data_8PVD # _model_server_result.job_id aGBLxKCuYf4HXVpunBPPZw _model_server_result.datetime_utc '2025-01-07 00:46:20' _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 8pvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 8PVD # _exptl.entry_id 8PVD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 745.421 _entity.id 2 _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 8PVD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PVD _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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 'point symmetry operation' ? ? -1 0 0 0 -1 0 0 0 1 211.328 211.328 0 3 'point symmetry operation' ? ? 1 0 0 0 -1 0 0 0 -1 0 211.328 211.328 4 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 211.328 0 211.328 # _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 # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id OH _struct_conn.ptnr1_label_comp_id TYR _struct_conn.ptnr1_label_seq_id 358 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id TYR _struct_conn.ptnr1_auth_seq_id 358 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id FE _struct_conn.ptnr2_label_comp_id HEM _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id HEM _struct_conn.ptnr2_auth_seq_id 602 _struct_conn.ptnr2_symmetry 1_555 _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 1.919 _struct_conn.pdbx_value_order ? # _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 8PVD _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 NDP A 1 601 601 NDP NDP . C 3 HEM A 1 602 602 HEM HEM . # 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 2 138.809 72.139 117.424 1 114.22 ? PA NDP 601 A 1 HETATM 2 O O1A NDP . . . B 2 138.636 70.655 117.457 1 114.48 ? O1A NDP 601 A 1 HETATM 3 O O2A NDP . . . B 2 139.512 72.786 118.569 1 118.45 ? O2A NDP 601 A 1 HETATM 4 O O5B NDP . . . B 2 137.402 72.865 117.25 1 112.21 ? O5B NDP 601 A 1 HETATM 5 C C5B NDP . . . B 2 136.414 72.301 116.379 1 110.17 ? C5B NDP 601 A 1 HETATM 6 C C4B NDP . . . B 2 135.107 72.996 116.653 1 109.73 ? C4B NDP 601 A 1 HETATM 7 O O4B NDP . . . B 2 134.151 72.504 115.688 1 107.04 ? O4B NDP 601 A 1 HETATM 8 C C3B NDP . . . B 2 134.463 72.793 118.045 1 113.36 ? C3B NDP 601 A 1 HETATM 9 O O3B NDP . . . B 2 134.327 74.03 118.745 1 111.37 ? O3B NDP 601 A 1 HETATM 10 C C2B NDP . . . B 2 133.111 72.138 117.755 1 112.07 ? C2B NDP 601 A 1 HETATM 11 O O2B NDP . . . B 2 132.049 72.694 118.55 1 113.35 ? O2B NDP 601 A 1 HETATM 12 C C1B NDP . . . B 2 132.885 72.512 116.292 1 106.81 ? C1B NDP 601 A 1 HETATM 13 N N9A NDP . . . B 2 132.04 71.615 115.517 1 105.15 ? N9A NDP 601 A 1 HETATM 14 C C8A NDP . . . B 2 131.961 70.242 115.546 1 107.4 ? C8A NDP 601 A 1 HETATM 15 N N7A NDP . . . B 2 131.12 69.752 114.674 1 106.23 ? N7A NDP 601 A 1 HETATM 16 C C5A NDP . . . B 