data_5LIY # _model_server_result.job_id gDrsrD4CeR6IKRLBuTzuzw _model_server_result.datetime_utc '2024-11-13 03:58:33' _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 5liy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5LIY # _exptl.entry_id 5LIY _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 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 120 _cell.entry_id 5LIY _cell.length_a 79.458 _cell.length_b 79.458 _cell.length_c 49.418 _cell.Z_PDB 3 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LIY _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A C VAL 32 X VAL 32 1_555 A N MLY 33 X MLY 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.363 ? covale ? covale2 A C MLY 33 X MLY 33 1_555 A N VAL 34 X VAL 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.279 ? covale ? covale3 A C GLU 61 X GLU 61 1_555 A N MLZ 62 X MLZ 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 A C MLZ 62 X MLZ 62 1_555 A N ILE 63 X ILE 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.243 ? covale ? covale5 A C GLU 94 X GLU 94 1_555 A N MLY 95 X MLY 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale6 A C MLY 95 X MLY 95 1_555 A N THR 96 X THR 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.273 ? covale ? covale7 A C VAL 154 X VAL 154 1_555 A N MLZ 155 X MLZ 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.313 ? covale ? covale8 A C MLZ 155 X MLZ 155 1_555 A N ALA 156 X ALA 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? covale ? covale9 A C LEU 176 X LEU 176 1_555 A N MLZ 177 X MLZ 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 A C MLZ 177 X MLZ 177 1_555 A N TYR 178 X TYR 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale11 A C SER 202 X SER 202 1_555 A N MLY 203 X MLY 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.264 ? covale ? covale12 A C MLY 203 X MLY 203 1_555 A N GLY 204 X GLY 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale13 A C HIS 241 X HIS 241 1_555 A N MLY 242 X MLY 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.271 ? covale ? covale14 A C MLY 242 X MLY 242 1_555 A N MLZ 243 X MLZ 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale15 A C MLZ 243 X MLZ 243 1_555 A N THR 244 X THR 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? covale ? covale16 A C PRO 262 X PRO 262 1_555 A N MLY 263 X MLY 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale17 A C MLY 263 X MLY 263 1_555 A N SER 264 X SER 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? # _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 338 n n PA O2A NAP sing 339 n n PA O5B NAP sing 340 n n PA O3 NAP sing 341 n n O2A HOA2 NAP sing 342 n n O5B C5B NAP sing 343 n n C5B C4B NAP sing 344 n n C5B H51A NAP sing 345 n n C5B H52A NAP sing 346 n n C4B O4B NAP sing 347 n n C4B C3B NAP sing 348 n n C4B H4B NAP sing 349 n n O4B C1B NAP sing 350 n n C3B O3B NAP sing 351 n n C3B C2B NAP sing 352 n n C3B H3B NAP sing 353 n n O3B HO3A NAP sing 354 n n C2B O2B NAP sing 355 n n C2B C1B NAP sing 356 n n C2B H2B NAP sing 357 n n O2B P2B NAP sing 358 n n C1B N9A NAP sing 359 n n C1B H1B NAP sing 360 n n N9A C8A NAP sing 361 n y N9A C4A NAP sing 362 n y C8A N7A NAP doub 363 n y C8A H8A NAP sing 364 n n N7A C5A NAP sing 365 n y C5A C6A NAP sing 366 n y C5A C4A NAP doub 367 n y