data_5PGX # _model_server_result.job_id GqiPnxLCUxaDqFscQjH53w _model_server_result.datetime_utc '2024-12-22 01:15:38' _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 5pgx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 5PGX # _exptl.entry_id 5PGX _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 4 _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 5PGX _cell.length_a 74.6 _cell.length_b 93.3 _cell.length_c 168.5 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5PGX _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K 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 296 n n PA O2A NAP sing 297 n n PA O5B NAP sing 298 n n PA O3 NAP sing 299 n n O2A HOA2 NAP sing 300 n n O5B C5B NAP sing 301 n n C5B C4B NAP sing 302 n n C5B H51A NAP sing 303 n n C5B H52A NAP sing 304 n n C4B O4B NAP sing 305 n n C4B C3B NAP sing 306 n n C4B H4B NAP sing 307 n n O4B C1B NAP sing 308 n n C3B O3B NAP sing 309 n n C3B C2B NAP sing 310 n n C3B H3B NAP sing 311 n n O3B HO3A NAP sing 312 n n C2B O2B NAP sing 313 n n C2B C1B NAP sing 314 n n C2B H2B NAP sing 315 n n O2B P2B NAP sing 316 n n C1B N9A NAP sing 317 n n C1B H1B NAP sing 318 n n N9A C8A NAP sing 319 n y N9A C4A NAP sing 320 n y C8A N7A NAP doub 321 n y C8A H8A NAP sing 322 n n N7A C5A NAP sing 323 n y C5A C6A NAP sing 324 n y C5A C4A NAP doub 325 n y C6A N6A NAP sing 326 n n C6A N1A NAP doub 327 n y N6A H61A NAP sing 328 n n N6A H62A NAP sing 329 n n N1A C2A NAP sing 330 n y C2A N3A NAP doub 331 n y C2A H2A NAP sing 332 n n N3A C4A NAP sing 333 n y O3 PN NAP sing 334 n n PN O1N NAP doub 335 n n PN O2N NAP sing 336 n n PN O5D NAP sing 337 n n O5D C5D NAP sing 338 n n C5D C4D NAP sing 339 n n C5D H51N NAP sing 340 n n C5D H52N NAP sing 341 n n C4D O4D NAP sing 342 n n C4D C3D NAP sing 343 n n C4D H4D NAP sing 344 n n O4D C1D NAP sing 345 n n C3D O3D NAP sing 346 n n C3D C2D NAP sing 347 n n C3D H3D NAP sing 348 n n O3D HO3N NAP sing 349 n n C2D O2D NAP sing 350 n n C2D C1D NAP sing 351 n n C2D H2D NAP sing 352 n n O2D HO2N NAP sing 353 n n C1D N1N NAP sing 354 n n C1D H1D NAP sing 355 n n N1N C2N NAP sing 356 n y N1N C6N NAP doub 357 n y C2N C3N NAP doub 358 n y C2N H2N NAP sing 359 n n C3N C7N NAP sing 360 n n C3N C4N NAP sing 361 n y C7N O7N NAP doub 362 n n C7N N7N NAP sing 363 n n N7N H71N NAP sing 364 n n N7N H72N NAP sing 365 n n C4N C5N NAP doub 366 n y C4N H4N NAP sing 367 n n C5N C6N NAP sing 368 n y C5N H5N NAP sing 369 n n C6N H6N NAP sing 370 n n P2B O1X NAP doub 371 n n P2B O2X NAP sing 372 n n P2B O3X NAP