data_7RDU # _model_server_result.job_id SV927QQV0czisYzlQgppqg _model_server_result.datetime_utc '2025-01-03 00:30:44' _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 7rdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 7RDU # _exptl.entry_id 7RDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 745.421 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADPH DIHYDRO-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 7RDU _cell.length_a 130.108 _cell.length_b 130.108 _cell.length_c 130.108 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RDU _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 metalc ? metalc1 A OD1 ASP 191 A ASP 192 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc2 A OE2 GLU 195 A GLU 196 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? metalc ? metalc3 A OE2 GLU 227 A GLU 228 1_555 B MG MG . A MG 401 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc4 A OE1 GLU 231 A GLU 232 1_555 B MG MG . A MG 401 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc5 B MG MG . A MG 401 1_555 F O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc6 B MG MG . A MG 401 1_555 F O HOH . A HOH 522 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc7 B MG MG . A MG 401 1_555 F O HOH . A HOH 534 3_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? # _chem_comp.formula 'C21 H30 N7 O17 P3' _chem_comp.formula_weight 745.421 _chem_comp.id NDP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 NDP doub 317 n n PA O2A NDP sing 318 n n PA O5B NDP sing 319 n n PA O3 NDP sing 320 n n O2A HOA2 NDP sing 321 n n O5B C5B NDP sing 322 n n C5B C4B NDP sing 323 n n C5B H51A NDP sing 324 n n C5B H52A NDP sing 325 n n C4B O4B NDP sing 326 n n C4B C3B NDP sing 327 n n C4B H4B NDP sing 328 n n O4B C1B NDP sing 329 n n C3B O3B NDP sing 330 n n C3B C2B NDP sing 331 n n C3B H3B NDP sing 332 n n O3B HO3A NDP sing 333 n n C2B O2B NDP sing 334 n n C2B C1B NDP sing 335 n n C2B H2B NDP sing 336 n n O2B P2B NDP sing 337 n n C1B N9A NDP sing 338 n n C1B H1B NDP sing 339 n n N9A C8A NDP sing 340 n y N9A C4A NDP sing 341 n y C8A N7A NDP doub 342 n y C8A H8A NDP sing 343 n n N7A C5A NDP sing 344 n y C5A C6A NDP sing 345 n y C5A C4A NDP doub 346 n y C6A N6A NDP sing 347 n n C6A N1A NDP doub 348 n y N6A H61A NDP sing 349 n n N6A H62A NDP sing 350 n n N1A C2A NDP sing 351 n y C2A N3A NDP doub 352 n y C2A H2A NDP sing 353 n n N3A C4A NDP sing 354 n y O3 PN NDP sing 355 n n PN O1N NDP doub 356 n n PN O2N NDP sing 357 n n PN O5D NDP sing 358 n n O2N H21N NDP sing 359 n n O5D C5D NDP sing 360 n n C5D C4D NDP sing 361 n n C5D H51N NDP sing 362 n n C5D H52N NDP sing 363 n n C4D O4D NDP sing 364 n n C4D C3D NDP sing 365 n n C4D H4D NDP sing 366 n n O4D C1D NDP sing 367 n n C3D O3D NDP sing 368 n n C3D C2D NDP sing 369 n n C3D H3D NDP sing 370 n n O3D HO3N NDP sing 371 n n C2D O2D NDP sing 372 n n C2D C1D NDP sing 373 n n C2D H2D NDP sing 374 n n O2D HO2N NDP sing 375 n n C1D N1N NDP sing 376 n n C1D H1D NDP sing 377 n