data_2VQB # _model_server_result.job_id d4-wt9foHR2Kez0ds_anGw _model_server_result.datetime_utc '2024-11-24 21:22:02' _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 2vqb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":501}' # _entry.id 2VQB # _exptl.entry_id 2VQB _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 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 120 _cell.entry_id 2VQB _cell.length_a 218.665 _cell.length_b 218.665 _cell.length_c 130.676 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VQB _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS dimeric 2 author_and_software_defined_assembly 1 PQS 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,D,E,F,G,H,I,J,W,X,Y,Z,AA,BA 1 1 B,C,K,L,M,N,O,P,Q,R,S,T,U,V 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 ? 3 F N N ? 3 L N N ? 3 R N N ? 3 X 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 359 n n PA O2A NAP sing 360 n n PA O5B NAP sing 361 n n PA O3 NAP sing 362 n n O2A HOA2 NAP sing 363 n n O5B C5B NAP sing 364 n n C5B C4B NAP sing 365 n n C5B H51A NAP sing 366 n n C5B H52A NAP sing 367 n n C4B O4B NAP sing 368 n n C4B C3B NAP sing 369 n n C4B H4B NAP sing 370 n n O4B C1B NAP sing 371 n n C3B O3B NAP sing 372 n n C3B C2B NAP sing 373 n n C3B H3B NAP sing 374 n n O3B HO3A NAP sing 375 n n C2B O2B NAP sing 376 n n C2B C1B NAP sing 377 n n C2B H2B NAP sing 378 n n O2B P2B NAP sing 379 n n C1B N9A NAP sing 380 n n C1B H1B NAP sing 381 n n N9A C8A NAP sing 382 n y N9A C4A NAP sing 383 n y C8A N7A NAP doub 384 n y C8A H8A NAP sing 385 n n N7A C5A NAP sing 386 n y C5A C6A NAP sing 387 n y C5A C4A NAP doub 388 n y C6A N6A NAP sing 389 n n C6A N1A NAP doub 390 n y N6A H61A NAP sing 391 n n N6A H62A NAP sing 392 n n N1A C2A NAP sing 393 n y C2A N3A NAP doub 394 n y C2A H2A NAP sing 395 n n N3A C4A NAP sing 396 n y O3 PN NAP sing 397 n n PN O1N NAP doub 398 n n PN O2N NAP sing 399 n n PN O5D NAP sing 400 n n O5D C5D NAP sing 401 n n C5D C4D NAP sing 402 n n C5D H51N NAP sing 403 n n C5D H52N NAP sing 404 n n C4D O4D NAP sing 405 n n C4D C3D NAP sing 406 n n C4D H4D NAP sing 407 n n O4D C1D NAP sing 408 n n C3D O3D NAP sing 409 n n C3D C2D NAP sing 410 n n C3D H3D NAP sing 411 n n O3D HO3N NAP sing 412 n n C2D O2D NAP sing 413 n n C2D C1D NAP sing 414 n n C2D H2D NAP sing 415 n n O2D HO2N NAP sing 416 n n C1D N1N NAP sing 417 n n C1D H1D NAP sing 418 n n N1N C2N NAP sing 419 n y N1N C6N NAP doub 420 n y C2N C3N NAP doub 421 n y C2N H2N NAP sing 422 n n C3N C7N NAP sing 423 n n C3N C4N NAP sing 424 n y C7N O7N NAP doub 425 n n C7N N7N NAP sing 426 n n N7N H71N NAP sing 