sing 373 n n O2X HOP2 NAP sing 374 n n O3X HOP3 NAP sing 375 n n # _atom_sites.entry_id 5PGX _atom_sites.fract_transf_matrix[1][1] 0.013405 _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] 0.010718 _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] 0.005935 _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 E 2 NAP A 1 301 301 NAP NAP . F 3 8KD A 1 302 302 8KD LG1 . G 2 NAP B 1 301 301 NAP NAP . H 3 8KD B 1 302 302 8KD LG1 . I 2 NAP D 1 301 301 NAP NAP . J 3 8KD D 1 302 302 8KD LG1 . K 2 NAP E 1 301 301 NAP NAP . L 3 8KD E 1 302 302 8KD LG1 . M 4 HOH A 1 401 9 HOH HOH . M 4 HOH A 2 402 3 HOH HOH . M 4 HOH A 3 403 30 HOH HOH . M 4 HOH A 4 404 8 HOH HOH . M 4 HOH A 5 405 5 HOH HOH . M 4 HOH A 6 406 18 HOH HOH . N 4 HOH B 1 401 35 HOH HOH . N 4 HOH B 2 402 19 HOH HOH . N 4 HOH B 3 403 14 HOH HOH . N 4 HOH B 4 404 31 HOH HOH . N 4 HOH B 5 405 11 HOH HOH . N 4 HOH B 6 406 23 HOH HOH . N 4 HOH B 7 407 2 HOH HOH . N 4 HOH B 8 408 10 HOH HOH . N 4 HOH B 9 409 24 HOH HOH . N 4 HOH B 10 410 33 HOH HOH . N 4 HOH B 11 411 32 HOH HOH . O 4 HOH D 1 401 7 HOH HOH . O 4 HOH D 2 402 4 HOH HOH . O 4 HOH D 3 403 37 HOH HOH . O 4 HOH D 4 404 16 HOH HOH . O 4 HOH D 5 405 12 HOH HOH . O 4 HOH D 6 406 1 HOH HOH . O 4 HOH D 7 407 13 HOH HOH . O 4 HOH D 8 408 6 HOH HOH . O 4 HOH D 9 409 29 HOH HOH . O 4 HOH D 10 410 15 HOH HOH . O 4 HOH D 11 411 22 HOH HOH . O 4 HOH D 12 412 28 HOH HOH . O 4 HOH D 13 413 17 HOH HOH . O 4 HOH D 14 414 36 HOH HOH . O 4 HOH D 15 415 25 HOH HOH . P 4 HOH E 1 401 39 HOH HOH . P 4 HOH E 2 402 20 HOH HOH . P 4 HOH E 3 403 21 HOH HOH . P 4 HOH E 4 404 38 HOH HOH . P 4 HOH E 5 405 34 HOH HOH . P 4 HOH E 6 406 27 HOH HOH . P 4 HOH E 7 407 26 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 2 54.81 60.536 78.109 1 35.52 ? PA NAP 301 A 1 HETATM 2 O O1A NAP . . . E 2 55.486 61.862 78.148 1 36.5 ? O1A NAP 301 A 1 HETATM 3 O O2A NAP . . . E 2 53.637 60.457 77.154 1 34.85 ? O2A NAP 301 A 1 HETATM 4 O O5B NAP . . . E 2 55.796 59.342 77.71 1 35.85 ? O5B NAP 301 A 1 HETATM 5 C C5B NAP . . . E 2 55.324 58.019 77.37 1 36.08 ? C5B NAP 301 A 1 HETATM 6 C C4B NAP . . . E 2 56.52 57.113 77.216 1 36.88 ? C4B NAP 301 A 1 HETATM 7 O O4B NAP . . . E 2 56.094 55.797 76.784 1 37.06 ? O4B NAP 301 A 1 HETATM 8 C C3B NAP . . . E 2 57.571 57.57 76.203 1 35.69 ? C3B NAP 301 A 1 HETATM 9 O O3B NAP . . . E 2 58.873 57.29 76.709 1 33.16 ? O3B NAP 301 A 1 HETATM 10 C C2B NAP . . . E 2 57.256 56.736 74.965 1 37.13 ? C2B NAP 301 A 1 HETATM 11 O O2B NAP . . . E 2 58.43 56.605 74.134 1 42.06 ? O2B NAP 