2 130.631 70.872 114.019 1 106.54 ? C5A NDP 601 A 1 HETATM 17 C C6A NDP . . . B 2 129.703 71.025 112.973 1 109.16 ? C6A NDP 601 A 1 HETATM 18 N N6A NDP . . . B 2 129.087 69.99 112.41 1 112.64 ? N6A NDP 601 A 1 HETATM 19 N N1A NDP . . . B 2 129.431 72.285 112.532 1 108.59 ? N1A NDP 601 A 1 HETATM 20 C C2A NDP . . . B 2 130.058 73.317 113.113 1 106.98 ? C2A NDP 601 A 1 HETATM 21 N N3A NDP . . . B 2 130.937 73.289 114.113 1 106.87 ? N3A NDP 601 A 1 HETATM 22 C C4A NDP . . . B 2 131.188 72.027 114.525 1 105.36 ? C4A NDP 601 A 1 HETATM 23 O O3 NDP . . . B 2 139.545 72.569 116.074 1 112.45 ? O3 NDP 601 A 1 HETATM 24 P PN NDP . . . B 2 140.232 73.945 115.62 1 117.39 ? PN NDP 601 A 1 HETATM 25 O O1N NDP . . . B 2 139.895 75.05 116.574 1 113.94 ? O1N NDP 601 A 1 HETATM 26 O O2N NDP . . . B 2 141.672 73.686 115.318 1 118.73 ? O2N NDP 601 A 1 HETATM 27 O O5D NDP . . . B 2 139.477 74.233 114.246 1 111.96 ? O5D NDP 601 A 1 HETATM 28 C C5D NDP . . . B 2 139.501 73.294 113.137 1 111.89 ? C5D NDP 601 A 1 HETATM 29 C C4D NDP . . . B 2 138.287 73.56 112.282 1 108.85 ? C4D NDP 601 A 1 HETATM 30 O O4D NDP . . . B 2 137.097 73.502 113.113 1 107.7 ? O4D NDP 601 A 1 HETATM 31 C C3D NDP . . . B 2 138.258 74.937 111.62 1 104.66 ? C3D NDP 601 A 1 HETATM 32 O O3D NDP . . . B 2 138.949 74.947 110.376 1 105.65 ? O3D NDP 601 A 1 HETATM 33 C C2D NDP . . . B 2 136.761 75.207 111.549 1 100.93 ? C2D NDP 601 A 1 HETATM 34 O O2D NDP . . . B 2 136.356 74.851 110.247 1 104.35 ? O2D NDP 601 A 1 HETATM 35 C C1D NDP . . . B 2 136.1 74.364 112.647 1 101.08 ? C1D NDP 601 A 1 HETATM 36 N N1N NDP . . . B 2 135.578 75.193 113.788 1 103.48 ? N1N NDP 601 A 1 HETATM 37 C C2N NDP . . . B 2 136.432 75.932 114.576 1 104.87 ? C2N NDP 601 A 1 HETATM 38 C C3N NDP . . . B 2 135.985 76.899 115.467 1 102.8 ? C3N NDP 601 A 1 HETATM 39 C C7N NDP . . . B 2 136.953 77.835 116.102 1 102.69 ? C7N NDP 601 A 1 HETATM 40 O O7N NDP . . . B 2 136.528 78.913 116.525 1 101.28 ? O7N NDP 601 A 1 HETATM 41 N N7N NDP . . . B 2 138.242 77.536 116.235 1 109.67 ? N7N NDP 601 A 1 HETATM 42 C C4N NDP . . . B 2 134.531 76.926 115.807 1 101.91 ? C4N NDP 601 A 1 HETATM 43 C C5N NDP . . . B 2 133.694 76.021 114.99 1 102.33 ? C5N NDP 601 A 1 HETATM 44 C C6N NDP . . . B 2 134.207 75.234 114.058 1 103.97 ? C6N NDP 601 A 1 HETATM 45 P P2B NDP . . . B 2 131.694 72.137 120.047 1 116.4 ? P2B NDP 601 A 1 HETATM 46 O O1X NDP . . . B 2 132.851 72.495 120.969 1 112.1 ? O1X NDP 601 A 1 HETATM 47 O O2X NDP . . . B 2 131.508 70.636 119.938 1 113.1 ? O2X NDP 601 A 1 HETATM 48 O O3X NDP . . . B 2 130.385 72.865 120.414 1 109.72 ? O3X NDP 601 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 159 _model_server_stats.create_model_time_ms 50 _model_server_stats.query_time_ms 488 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 48 #