data_7DI8 # _model_server_result.job_id fv6khNaQvCf0a9ndS3kKIg _model_server_result.datetime_utc '2024-11-15 16:30:54' _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 7di8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":602}' # _entry.id 7DI8 # _exptl.entry_id 7DI8 _exptl.method 'ELECTRON CRYSTALLOGRAPHY' # _entity.details ? _entity.formula_weight 745.421 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADPH DIHYDRO-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 7DI8 _cell.length_a 69.98 _cell.length_b 174.02 _cell.length_c 199.45 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DI8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _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 # 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 H N N ? 3 J N N ? 3 L N 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 OH TYR 358 A TYR 357 1_555 E FE HEM . A HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc2 B OH TYR 358 B TYR 357 1_555 G FE HEM . B HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc3 C OH TYR 358 C TYR 357 1_555 I FE HEM . C HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc4 D OH TYR 358 D TYR 357 1_555 K FE HEM . D HEM 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? # _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 7DI8 _atom_sites.fract_transf_matrix[1][1] 0.01429 _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] 0.005746 _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] 0.005014 _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 HEM A 1 601 527 HEM HEM . F 3 NDP A 1 602 528 NDP NDP . G 2 HEM B 1 601 527 HEM HEM . H 3 NDP B 1 602 528 NDP NDP . I 2 HEM C 1 601 527 HEM HEM . J 3 NDP C 1 602 528 NDP NDP . K 2 HEM D 1 601 527 HEM HEM . L 3 NDP D 1 602 528 NDP NDP . # 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 . . . H 3 56.767 106.476 106.22 1 30.76 ? PA NDP 602 B 1 HETATM 2 O O1A NDP . . . H 3 56.208 106.006 104.922 1 30.79 ? O1A NDP 602 B 1 HETATM 3 O O2A NDP . . . H 3 57.843 107.52 106.276 1 30.76 ? O2A NDP 602 B 1 HETATM 4 O O5B NDP . . . H 3 57.203 105.183 107.15 1 30.72 ? O5B NDP 602 B 1 HETATM 5 C C5B NDP . . . H 3 57.265 104.108 106.261 1 33.35 ? C5B NDP 602 B 1 HETATM 6 C C4B NDP . . . H 3 57.942 102.941 106.946 1 37.99 ? C4B NDP 602 B 1 HETATM 7 O O4B NDP . . . H 3 57.202 101.776 106.678 1 35.34 ? O4B NDP 602 B 1 HETATM 8 C C3B NDP . . . H 3 59.381 102.787 106.373 1 43.16 ? C3B NDP 602 B 1 HETATM 9 O O3B NDP . . . H 3 60.332 102.991 107.37 1 50.27 ? O3B NDP 602 B 1 HETATM 10 C C2B NDP . . . H 3 59.444 101.303 105.932 1 37.08 ? C2B NDP 