301 A 1 HETATM 12 C C1B NAP . . . E 2 56.792 55.431 75.607 1 36.58 ? C1B NAP 301 A 1 HETATM 13 N N9A NAP . . . E 2 55.927 54.57 74.806 1 35.79 ? N9A NAP 301 A 1 HETATM 14 C C8A NAP . . . E 2 54.874 54.945 74.012 1 36.3 ? C8A NAP 301 A 1 HETATM 15 N N7A NAP . . . E 2 54.351 53.963 73.318 1 35.92 ? N7A NAP 301 A 1 HETATM 16 C C5A NAP . . . E 2 55.108 52.86 73.688 1 34.9 ? C5A NAP 301 A 1 HETATM 17 C C6A NAP . . . E 2 55.073 51.504 73.297 1 32.96 ? C6A NAP 301 A 1 HETATM 18 N N6A NAP . . . E 2 54.227 51.009 72.389 1 32.17 ? N6A NAP 301 A 1 HETATM 19 N N1A NAP . . . E 2 55.957 50.66 73.879 1 33.05 ? N1A NAP 301 A 1 HETATM 20 C C2A NAP . . . E 2 56.808 51.144 74.789 1 31.69 ? C2A NAP 301 A 1 HETATM 21 N N3A NAP . . . E 2 56.933 52.396 75.236 1 32.6 ? N3A NAP 301 A 1 HETATM 22 C C4A NAP . . . E 2 56.063 53.215 74.627 1 35.05 ? C4A NAP 301 A 1 HETATM 23 O O3 NAP . . . E 2 54.274 59.93 79.487 1 36.68 ? O3 NAP 301 A 1 HETATM 24 P PN NAP . . . E 2 53.823 60.636 80.846 1 36.87 ? PN NAP 301 A 1 HETATM 25 O O1N NAP . . . E 2 52.791 61.643 80.506 1 36.28 ? O1N NAP 301 A 1 HETATM 26 O O2N NAP . . . E 2 55.036 61.056 81.581 1 36.08 ? O2N NAP 301 A 1 HETATM 27 O O5D NAP . . . E 2 53.104 59.43 81.607 1 39.18 ? O5D NAP 301 A 1 HETATM 28 C C5D NAP . . . E 2 53.846 58.387 82.288 1 35.92 ? C5D NAP 301 A 1 HETATM 29 C C4D NAP . . . E 2 52.903 57.554 83.124 1 29.14 ? C4D NAP 301 A 1 HETATM 30 O O4D NAP . . . E 2 52.135 58.417 83.994 1 29.49 ? O4D NAP 301 A 1 HETATM 31 C C3D NAP . . . E 2 51.865 56.747 82.355 1 25.33 ? C3D NAP 301 A 1 HETATM 32 O O3D NAP . . . E 2 51.717 55.417 82.839 1 21.74 ? O3D NAP 301 A 1 HETATM 33 C C2D NAP . . . E 2 50.604 57.57 82.578 1 26.64 ? C2D NAP 301 A 1 HETATM 34 O O2D NAP . . . E 2 49.424 56.785 82.538 1 24.03 ? O2D NAP 301 A 1 HETATM 35 C C1D NAP . . . E 2 50.792 58.037 84.023 1 29.67 ? C1D NAP 301 A 1 HETATM 36 N N1N NAP . . . E 2 49.94 59.272 84.252 1 32.15 ? N1N NAP 301 A 1 HETATM 37 C C2N NAP . . . E 2 50.326 60.492 83.69 1 33.49 ? C2N NAP 301 A 1 HETATM 38 C C3N NAP . . . E 2 49.526 61.613 83.828 1 35.66 ? C3N NAP 301 A 1 HETATM 39 C C7N NAP . . . E 2 49.848 62.924 83.135 1 37.15 ? C7N NAP 301 A 1 HETATM 40 O O7N NAP . . . E 2 49.142 63.932 83.364 1 33.75 ? O7N NAP 301 A 1 HETATM 41 N N7N NAP . . . E 2 50.925 62.967 82.308 1 39.28 ? N7N NAP 301 A 1 HETATM 42 C C4N NAP . . . E 2 48.357 61.502 84.573 1 36.6 ? C4N NAP 301 A 1 HETATM 43 C C5N NAP . . . E 2 47.991 60.286 85.127 1 35.17 ? C5N NAP 301 A 1 HETATM 44 C C6N NAP . . . E 2 48.788 59.175 84.939 1 32.11 ? C6N NAP 301 A 