data_5PGX # _model_server_result.job_id sLYzO3iEaW9aEE46_dpZjA _model_server_result.datetime_utc '2024-12-22 01:02:24' _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":"G","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 . . . G 2 28.728 29.393 85.54 1 31.66 ? PA NAP 301 B 1 HETATM 2 O O1A NAP . . . G 2 27.796 28.409 86.144 1 29.34 ? O1A NAP 301 B 1 HETATM 3 O O2A NAP . . . G 2 30.181 28.939 85.457 1 32.27 ? O2A NAP 301 B 1 HETATM 4 O O5B NAP . . . G 2 28.31 29.756 84.04 1 34.01 ? O5B NAP 301 B 1 HETATM 5 C C5B NAP . . . G 2 29.227 30.298 83.06 1 36.23 ? C5B NAP 301 B 1 HETATM 6 C C4B NAP . . . G 2 28.463 30.492 81.777 1 38.52 ? C4B NAP 301 B 1 HETATM 7 O O4B NAP . . . G 2 29.321 31.077 80.772 1 38.27 ? O4B NAP 301 B 1 HETATM 8 C C3B NAP . . . G 2 27.912 29.213 81.151 1 40.01 ? C3B NAP 301 B 1 HETATM 9 O O3B NAP . . . G 2 26.703 29.505 80.467 1 39.34 ? O3B NAP 301 B 1 HETATM 10 C C2B NAP . . . G 2 29.023 28.83 80.181 1 41.19 ? C2B NAP 301 B 1 HETATM 11 O O2B NAP . . . G 2 28.59 27.902 79.162 1 43.63 ? O2B NAP 301 B 1 HETATM 12 C C1B NAP . . . G 2 29.423 30.206 79.661 1 36.32 ? C1B NAP 301 B 1 HETATM 13 N N9A NAP . . . G 2 30.778 30.303 79.128 1 34.28 ? N9A NAP 301 B 1 HETATM 14 C C8A NAP . . . G 2 31.935 29.875 79.727 1 34.75 ? C8A NAP 301 B 1 HETATM 15 N N7A NAP . . . G 2 33.012 30.051 78.998 1 33.68 ? N7A NAP 301 B 1 HETATM 16 C C5A NAP . . . G 2 32.529 30.628 77.832 1 33.06 ? C5A NAP 301 B 1 HETATM 17 C C6A NAP . . . G 2 33.163 31.04 76.641 1 35.14 ? C6A NAP 301 B 1 HETATM 18 N N6A NAP . . . G 2 34.455 30.821 76.373 1 36.14 ? N6A NAP 301 B 1 HETATM 19 N N1A NAP . . . G 2 32.394 31.628 75.692 1 33.83 ? N1A NAP 301 B 1 HETATM 20 C C2A NAP . . . G 2 31.082 31.768 75.918 1 30.61 ? C2A NAP 301 B 1 HETATM 21 N N3A NAP . . . G 2 30.371 31.387 76.983 1 30.82 ? N3A NAP 301 B 1 HETATM 22 C C4A NAP . . . G 2 31.156 30.812 77.908 1 32.73 ? C4A NAP 301 B 1 HETATM 23 O O3 NAP . . . G 2 28.845 30.862 86.158 1 34.46 ? O3 NAP 301 B 1 HETATM 24 P PN NAP . . . G 2 28.263 31.655 87.419 1 34 ? PN NAP 301 B 1 HETATM 25 O O1N NAP . . . G 2 28.964 31.164 88.627 1 32.26 ? O1N NAP 301 B 1 HETATM 26 O O2N NAP . . . G 2 26.78 31.645 87.359 1 30.32 ? O2N NAP 301 B 1 HETATM 27 O O5D NAP . . . G 2 28.783 33.131 87.117 1 33.85 ? O5D NAP 301 B 1 HETATM 28 C C5D NAP . . . G 2 28.037 34.003 86.238 1 34.87 ? C5D NAP 301 B 1 HETATM 29 C C4D NAP . . . G 2 28.586 35.404 86.349 1 35.22 ? C4D NAP 301 B 1 HETATM 30 O O4D NAP . . . G 2 28.48 35.858 87.714 1 34.08 ? O4D NAP 301 B 1 HETATM 31 C C3D NAP . . . G 2 30.055 35.578 85.983 1 36.1 ? C3D NAP 301 B 1 HETATM 32 O O3D NAP . . . G 2 30.277 36.858 85.401 1 34.2 ? O3D NAP 301 B 1 HETATM 33 C C2D NAP . . . G 2 30.731 35.499 87.345 1 36.4 ? C2D NAP 301 B 1 HETATM 34 O O2D NAP . . . G 2 31.985 36.165 87.32 1 38.96 ? O2D NAP 301 B 1 HETATM 35 C C1D NAP . . . G 2 29.726 36.357 88.15 1 34.24 ? C1D NAP 301 B 1 HETATM 36 N N1N NAP . . . G 2 29.877 36.09 89.643 1 28.41 ? N1N NAP 301 B 1 HETATM 37 C C2N NAP . . . G 2 29.589 34.828 90.162 1 27.11 ? C2N NAP 301 B 1 HETATM 38 C C3N NAP . . . G 2 29.891 34.546 91.484 1 26.73 ? C3N NAP 301 B 1 HETATM 39 C C7N NAP . . . G 2 29.693 33.201 92.119 1 23.67 ? C7N NAP 301 B 1 HETATM 40 O O7N NAP . . . G 2 30.115 33.005 93.29 1 20.05 ? O7N NAP 301 B 1 HETATM 41 N N7N NAP . . . G 2 29.092 32.228 91.389 1 24.78 ? N7N NAP 301 B 1 HETATM 42 C C4N NAP . . . G 2 30.433 35.557 92.273 1 26.51 ? C4N NAP 301 B 1 HETATM 43 C C5N NAP . . . G 2 30.661 36.812 91.744 1 27.06 ? C5N NAP 301 B 1 HETATM 44 C C6N NAP . . . G 2 30.388 37.057 90.424 1 28.05 ? C6N NAP 301 B 1 HETATM 45 P P2B NAP . . . G 2 29.572 27.066 78.217 1 43.63 ? P2B NAP 301 B 1 HETATM 46 O O1X NAP . . . G 2 30.032 27.94 77.149 1 44.78 ? O1X NAP 301 B 1 HETATM 47 O O2X NAP . . . G 2 30.738 26.522 79.071 1 41.77 ? O2X NAP 301 B 1 HETATM 48 O O3X NAP . . . G 2 28.754 25.89 77.73 1 44.73 ? O3X NAP 301 B 1 HETATM 49 H HOA2 NAP . . . G 2 30.998 29.418 85.16 0 32.22 ? HOA2 NAP 301 B 1 HETATM 50 H H51A NAP . . . G 2 29.531 31.261 83.469 0 36.19 ? H51A NAP 301 B 1 HETATM 51 H H52A NAP . . . G 2 30.117 29.683 82.935 0 36.19 ? H52A NAP 301 B 1 HETATM 52 H H4B NAP . . . G 2 27.693 31.246 81.922 0 38.48 ? H4B NAP 301 B 1 HETATM 53 H H3B NAP . . . G 2 27.752 28.447 81.906 0 40.06 ? H3B NAP 301 B 1 HETATM 54 H HO3A NAP . . . G 2 26.004 29.519 81.171 0 39.36 ? HO3A NAP 301 B 1 HETATM 55 H H2B NAP . . . G 2 29.819 28.366 80.762 0 41.22 ? H2B NAP 301 B 1 HETATM 56 H H1B NAP . . . G 2 28.743 30.58 78.897 0 36.29 ? H1B NAP 301 B 1 HETATM 57 H H8A NAP . . . G 2 31.962 29.436 80.723 0 34.75 ? H8A NAP 301 B 1 HETATM 58 H H61A NAP . . . G 2 35.048 30.339 77.041 0 36.18 ? H61A NAP 301 B 1 HETATM 59 H H62A NAP . . . G 2 34.88 31.127 75.503 0 36.18 ? H62A NAP 301 B 1 HETATM 60 H H2A NAP . . . G 2 30.509 32.246 75.126 0 30.64 ? H2A NAP 301 B 1 HETATM 61 H H51N NAP . . . G 2 26.959 34.006 86.393 0 34.81 ? H51N NAP 301 B 1 HETATM 62 H H52N NAP . . . G 2 28.199 33.582 85.247 0 34.81 ? H52N NAP 301 B 1 HETATM 63 H H4D NAP . . . G 2 27.973 36.091 85.769 0 35.25 ? H4D NAP 301 B 1 HETATM 64 H H3D NAP . . . G 2 30.443 34.791 85.338 0 36.1 ? H3D NAP 301 B 1 HETATM 65 H HO3N NAP . . . G 2 30.172 36.73 84.423 0 34.27 ? HO3N NAP 301 B 1 HETATM 66 H H2D NAP . . . G 2 30.855 34.485 87.719 0 36.4 ? H2D NAP 301 B 1 HETATM 67 H HO2N NAP . . . G 2 32.657 35.555 86.917 0 38.95 ? HO2N NAP 301 B 1 HETATM 68 H H1D NAP . . . G 2 29.763 37.434 87.993 0 34.25 ? H1D NAP 301 B 1 HETATM 69 H H2N NAP . . . G 2 29.132 34.097 89.499 0 27.08 ? H2N NAP 301 B 1 HETATM 70 H H71N NAP . . . G 2 28.932 31.315 91.801 0 24.75 ? H71N NAP 301 B 1 HETATM 71 H H72N NAP . . . G 2 28.754 32.313 90.437 0 24.75 ? H72N NAP 301 B 1 HETATM 72 H H4N NAP . . . G 2 30.728 35.386 93.307 0 26.5 ? H4N NAP 301 B 1 HETATM 73 H H5N NAP . . . G 2 31.085 37.606 92.354 0 27.09 ? H5N NAP 301 B 1 HETATM 74 H H6N NAP . . . G 2 30.66 38.016 89.991 0 28.09 ? H6N NAP 301 B 1 HETATM 75 H HOP2 NAP . . . G 2 30.505 25.967 79.86 0 41.76 ? HOP2 NAP 301 B 1 HETATM 76 H HOP3 NAP . . . G 2 28.217 25.297 78.318 0 44.71 ? HOP3 NAP 301 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 76 #