602 B 1 HETATM 11 O O2B NDP . . . H 3 60.506 100.653 106.4 1 33.45 ? O2B NDP 602 B 1 HETATM 12 C C1B NDP . . . H 3 58.131 100.717 106.6 1 34.03 ? C1B NDP 602 B 1 HETATM 13 N N9A NDP . . . H 3 57.501 99.664 105.786 1 30.66 ? N9A NDP 602 B 1 HETATM 14 C C8A NDP . . . H 3 57.314 99.632 104.388 1 30.68 ? C8A NDP 602 B 1 HETATM 15 N N7A NDP . . . H 3 56.685 98.517 103.958 1 30.69 ? N7A NDP 602 B 1 HETATM 16 C C5A NDP . . . H 3 56.443 97.788 105.138 1 30.67 ? C5A NDP 602 B 1 HETATM 17 C C6A NDP . . . H 3 55.824 96.546 105.37 1 30.66 ? C6A NDP 602 B 1 HETATM 18 N N6A NDP . . . H 3 55.316 95.816 104.313 1 30.68 ? N6A NDP 602 B 1 HETATM 19 N N1A NDP . . . H 3 55.702 96.03 106.637 1 30.64 ? N1A NDP 602 B 1 HETATM 20 C C2A NDP . . . H 3 56.231 96.819 107.64 1 30.62 ? C2A NDP 602 B 1 HETATM 21 N N3A NDP . . . H 3 56.847 98.014 107.584 1 30.63 ? N3A NDP 602 B 1 HETATM 22 C C4A NDP . . . H 3 56.944 98.49 106.288 1 30.65 ? C4A NDP 602 B 1 HETATM 23 O O3 NDP . . . H 3 55.431 107.181 106.859 1 30.8 ? O3 NDP 602 B 1 HETATM 24 P PN NDP . . . H 3 55.63 107.264 108.427 1 30.77 ? PN NDP 602 B 1 HETATM 25 O O1N NDP . . . H 3 54.675 108.256 108.96 1 30.8 ? O1N NDP 602 B 1 HETATM 26 O O2N NDP . . . H 3 57.074 107.17 108.869 1 30.73 ? O2N NDP 602 B 1 HETATM 27 O O5D NDP . . . H 3 54.984 105.784 109.125 1 30.75 ? O5D NDP 602 B 1 HETATM 28 C C5D NDP . . . H 3 53.651 105.793 108.81 1 30.78 ? C5D NDP 602 B 1 HETATM 29 C C4D NDP . . . H 3 53.107 104.405 109.032 1 30.77 ? C4D NDP 602 B 1 HETATM 30 O O4D NDP . . . H 3 54.076 103.46 108.563 1 30.74 ? O4D NDP 602 B 1 HETATM 31 C C3D NDP . . . H 3 52.988 104.175 110.559 1 30.75 ? C3D NDP 602 B 1 HETATM 32 O O3D NDP . . . H 3 51.701 104.503 110.983 1 30.78 ? O3D NDP 602 B 1 HETATM 33 C C2D NDP . . . H 3 53.209 102.685 110.683 1 30.73 ? C2D NDP 602 B 1 HETATM 34 O O2D NDP . . . H 3 52.035 101.97 110.507 1 30.74 ? O2D NDP 602 B 1 HETATM 35 C C1D NDP . . . H 3 54.156 102.37 109.473 1 30.71 ? C1D NDP 602 B 1 HETATM 36 N N1N NDP . . . H 3 55.562 102.252 109.926 1 30.68 ? N1N NDP 602 B 1 HETATM 37 C C2N NDP . . . H 3 56.14 103.267 110.665 1 30.67 ? C2N NDP 602 B 1 HETATM 38 C C3N NDP . . . H 3 57.43 103.192 111.075 1 30.64 ? C3N NDP 602 B 1 HETATM 39 C C7N NDP . . . H 3 57.939 104.302 111.859 1 30.63 ? C7N NDP 602 B 1 HETATM 40 O O7N NDP . . . H 3 58.686 104.16 112.832 1 30.6 ? O7N NDP 602 B 1 HETATM 41 N N7N NDP . . . H 3 57.564 105.589 111.495 1 30.66 ? N7N NDP 602 B 1 HETATM 42 C C4N NDP . . . H 3 58.302 102.041 110.77 1 30.6 ? C4N NDP 602 B 1 HETATM 43 C C5N NDP . . . H 3 57.598 100.986 109.978 1 30.61 ? C5N NDP 602 B 1 HETATM 44 C C6N