C6A N6A NAP sing 368 n n C6A N1A NAP doub 369 n y N6A H61A NAP sing 370 n n N6A H62A NAP sing 371 n n N1A C2A NAP sing 372 n y C2A N3A NAP doub 373 n y C2A H2A NAP sing 374 n n N3A C4A NAP sing 375 n y O3 PN NAP sing 376 n n PN O1N NAP doub 377 n n PN O2N NAP sing 378 n n PN O5D NAP sing 379 n n O5D C5D NAP sing 380 n n C5D C4D NAP sing 381 n n C5D H51N NAP sing 382 n n C5D H52N NAP sing 383 n n C4D O4D NAP sing 384 n n C4D C3D NAP sing 385 n n C4D H4D NAP sing 386 n n O4D C1D NAP sing 387 n n C3D O3D NAP sing 388 n n C3D C2D NAP sing 389 n n C3D H3D NAP sing 390 n n O3D HO3N NAP sing 391 n n C2D O2D NAP sing 392 n n C2D C1D NAP sing 393 n n C2D H2D NAP sing 394 n n O2D HO2N NAP sing 395 n n C1D N1N NAP sing 396 n n C1D H1D NAP sing 397 n n N1N C2N NAP sing 398 n y N1N C6N NAP doub 399 n y C2N C3N NAP doub 400 n y C2N H2N NAP sing 401 n n C3N C7N NAP sing 402 n n C3N C4N NAP sing 403 n y C7N O7N NAP doub 404 n n C7N N7N NAP sing 405 n n N7N H71N NAP sing 406 n n N7N H72N NAP sing 407 n n C4N C5N NAP doub 408 n y C4N H4N NAP sing 409 n n C5N C6N NAP sing 410 n y C5N H5N NAP sing 411 n n C6N H6N NAP sing 412 n n P2B O1X NAP doub 413 n n P2B O2X NAP sing 414 n n P2B O3X NAP sing 415 n n O2X HOP2 NAP sing 416 n n O3X HOP3 NAP sing 417 n n # _atom_sites.entry_id 5LIY _atom_sites.fract_transf_matrix[1][1] 0.012585 _atom_sites.fract_transf_matrix[1][2] 0.007266 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014532 _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] 0.020236 _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 B 2 NAP X 1 401 350 NAP NAP . C 3 DQP X 1 402 900 DQP DQP . D 4 EDO X 1 403 1 EDO EDO . E 5 HOH X 1 501 4 HOH HOH . E 5 HOH X 2 502 1 HOH HOH . E 5 HOH X 3 503 10 HOH HOH . E 5 HOH X 4 504 17 HOH HOH . E 5 HOH X 5 505 1 HOH HOH . E 5 HOH X 6 506 15 HOH HOH . E 5 HOH X 7 507 14 HOH HOH . E 5 HOH X 8 508 11 HOH HOH . E 5 HOH X 9 509 20 HOH HOH . E 5 HOH X 10 510 6 HOH HOH . E 5 HOH X 11 511 5 HOH HOH . E 5 HOH X 12 512 7 HOH HOH . E 5 HOH X 13 513 3 HOH HOH . E 5 HOH X 14 514 3 HOH HOH . E 5 HOH X 15 515 12 HOH HOH . E 5 HOH X 16 516 13 HOH HOH . E 5 HOH X 17 517 11 HOH HOH . E 5 HOH X 18 518 5 HOH HOH . E 5 HOH X 19 519 8 HOH HOH . E 5 HOH X 20 520 13 HOH HOH . E 5 HOH X 21 521 10 HOH HOH . E 5 HOH X 22 522 19 HOH HOH . E 5 HOH X 23 523 18 HOH HOH . E 5 HOH X 24 524 9 HOH HOH . E 5 HOH X 25 525 23 HOH HOH . E 5 HOH X 26 526 4 HOH HOH . E 5 HOH X 27 527 21 HOH HOH . E 5 HOH X 28 528 4 HOH HOH . E 5 HOH X 29 529 22 HOH HOH . E 5 HOH X 30 530 15 HOH HOH . E 5 HOH X 31 531 6 HOH HOH . E 5 HOH X 32 532 8 HOH HOH . E 5 HOH X 33 533 2 HOH HOH . E 5 HOH X 34 534 12 HOH HOH . E 5 HOH X 35 535 9 HOH HOH . E 5 HOH X 36 536 2 HOH HOH . E 5 HOH X 37 537 14 HOH HOH . E 5 HOH X 38 538 2 HOH HOH . E 5 HOH X 39 539 16 HOH HOH . E 5 HOH X 40 540 16 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 . . . B 2 -9.719 35.651 -3.54 1 29.33 ? PA NAP 401 X 1 HETATM 2 O O1A NAP . . . B 2 -10.574 35.407 -4.751 1 25.87 ? O1A NAP 401 X 1 HETATM 3 O O2A NAP . . . B 2 -10.318 35.587 -2.156 1 27.67 ? O2A NAP 401 X 1 HETATM 4 O O5B NAP . . . B 2 -9.032 37.089 -3.69 1 27.26 ? O5B NAP 401 X 1 HETATM 5 C C5B NAP . . . B 2 -8.012 37.505 -2.779 1 27.51 ? C5B NAP 401 X 1 HETATM 6 C C4B NAP . . . B 2 -7.418 38.821 -3.284 1 31.79 ? C4B NAP 401 X 1 HETATM 7 O O4B NAP . . . B 2 -8.456 39.783 -3.488 1 32.33 ? O4B NAP 401 X 1 HETATM 8 C C3B NAP . . . B 2 -6.44 39.475 -2.327 1 28.93 ? C3B NAP 401 X 1 HETATM 9 O O3B NAP . . . B 2 -5.39 40.084 -3.079 1 33.52 ? O3B NAP 401 X 1 HETATM 10 C C2B NAP . . . B 2 -7.216 40.59 -1.682 1 28.71 ? C2B NAP 401 X 1 HETATM 11 O O2B NAP . . . B 2 -6.342 41.67 -1.38 1 24.83 ? O2B NAP 401 X 1 HETATM 12 C C1B NAP . . . B 2 -8.197 40.987 -2.758 1 25.87 ? C1B NAP 401 X 1 HETATM 13 N N9A NAP . . . B 2 -9.502 41.456 -2.218 1 26.71 ? N9A NAP 401 X 1 HETATM 14 C C8A NAP . . . B 2 -10.182 40.905 -1.194 1 33.15 ? C8A NAP 401 X 1 HETATM 15 N N7A NAP . . . B 2 -11.333 41.603 -1.014 1 31.05 ? N7A NAP 401 X 1 HETATM 16 C C5A NAP . . . B 2 -11.366 42.584 -1.938 1 27.38 ? C5A NAP 401 X 1 HETATM 17 C C6A NAP . . . B 2 -12.28 43.579 -2.233 1 27.78 ? C6A NAP 401 X 1 HETATM 18 N N6A NAP . . . B 2 -13.412 43.7 -1.505 1 26.88 ? N6A NAP 401 X 1 HETATM 19 N N1A NAP . . . B 2 -12.014 44.435 -3.243 1 32 ? N1A NAP 401 X 1 HETATM 20 C C2A NAP . . . B 2 -10.889 44.341 -3.964 1 29.42 ? C2A NAP 401 X 1 HETATM 21 N N3A NAP . . . B 2 -9.989 43.378 -3.703 1 30.45 ? N3A NAP 401 X 1 HETATM 22 C C4A NAP . . . B 2 -10.209 42.492 -2.692 1 29.7 ? C4A NAP 401 X 1 HETATM 23 O O3 NAP . . . B 2 -8.367 34.794 -3.668 1 32.82 ? O3 NAP 401 X 1 HETATM 24 P PN NAP . . . B 2 -7.938 33.436 -2.906 1 34.41 ? PN NAP 401 X 1 HETATM 25 O O1N NAP . . . B 2 -7.174 33.884 -1.678 1 36.84 ? O1N NAP 401 X 1 HETATM 26 O O2N NAP . . . B 2 -7.24 32.559 -3.915 1 39.68 ? O2N NAP 401 X 1 HETATM 27 O O5D NAP . . . B 2 -9.285 32.658 -2.474 1 37.51 ? O5D NAP 401 X 1 HETATM 28 C C5D NAP . . . B 2 -9.832 32.81 -1.174 1 22.5 ? C5D NAP 401 X 1 HETATM 29 C C4D NAP . . . B 2 -9.41 31.678 -0.224 1 23.37 ? C4D NAP 401 X 1 HETATM 30 O O4D NAP . . . B 2 -9.692 30.38 -0.767 1 37.06 ? O4D NAP 401 X 1 HETATM 31 C C3D NAP . . . B 2 -7.927 31.581 0.079 1 26.19 ? C3D NAP 401 X 1 HETATM 32 O O3D NAP . . . B 2 -7.385 32.657 0.867 1 34.02 ? O3D NAP 401 X 1 HETATM 33 C C2D NAP . . . B 2 -7.855 30.221 0.741 1 28.65 ? C2D NAP 401 X 1 HETATM 34 O O2D NAP . . . B 2 -8.233 30.302 2.143 1 30.82 ? O2D NAP 401 X 1 HETATM 35 C C1D NAP . . . B 2 -8.812 29.422 -0.154 1 37.11 ? C1D NAP 401 X 1 HETATM 36 N N1N NAP . . . B 2 -7.939 28.735 -1.139 1 36.32 ? N1N NAP 401 X 1 HETATM 37 C C2N NAP . . . B 2 -8.03 27.327 -1.182 1 32.92 ? C2N NAP 401 X 1 HETATM 38 C C3N NAP . . . B 2 -7.531 26.61 -2.26 1 33.36 ? C3N NAP 401 X 1 HETATM 39 C C7N NAP . . . B 2 -7.594 25.117 -2.206 1 37.25 ? C7N NAP 401 X 1 HETATM 40 O O7N NAP . . . B 2 -6.963 24.48 -3.031 1 31.29 ? O7N NAP 401 X 1 HETATM 41 N N7N NAP . . . B 2 -8.369 24.558 -1.261 1 25.23 ? N7N NAP 401 X 1 HETATM 42 C C4N NAP . . . B 2 -7.046 27.262 -3.384 1 36.27 ? C4N NAP 401 X 1 HETATM 43 C C5N NAP . . . B 2 -7.026 28.655 -3.427 1 36.41 ? C5N NAP 401 X 1 HETATM 44 C C6N NAP . . . B 2 -7.522 29.381 -2.337 1 40.22 ? C6N NAP 401 X 1 HETATM 45 P P2B NAP . . . B 2 -5.82 41.972 0.122 1 31.84 ? P2B NAP 401 X 1 HETATM 46 O O1X NAP . . . B 2 -5.611 40.639 0.793 1 31.08 ? O1X NAP 401 X 1 HETATM 47 O O2X NAP . . . B 2 -4.533 42.743 -0.041 1 32.64 ? O2X NAP 401 X 1 HETATM 48 O O3X NAP . . . B 2 -6.96 42.744 0.729 1 31.95 ? O3X NAP 401 X 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 48 #