data_3RU3 # _model_server_result.job_id yu5LuBhMVELy4PKtMK_b-g _model_server_result.datetime_utc '2024-11-15 00:19:16' _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 3ru3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":493}' # _entry.id 3RU3 # _exptl.entry_id 3RU3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 745.421 _entity.id 5 _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 3RU3 _cell.length_a 120.943 _cell.length_b 120.943 _cell.length_c 154.802 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RU3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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,G,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 6 'crystal symmetry operation' 6_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 7 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _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 ASN 64 A ASN 52 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc2 A O ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.887 ? metalc ? metalc3 A OD1 ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.498 ? metalc ? metalc4 A O PHE 129 A PHE 117 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc5 A O VAL 158 A VAL 146 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.246 ? metalc ? metalc6 A O VAL 160 A VAL 148 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc7 A OG SER 162 A SER 150 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? metalc ? metalc8 D MG MG . A MG 492 1_555 F O1B ATP . A ATP 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc9 D MG MG . A MG 492 1_555 H O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? # _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 286 n n PA O2A NDP sing 287 n n PA O5B NDP sing 288 n n PA O3 NDP sing 289 n n O2A HOA2 NDP sing 290 n n O5B C5B NDP sing 291 n n C5B C4B NDP sing 292 n n C5B H51A NDP sing 293 n n C5B H52A NDP sing 294 n n C4B O4B NDP sing 295 n n C4B C3B NDP sing 296 n n C4B H4B NDP sing 297 n n O4B C1B NDP sing 298 n n C3B O3B NDP sing 299 n n C3B C2B NDP sing 300 n n C3B H3B NDP sing 301 n n O3B HO3A NDP sing 302 n n C2B O2B NDP sing 303 n n C2B C1B NDP sing 304 n n C2B H2B NDP sing 305 n n O2B P2B NDP sing 306 n n C1B N9A NDP sing 307 n n C1B H1B NDP sing 308 n n N9A C8A NDP sing 309 n y N9A C4A NDP sing 310 n y C8A N7A NDP doub 311 n y C8A H8A NDP sing 312 n n N7A C5A NDP sing 313 n y C5A C6A NDP sing 314 n y C5A C4A NDP doub 315 n y C6A N6A NDP sing 316 n n C6A N1A NDP doub 317 n y N6A H61A NDP sing 318 n n N6A H62A NDP sing 319 n n N1A C2A NDP sing 320 n y C2A N3A NDP doub 321 n y C2A H2A NDP sing 322 n n N3A C4A NDP sing 323 n y O3 PN NDP sing 324 n n PN O1N NDP doub 325 n n PN O2N NDP