n N1N C2N NDP sing 378 n n N1N C6N NDP sing 379 n n C2N C3N NDP doub 380 n n C2N H2N NDP sing 381 n n C3N C7N NDP sing 382 n n C3N C4N NDP sing 383 n n C7N O7N NDP doub 384 n n C7N N7N NDP sing 385 n n N7N H71N NDP sing 386 n n N7N H72N NDP sing 387 n n C4N C5N NDP sing 388 n n C4N H41N NDP sing 389 n n C4N H42N NDP sing 390 n n C5N C6N NDP doub 391 n n C5N H5N NDP sing 392 n n C6N H6N NDP sing 393 n n P2B O1X NDP doub 394 n n P2B O2X NDP sing 395 n n P2B O3X NDP sing 396 n n O2X HOP2 NDP sing 397 n n O3X HOP3 NDP sing 398 n n # _atom_sites.entry_id 7RDU _atom_sites.fract_transf_matrix[1][1] 0.007686 _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] 0.007686 _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] 0.007686 _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 MG A 1 401 341 MG MG . C 2 MG A 1 402 342 MG MG . D 3 NAP A 1 403 1 NAP RED . E 4 NDP A 1 404 1 NDP NDP . F 5 HOH A 1 501 27 HOH HOH . F 5 HOH A 2 502 38 HOH HOH . F 5 HOH A 3 503 2 HOH HOH . F 5 HOH A 4 504 37 HOH HOH . F 5 HOH A 5 505 45 HOH HOH . F 5 HOH A 6 506 24 HOH HOH . F 5 HOH A 7 507 36 HOH HOH . F 5 HOH A 8 508 13 HOH HOH . F 5 HOH A 9 509 25 HOH HOH . F 5 HOH A 10 510 1 HOH HOH . F 5 HOH A 11 511 4 HOH HOH . F 5 HOH A 12 512 26 HOH HOH . F 5 HOH A 13 513 10 HOH HOH . F 5 HOH A 14 514 30 HOH HOH . F 5 HOH A 15 515 15 HOH HOH . F 5 HOH A 16 516 16 HOH HOH . F 5 HOH A 17 517 6 HOH HOH . F 5 HOH A 18 518 20 HOH HOH . F 5 HOH A 19 519 22 HOH HOH . F 5 HOH A 20 520 11 HOH HOH . F 5 HOH A 21 521 14 HOH HOH . F 5 HOH A 22 522 42 HOH HOH . F 5 HOH A 23 523 19 HOH HOH . F 5 HOH A 24 524 5 HOH HOH . F 5 HOH A 25 525 23 HOH HOH . F 5 HOH A 26 526 34 HOH HOH . F 5 HOH A 27 527 7 HOH HOH . F 5 HOH A 28 528 8 HOH HOH . F 5 HOH A 29 529 35 HOH HOH . F 5 HOH A 30 530 31 HOH HOH . F 5 HOH A 31 531 17 HOH HOH . F 5 HOH A 32 532 9 HOH HOH . F 5 HOH A 33 533 12 HOH HOH . F 5 HOH A 34 534 43 HOH HOH . F 5 HOH A 35 535 32 HOH HOH . F 5 HOH A 36 536 39 HOH HOH . F 5 HOH A 37 537 21 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 NDP . B . E 4 -12.728 45.914 -17.171 0.55 75.84 ? PA NDP 404 A 1 HETATM 2 O O1A NDP . B . E 4 -11.958 46.824 -16.278 0.55 74.43 -1 O1A NDP 404 A 1 HETATM 3 O O2A NDP . B . E 4 -14.012 45.277 -16.721 0.55 75.06 ? O2A NDP 404 A 1 HETATM 4 O O5B NDP . B . E 4 -12.956 46.653 -18.621 0.55 75.5 ? O5B NDP 404 A 1 HETATM 5 C C5B NDP . B . E 4 -14.333 46.615 -18.802 0.55 75.28 ? C5B NDP 404 A 1 HETATM 6 C C4B NDP . B . E 4 -14.687 47.504 -19.966 0.55 75.62 ? C4B NDP 404 A 1 HETATM 7 O O4B NDP . B . E 4 -15.301 46.724 -20.994 0.55 76.07 ? O4B NDP 404 A 1 HETATM 8 C C3B NDP . B . E 4 -15.687 48.561 -19.449 0.55 76.05 ? C3B NDP 404 A 1 HETATM 9 O O3B NDP . B . E 4 -15.476 49.769 -20.11 0.55 74.95 ? O3B NDP 404 A 1 HETATM 10 C C2B NDP . B . E 4 -17.028 47.955 -19.907 0.55 75.95 ? C2B NDP 404 A 1 HETATM 11 O O2B NDP . B . E 4 -17.986 48.855 -20.115 0.55 76.81 ? O2B NDP 404 A 1 HETATM 12 C C1B NDP . B . E 4 -16.559 47.335 -21.267 0.55 76.08 ? C1B