427 n n N7N H72N NAP sing 428 n n C4N C5N NAP doub 429 n y C4N H4N NAP sing 430 n n C5N C6N NAP sing 431 n y C5N H5N NAP sing 432 n n C6N H6N NAP sing 433 n n P2B O1X NAP doub 434 n n P2B O2X NAP sing 435 n n P2B O3X NAP sing 436 n n O2X HOP2 NAP sing 437 n n O3X HOP3 NAP sing 438 n n # _atom_sites.entry_id 2VQB _atom_sites.fract_transf_matrix[1][1] 0.004573 _atom_sites.fract_transf_matrix[1][2] 0.00264 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005281 _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] 0.007653 _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 FAD A 1 500 500 FAD FAD . F 3 NAP A 1 501 501 NAP NAP . G 4 CL A 1 1451 1451 CL CL . H 5 EPE A 1 1452 1452 EPE EPE . I 6 OXY A 1 1453 1453 OXY OXY . J 6 OXY A 1 1454 1454 OXY OXY . K 2 FAD B 1 500 500 FAD FAD . L 3 NAP B 1 501 501 NAP NAP . M 4 CL B 1 1451 1451 CL CL . N 5 EPE B 1 1452 1452 EPE EPE . O 6 OXY B 1 1453 1453 OXY OXY . P 6 OXY B 1 1454 1454 OXY OXY . Q 2 FAD C 1 500 500 FAD FAD . R 3 NAP C 1 501 501 NAP NAP . S 5 EPE C 1 1451 1451 EPE EPE . T 6 OXY C 1 1452 1452 OXY OXY . U 6 OXY C 1 1453 1453 OXY OXY . V 4 CL C 1 1454 1454 CL CL . W 2 FAD D 1 500 500 FAD FAD . X 3 NAP D 1 501 501 NAP NAP . Y 4 CL D 1 1451 1451 CL CL . Z 5 EPE D 1 1452 1452 EPE EPE . AA 6 OXY D 1 1453 1453 OXY OXY . BA 6 OXY D 1 1454 1454 OXY OXY . # 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 . . . R 3 -24.674 229.255 -13.755 1 45.37 ? PA NAP 501 C 1 HETATM 2 O O1A NAP . . . R 3 -25.053 230.407 -14.615 1 44.65 ? O1A NAP 501 C 1 HETATM 3 O O2A NAP . . . R 3 -25.705 228.03 -13.999 1 43.58 ? O2A NAP 501 C 1 HETATM 4 O O5B NAP . . . R 3 -23.185 228.689 -14.048 1 46.41 ? O5B NAP 501 C 1 HETATM 5 C C5B NAP . . . R 3 -22.954 227.31 -13.712 1 44.71 ? C5B NAP 501 C 1 HETATM 6 C C4B NAP . . . R 3 -21.428 227.12 -13.854 1 45.15 ? C4B NAP 501 C 1 HETATM 7 O O4B NAP . . . R 3 -20.874 226.25 -12.851 1 44.76 ? O4B NAP 501 C 1 HETATM 8 C C3B NAP . . . R 3 -21.047 226.518 -15.234 1 45.94 ? C3B NAP 501 C 1 HETATM 9 O O3B NAP . . . R 3 -19.92 227.242 -15.775 1 47.35 ? O3B NAP 501 C 1 HETATM 10 C C2B NAP . . . R 3 -20.694 225.039 -14.893 1 45.27 ? C2B NAP 501 C 1 HETATM 11 O O2B NAP . . . R 3 -19.652 224.429 -15.667 1 47.88 ? O2B NAP 501 C 1 HETATM 12 C C1B NAP . . . R 3 -20.012 225.305 -13.542 1 44.62 ? C1B NAP 501 C 1 HETATM 13 N N9A NAP . . . R 3 -19.854 224.031 -12.852 1 44.62 ? N9A NAP 501 C 1 HETATM 14 C C8A NAP . . . R 3 -20.87 223.198 -12.442 1 44.03 ? C8A NAP 501 C 1 HETATM 15 N N7A NAP . . . R 3 -20.391 222.121 -11.857 1 43.73 ? N7A NAP 501 C 1 HETATM 16 C C5A NAP . . . R 3 -19.029 222.198 -11.857 1 43.7 ? C5A NAP 501 C 1 HETATM 17 C C6A NAP . . . R 3 -18.01 221.336 -11.376 1 44.39 ? C6A NAP 501 C 1 HETATM 18 N N6A NAP . . . R 3 -18.366 220.146 -10.742 1 44.49 ? N6A NAP 501 C 1 HETATM 19 N N1A NAP . . . R 3 -16.732 221.707 -11.54 1 44.59 ? N1A NAP 501 C 1 HETATM 20 C C2A NAP . . . R 3 -16.452 222.867 -12.169 1 44.43 ? C2A NAP 501 C 1 HETATM 21 N N3A NAP . . . R 3 -17.364 223.72 -12.66 1 43.9 ? N3A NAP 501 C 1 HETATM 22 C C4A NAP . . . R 3 -18.663 223.421 -12.517 1 43.72 ? C4A NAP 501 C 1 HETATM 23 O O3 NAP . . . R 3 -24.703 229.775 -12.239 1 45.31 ? O3 NAP 501 C 1 HETATM 24 P PN NAP . . . R 3 -23.922 231.169 -11.885 1 45.66 ? PN NAP 501 C 1 HETATM 25 O O1N NAP . . . R 3 -22.707 231.432 -12.825 1 45.83 ? O1N NAP 501 C 1 HETATM 26 O O2N NAP . . . R 3 -23.419 231.034 -10.398 1 44.61 ? O2N NAP 501 C 1 HETATM 27 O O5D NAP . . . R 3 -24.889 232.46 -11.945 1 44.37 ? O5D NAP 501 C 1 HETATM 28 C C5D NAP . . . R 3 -26.238 232.076 -12.241 1 42.14 ? C5D NAP 501 C 1 HETATM 29 C C4D NAP . . . R 3 -27.131 233.306 -12.099 1 41.7 ? C4D NAP 501 C 1 HETATM 30 O O4D NAP . . . R 3 -26.562 234.267 -11.159 1 43.18 ? O4D NAP 501 C 1 HETATM 31 C C3D NAP . . . R 3 -27.268 234.034 -13.441 1 41.35 ? C3D NAP 501 C 1 HETATM 32 O O3D NAP . . . R 3 -28.628 234.422 -13.554 1 41.25 ? O3D NAP 501 C 1 HETATM 33 C C2D NAP . . . R 3 -26.342 235.279 -13.332 1 41.71 ? C2D NAP 501 C 1 HETATM 34 O O2D NAP . . . R 3 -26.856 236.412 -14.04 1 43.8 ? O2D NAP 501 C 1 HETATM 35 C C1D NAP . . . R 3 -26.4 235.567 -11.826 1 42.48 ? C1D NAP 501 C 1 HETATM 36 N N1N NAP . . . R 3 -25.236 236.338 -11.325 1 42.63 ? N1N NAP 501 C 1 HETATM 37 C C2N NAP . . . R 3 -25.164 237.639 -11.575 1 42.12 ? C2N NAP 501 C 1 HETATM 38 C C3N NAP . . . R 3 -24.1 238.432 -11.09 1 43.13 ? C3N NAP 501 C 1 HETATM 39 C C7N NAP . . . R 3 -24.042 239.89 -11.38 1 43.83 ? C7N NAP 501 C 1 HETATM 40 O O7N NAP . . . R 3 -22.938 240.411 -11.501 1 47.32 ? O7N NAP 501 C 1 HETATM 41 N N7N NAP . . . R 3 -25.176 240.649 -11.501 1 42.96 ? N7N NAP 501 C 1 HETATM 42 C C4N NAP . . . R 3 -23.082 237.823 -10.327 1 41.51 ? C4N NAP 501 C 1 HETATM 43 C C5N NAP . . . R 3 -23.197 236.443 -10.095 1 41.66 ? C5N NAP 501 C 1 HETATM 44 C C6N NAP . . . R 3 -24.291 235.732 -10.606 1 41.87 ? C6N NAP 501 C 1 HETATM 45 P P2B NAP . . . R 3 -20.187 224.044 -17.149 1 52.07 ? P2B NAP 501 C 1 HETATM 46 O O1X NAP . . . R 3 -20.209 225.28 -18 1 50.53 ? O1X NAP 501 C 1 HETATM 47 O O2X NAP . . . R 3 -19.169 222.952 -17.793 1 50.82 ? O2X NAP 501 C 1 HETATM 48 O O3X NAP . . . R 3 -21.678 223.404 -17.058 1 50.33 ? O3X NAP 501 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 48 #