sing 326 n n PN O5D NDP sing 327 n n O2N H21N NDP sing 328 n n O5D C5D NDP sing 329 n n C5D C4D NDP sing 330 n n C5D H51N NDP sing 331 n n C5D H52N NDP sing 332 n n C4D O4D NDP sing 333 n n C4D C3D NDP sing 334 n n C4D H4D NDP sing 335 n n O4D C1D NDP sing 336 n n C3D O3D NDP sing 337 n n C3D C2D NDP sing 338 n n C3D H3D NDP sing 339 n n O3D HO3N NDP sing 340 n n C2D O2D NDP sing 341 n n C2D C1D NDP sing 342 n n C2D H2D NDP sing 343 n n O2D HO2N NDP sing 344 n n C1D N1N NDP sing 345 n n C1D H1D NDP sing 346 n n N1N C2N NDP sing 347 n n N1N C6N NDP sing 348 n n C2N C3N NDP doub 349 n n C2N H2N NDP sing 350 n n C3N C7N NDP sing 351 n n C3N C4N NDP sing 352 n n C7N O7N NDP doub 353 n n C7N N7N NDP sing 354 n n N7N H71N NDP sing 355 n n N7N H72N NDP sing 356 n n C4N C5N NDP sing 357 n n C4N H41N NDP sing 358 n n C4N H42N NDP sing 359 n n C5N C6N NDP doub 360 n n C5N H5N NDP sing 361 n n C6N H6N NDP sing 362 n n P2B O1X NDP doub 363 n n P2B O2X NDP sing 364 n n P2B O3X NDP sing 365 n n O2X HOP2 NDP sing 366 n n O3X HOP3 NDP sing 367 n n # _atom_sites.entry_id 3RU3 _atom_sites.fract_transf_matrix[1][1] 0.008268 _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] 0.008268 _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] 0.00646 _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 C 3 K A 1 491 1 K K . D 4 MG A 1 492 2 MG MG . E 5 NDP A 1 493 3 NDP NDP . F 6 ATP A 1 494 4 ATP ATP . G 7 NPW A 1 495 5 NPW NPW . H 8 HOH A 1 496 1 HOH HOH . H 8 HOH A 2 497 2 HOH HOH . H 8 HOH A 3 498 3 HOH HOH . H 8 HOH A 4 499 4 HOH HOH . H 8 HOH A 5 500 5 HOH HOH . H 8 HOH A 6 501 7 HOH HOH . H 8 HOH A 7 502 8 HOH HOH . H 8 HOH A 8 503 9 HOH HOH . H 8 HOH A 9 504 10 HOH HOH . H 8 HOH A 10 505 11 HOH HOH . H 8 HOH A 11 506 12 HOH HOH . H 8 HOH A 12 507 13 HOH HOH . H 8 HOH A 13 508 14 HOH HOH . H 8 HOH A 14 509 15 HOH HOH . H 8 HOH A 15 510 16 HOH HOH . H 8 HOH A 16 511 17 HOH HOH . H 8 HOH A 17 512 18 HOH HOH . H 8 HOH A 18 513 19 HOH HOH . H 8 HOH A 19 514 20 HOH HOH . H 8 HOH A 20 515 21 HOH HOH . H 8 HOH A 21 516 22 HOH HOH . H 8 HOH A 22 517 23 HOH HOH . H 8 HOH A 23 518 24 HOH HOH . H 8 HOH A 24 519 25 HOH HOH . H 8 HOH A 25 520 26 HOH HOH . H 8 HOH A 26 521 27 HOH HOH . I 8 HOH B 1 8 6 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 . . . E 5 -51.224 11.907 -15.563 1 52.16 ? PA NDP 493 A 1 HETATM 2 O O1A NDP . . . E 5 -50.04 11.293 -16.215 1 47.8 ? O1A NDP 493 A 1 HETATM 3 O O2A NDP . . . E 5 -51.205 12.163 -14.08 1 43.45 ? O2A NDP 493 A 1 HETATM 4 O O5B NDP . . . E 5 -51.588 13.287 -16.277 1 54.93 ? O5B NDP 493 A 1 HETATM 5 C C5B NDP . . . E 5 -52.939 13.607 -16.408 1 59.54 ? C5B NDP 493 A 1 HETATM 6 C C4B NDP . . . E 5 -53.161 14.893 -15.706 1 64.46 ? C4B NDP 493 A 