NDP 404 A 1 HETATM 13 N N9A NDP . B . E 4 -17.483 46.304 -21.765 0.55 75.94 ? N9A NDP 404 A 1 HETATM 14 C C8A NDP . B . E 4 -18.013 45.196 -21.078 0.55 76.05 ? C8A NDP 404 A 1 HETATM 15 N N7A NDP . B . E 4 -18.84 44.442 -21.836 0.55 75.93 ? N7A NDP 404 A 1 HETATM 16 C C5A NDP . B . E 4 -18.844 45.103 -23.08 0.55 76.22 ? C5A NDP 404 A 1 HETATM 17 C C6A NDP . B . E 4 -19.504 44.826 -24.291 0.55 76.94 ? C6A NDP 404 A 1 HETATM 18 N N6A NDP . B . E 4 -20.331 43.724 -24.4 0.55 76.27 ? N6A NDP 404 A 1 HETATM 19 N N1A NDP . B . E 4 -19.349 45.629 -25.387 0.55 77.2 ? N1A NDP 404 A 1 HETATM 20 C C2A NDP . B . E 4 -18.509 46.707 -25.204 0.55 76.8 ? C2A NDP 404 A 1 HETATM 21 N N3A NDP . B . E 4 -17.814 47.105 -24.126 0.55 75.96 ? N3A NDP 404 A 1 HETATM 22 C C4A NDP . B . E 4 -18.003 46.264 -23.049 0.55 75.87 ? C4A NDP 404 A 1 HETATM 23 O O3 NDP . B . E 4 -11.654 44.682 -17.368 0.55 73.72 ? O3 NDP 404 A 1 HETATM 24 P PN NDP . B . E 4 -10.21 45.304 -17.619 0.55 72.2 ? PN NDP 404 A 1 HETATM 25 O O1N NDP . B . E 4 -10.295 46.3 -18.707 0.55 73.43 -1 O1N NDP 404 A 1 HETATM 26 O O2N NDP . B . E 4 -9.396 45.505 -16.36 0.55 72.96 ? O2N NDP 404 A 1 HETATM 27 O O5D NDP . B . E 4 -9.263 44.057 -18.407 0.55 70.63 ? O5D NDP 404 A 1 HETATM 28 C C5D NDP . B . E 4 -9.274 44.365 -19.741 0.55 70.37 ? C5D NDP 404 A 1 HETATM 29 C C4D NDP . B . E 4 -8.213 43.534 -20.419 0.55 68.79 ? C4D NDP 404 A 1 HETATM 30 O O4D NDP . B . E 4 -6.92 43.928 -19.925 0.55 68.68 ? O4D NDP 404 A 1 HETATM 31 C C3D NDP . B . E 4 -8.442 42.052 -20.007 0.55 68.46 ? C3D NDP 404 A 1 HETATM 32 O O3D NDP . B . E 4 -8.435 41.27 -21.155 0.55 66.29 ? O3D NDP 404 A 1 HETATM 33 C C2D NDP . B . E 4 -7.239 41.743 -19.094 0.55 68.68 ? C2D NDP 404 A 1 HETATM 34 O O2D NDP . B . E 4 -6.731 40.459 -19.281 0.55 66.85 ? O2D NDP 404 A 1 HETATM 35 C C1D NDP . B . E 4 -6.185 42.767 -19.611 0.55 68.3 ? C1D NDP 404 A 1 HETATM 36 N N1N NDP . B . E 4 -5.218 43.104 -18.542 0.55 68.36 ? N1N NDP 404 A 1 HETATM 37 C C2N NDP . B . E 4 -5.681 43.58 -17.338 0.55 69.55 ? C2N NDP 404 A 1 HETATM 38 C C3N NDP . B . E 4 -4.842 43.73 -16.277 0.55 69.7 ? C3N NDP 404 A 1 HETATM 39 C C7N NDP . B . E 4 -5.443 44.247 -15.059 0.55 69.71 ? C7N NDP 404 A 1 HETATM 40 O O7N NDP . B . E 4 -4.847 44.386 -13.982 0.55 69.77 ? O7N NDP 404 A 1 HETATM 41 N N7N NDP . B . E 4 -6.78 44.609 -15.137 0.55 69.64 ? N7N NDP 404 A 1 HETATM 42 C C4N NDP . B . E 4 -3.391 43.385 -16.348 0.55 68.24 ? C4N NDP 404 A 1 HETATM 43 C C5N NDP . B . E 4 -2.954 43.099 -17.742 0.55 66.96 ? C5N NDP 404 A 1 HETATM 44 C C6N NDP . B . E 4 -3.826 42.967 -18.748 0.55 66.91 ? C6N NDP 404 A 1 HETATM 45 P P2B NDP . B . E 4 -18.987 49.14 -18.597 0.55 77.24 ? P2B NDP 404 A 1 HETATM 46 O O1X NDP . B . E 4 -18.051 50.116 -17.955 0.55 75.1 ? O1X NDP 404 A 1 HETATM 47 O O2X NDP . B . E 4 -19.101 47.75 -17.963 0.55 76.88 -1 O2X NDP 404 A 1 HETATM 48 O O3X NDP . B . E 4 -20.214 49.693 -19.267 0.55 77.69 ? O3X NDP 404 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 48 #