1 HETATM 45 P P2B NAP . . . E 2 58.493 56.103 72.616 1 48.43 ? P2B NAP 301 A 1 HETATM 46 O O1X NAP . . . E 2 58.28 54.633 72.55 1 47.83 ? O1X NAP 301 A 1 HETATM 47 O O2X NAP . . . E 2 57.432 56.906 71.885 1 52.64 ? O2X NAP 301 A 1 HETATM 48 O O3X NAP . . . E 2 59.829 56.547 72.016 1 48.98 ? O3X NAP 301 A 1 HETATM 49 H HOA2 NAP . . . E 2 53.031 59.707 76.915 0 34.9 ? HOA2 NAP 301 A 1 HETATM 50 H H51A NAP . . . E 2 54.727 57.701 78.223 0 36.1 ? H51A NAP 301 A 1 HETATM 51 H H52A NAP . . . E 2 54.683 58.029 76.49 0 36.1 ? H52A NAP 301 A 1 HETATM 52 H H4B NAP . . . E 2 56.958 56.912 78.192 0 36.91 ? H4B NAP 301 A 1 HETATM 53 H H3B NAP . . . E 2 57.469 58.632 75.988 0 35.64 ? H3B NAP 301 A 1 HETATM 54 H HO3A NAP . . . E 2 59.067 57.997 77.38 0 33.1 ? HO3A NAP 301 A 1 HETATM 55 H H2B NAP . . . E 2 56.467 57.234 74.404 0 37.09 ? H2B NAP 301 A 1 HETATM 56 H H1B NAP . . . E 2 57.634 54.82 75.929 0 36.63 ? H1B NAP 301 A 1 HETATM 57 H H8A NAP . . . E 2 54.497 55.966 73.965 0 36.31 ? H8A NAP 301 A 1 HETATM 58 H H61A NAP . . . E 2 53.551 51.611 71.93 0 32.17 ? H61A NAP 301 A 1 HETATM 59 H H62A NAP . . . E 2 54.234 50.028 72.13 0 32.17 ? H62A NAP 301 A 1 HETATM 60 H H2A NAP . . . E 2 57.542 50.446 75.187 0 31.72 ? H2A NAP 301 A 1 HETATM 61 H H51N NAP . . . E 2 54.678 58.748 82.89 0 35.9 ? H51N NAP 301 A 1 HETATM 62 H H52N NAP . . . E 2 54.29 57.809 81.479 0 35.9 ? H52N NAP 301 A 1 HETATM 63 H H4D NAP . . . E 2 53.485 56.904 83.774 0 29.15 ? H4D NAP 301 A 1 HETATM 64 H H3D NAP . . . E 2 52.071 56.719 81.287 0 25.34 ? H3D NAP 301 A 1 HETATM 65 H HO3N NAP . . . E 2 51.647 55.458 83.829 0 21.75 ? HO3N NAP 301 A 1 HETATM 66 H H2D NAP . . . E 2 50.518 58.394 81.872 0 26.62 ? H2D NAP 301 A 1 HETATM 67 H HO2N NAP . . . E 2 49.094 56.773 81.602 0 24.02 ? HO2N NAP 301 A 1 HETATM 68 H H1D NAP . . . E 2 50.598 57.329 84.827 0 29.65 ? H1D NAP 301 A 1 HETATM 69 H H2N NAP . . . E 2 51.272 60.525 83.156 0 33.46 ? H2N NAP 301 A 1 HETATM 70 H H71N NAP . . . E 2 51.177 63.838 81.854 0 39.27 ? H71N NAP 301 A 1 HETATM 71 H H72N NAP . . . E 2 51.527 62.189 82.063 0 39.27 ? H72N NAP 301 A 1 HETATM 72 H H4N NAP . . . E 2 47.689 62.348 84.726 0 36.56 ? H4N NAP 301 A 1 HETATM 73 H H5N NAP . . . E 2 47.073 60.194 85.704 0 35.15 ? H5N NAP 301 A 1 HETATM 74 H H6N NAP . . . E 2 48.461 58.199 85.288 0 32.07 ? H6N NAP 301 A 1 HETATM 75 H HOP2 NAP . . . E 2 57.237 57.821 72.219 0 52.6 ? HOP2 NAP 301 A 1 HETATM 76 H HOP3 NAP . . . E 2 60.492 57.12 72.481 0 49.09 ? HOP3 NAP 301 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 76 #