1 HETATM 7 O O4B NDP . . . E 5 -52.564 15.926 -16.459 1 66.21 ? O4B NDP 493 A 1 HETATM 8 C C3B NDP . . . E 5 -54.634 15.203 -15.684 1 69.19 ? C3B NDP 493 A 1 HETATM 9 O O3B NDP . . . E 5 -54.869 16.03 -14.554 1 72.18 ? O3B NDP 493 A 1 HETATM 10 C C2B NDP . . . E 5 -54.823 15.961 -16.975 1 70.03 ? C2B NDP 493 A 1 HETATM 11 O O2B NDP . . . E 5 -55.936 16.806 -16.884 1 74.11 ? O2B NDP 493 A 1 HETATM 12 C C1B NDP . . . E 5 -53.54 16.764 -17.066 1 67.87 ? C1B NDP 493 A 1 HETATM 13 N N9A NDP . . . E 5 -53.04 17.081 -18.414 1 66.16 ? N9A NDP 493 A 1 HETATM 14 C C8A NDP . . . E 5 -52.82 16.199 -19.467 1 63.87 ? C8A NDP 493 A 1 HETATM 15 N N7A NDP . . . E 5 -52.308 16.925 -20.493 1 62.56 ? N7A NDP 493 A 1 HETATM 16 C C5A NDP . . . E 5 -52.207 18.224 -20.105 1 59.76 ? C5A NDP 493 A 1 HETATM 17 C C6A NDP . . . E 5 -51.768 19.335 -20.763 1 59.87 ? C6A NDP 493 A 1 HETATM 18 N N6A NDP . . . E 5 -51.334 19.187 -22.008 1 61.76 ? N6A NDP 493 A 1 HETATM 19 N N1A NDP . . . E 5 -51.748 20.561 -20.124 1 60.93 ? N1A NDP 493 A 1 HETATM 20 C C2A NDP . . . E 5 -52.202 20.663 -18.82 1 60.94 ? C2A NDP 493 A 1 HETATM 21 N N3A NDP . . . E 5 -52.647 19.53 -18.157 1 60.26 ? N3A NDP 493 A 1 HETATM 22 C C4A NDP . . . E 5 -52.642 18.34 -18.801 1 61.97 ? C4A NDP 493 A 1 HETATM 23 O O3 NDP . . . E 5 -52.382 10.884 -15.991 1 45.29 ? O3 NDP 493 A 1 HETATM 24 P PN NDP . . . E 5 -52.831 9.674 -15.092 1 45.51 ? PN NDP 493 A 1 HETATM 25 O O1N NDP . . . E 5 -53.603 10.131 -13.924 1 45.63 ? O1N NDP 493 A 1 HETATM 26 O O2N NDP . . . E 5 -53.117 8.56 -15.971 1 42.96 ? O2N NDP 493 A 1 HETATM 27 O O5D NDP . . . E 5 -51.456 9.242 -14.326 1 50.22 ? O5D NDP 493 A 1 HETATM 28 C C5D NDP . . . E 5 -50.567 8.228 -14.793 1 47.85 ? C5D NDP 493 A 1 HETATM 29 C C4D NDP . . . E 5 -49.388 8.197 -13.852 1 47.26 ? C4D NDP 493 A 1 HETATM 30 O O4D NDP . . . E 5 -49.769 7.522 -12.662 1 47.75 ? O4D NDP 493 A 1 HETATM 31 C C3D NDP . . . E 5 -48.162 7.458 -14.411 1 46.89 ? C3D NDP 493 A 1 HETATM 32 O O3D NDP . . . E 5 -47.217 8.271 -15.093 1 43.83 ? O3D NDP 493 A 1 HETATM 33 C C2D NDP . . . E 5 -47.608 6.929 -13.118 1 45.12 ? C2D NDP 493 A 1 HETATM 34 O O2D NDP . . . E 5 -47.045 8.032 -12.444 1 41.86 ? O2D NDP 493 A 1 HETATM 35 C C1D NDP . . . E 5 -48.854 6.467 -12.364 1 45.42 ? C1D NDP 493 A 1 HETATM 36 N N1N NDP . . . E 5 -49.306 5.142 -12.824 1 39.59 ? N1N NDP 493 A 1 HETATM 37 P P2B NDP . . . E 5 -57.196 16.496 -17.842 1 77.56 ? P2B NDP 493 A 1 HETATM 38 O O1X NDP . . . E 5 -57.084 17.558 -18.931 1 73.39 ? O1X NDP 493 A 1 HETATM 39 O O2X NDP . . . E 5 -58.414 16.553 -16.934 1 78.31 ? O2X NDP 493 A 1 HETATM 40 O O3X NDP . . . E 5 -57.182 15.095 -18.418 1 75.26 ? O3X NDP 493 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 40 #