592 61.9 23.685 1 44.3 ? C1D NAP 401 B 1 HETATM 36 N N1N NAP . . . E 3 19.294 61.996 24.402 1 44.18 ? N1N NAP 401 B 1 HETATM 37 C C2N NAP . . . E 3 19.239 62.407 25.68 1 43.7 ? C2N NAP 401 B 1 HETATM 38 C C3N NAP . . . E 3 17.997 62.475 26.333 1 45.16 ? C3N NAP 401 B 1 HETATM 39 C C7N NAP . . . E 3 17.9 62.952 27.801 1 46.25 ? C7N NAP 401 B 1 HETATM 40 O O7N NAP . . . E 3 18.865 63.118 28.428 1 45.74 ? O7N NAP 401 B 1 HETATM 41 N N7N NAP . . . E 3 16.609 63.183 28.39 1 45.56 ? N7N NAP 401 B 1 HETATM 42 C C4N NAP . . . E 3 16.852 62.119 25.68 1 44.91 ? C4N NAP 401 B 1 HETATM 43 C C5N NAP . . . E 3 16.915 61.697 24.408 1 44.53 ? C5N NAP 401 B 1 HETATM 44 C C6N NAP . . . E 3 18.147 61.63 23.748 1 44.14 ? C6N NAP 401 B 1 HETATM 45 P P2B NAP . . . E 3 31.988 62.964 30.854 1 44.21 ? P2B NAP 401 B 1 HETATM 46 O O1X NAP . . . E 3 32.977 62.077 31.59 1 47.7 ? O1X NAP 401 B 1 HETATM 47 O O2X NAP . . . E 3 32.669 64.2 30.389 1 48.45 ? O2X NAP 401 B 1 HETATM 48 O O3X NAP . . . E 3 30.848 63.33 31.786 1 44.49 ? O3X NAP 401 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 48 #