NDP . . . H 3 56.317 101.108 109.6 1 30.65 ? C6N NDP 602 B 1 HETATM 45 P P2B NDP . . . H 3 62.028 100.928 105.398 1 40 ? P2B NDP 602 B 1 HETATM 46 O O1X NDP . . . H 3 61.358 101.344 104.125 1 41.26 ? O1X NDP 602 B 1 HETATM 47 O O2X NDP . . . H 3 62.693 99.549 105.426 1 44.41 ? O2X NDP 602 B 1 HETATM 48 O O3X NDP . . . H 3 62.643 102.009 106.243 1 40.59 ? O3X NDP 602 B 1 HETATM 49 H H51A NDP . . . H 3 56.39 103.871 105.916 1 40.19 ? H51A NDP 602 B 1 HETATM 50 H H52A NDP . . . H 3 57.796 104.366 105.491 1 40.19 ? H52A NDP 602 B 1 HETATM 51 H H4B NDP . . . H 3 57.942 103.079 107.907 1 45.76 ? H4B NDP 602 B 1 HETATM 52 H H3B NDP . . . H 3 59.536 103.352 105.6 1 51.97 ? H3B NDP 602 B 1 HETATM 53 H HO3A NDP . . . H 3 60.931 103.48 107.018 1 60.5 ? HO3A NDP 602 B 1 HETATM 54 H H2B NDP . . . H 3 59.312 101.277 104.971 1 44.67 ? H2B NDP 602 B 1 HETATM 55 H H1B NDP . . . H 3 58.309 100.343 107.477 1 41.02 ? H1B NDP 602 B 1 HETATM 56 H H8A NDP . . . H 3 57.612 100.325 103.844 1 37 ? H8A NDP 602 B 1 HETATM 57 H H61A NDP . . . H 3 55.817 95.237 103.919 1 36.99 ? H61A NDP 602 B 1 HETATM 58 H H62A NDP . . . H 3 54.505 95.946 104.058 1 36.99 ? H62A NDP 602 B 1 HETATM 59 H H2A NDP . . . H 3 56.139 96.452 108.489 1 36.93 ? H2A NDP 602 B 1 HETATM 60 H H51N NDP . . . H 3 53.171 106.396 109.398 1 37.12 ? H51N NDP 602 B 1 HETATM 61 H H52N NDP . . . H 3 53.474 106.121 107.915 1 37.12 ? H52N NDP 602 B 1 HETATM 62 H H4D NDP . . . H 3 52.262 104.3 108.567 1 37.11 ? H4D NDP 602 B 1 HETATM 63 H H3D NDP . . . H 3 53.678 104.666 111.032 1 37.08 ? H3D NDP 602 B 1 HETATM 64 H HO3N NDP . . . H 3 51.718 104.45 111.831 1 37.12 ? HO3N NDP 602 B 1 HETATM 65 H H2D NDP . . . H 3 53.636 102.461 111.524 1 37.05 ? H2D NDP 602 B 1 HETATM 66 H HO2N NDP . . . H 3 52.272 101.217 110.191 1 37.07 ? HO2N NDP 602 B 1 HETATM 67 H H1D NDP . . . H 3 53.907 101.555 109.011 1 37.04 ? H1D NDP 602 B 1 HETATM 68 H H2N NDP . . . H 3 55.612 104.003 110.878 1 36.98 ? H2N NDP 602 B 1 HETATM 69 H H71N NDP . . . H 3 57.855 106.261 111.947 1 36.97 ? H71N NDP 602 B 1 HETATM 70 H H72N NDP . . . H 3 57.046 105.738 110.825 1 36.97 ? H72N NDP 602 B 1 HETATM 71 H H41N NDP . . . H 3 59.087 102.331 110.28 1 36.91 ? H41N NDP 602 B 1 HETATM 72 H H42N NDP . . . H 3 58.633 101.657 111.597 1 36.91 ? H42N NDP 602 B 1 HETATM 73 H H5N NDP . . . H 3 58.067 100.217 109.746 1 36.92 ? H5N NDP 602 B 1 HETATM 74 H H6N NDP . . . H 3 55.881 100.451 109.107 1 36.96 ? H6N NDP 602 B 1 # _model_server_stats.io_time_ms 39 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 42 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 74 #