data_3D8X # _model_server_result.job_id pyCLInXdU0QwWWzzDLapkA _model_server_result.datetime_utc '2025-01-11 02:03:27' _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 3d8x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":481}' # _entry.id 3D8X # _exptl.entry_id 3D8X _exptl.method 'X-RAY DIFFRACTION' # _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 114.16 _cell.angle_gamma 90 _cell.entry_id 3D8X _cell.length_a 54.229 _cell.length_b 125.004 _cell.length_c 60.967 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D8X _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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,G _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 3 _struct_asym.id D _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 disulf ? disulf1 A SG CYS 149 A CYS 142 1_555 A SG CYS 152 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 149 B CYS 142 1_555 B SG CYS 152 B CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _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 328 n n PA O2A NDP sing 329 n n PA O5B NDP sing 330 n n PA O3 NDP sing 331 n n O2A HOA2 NDP sing 332 n n O5B C5B NDP sing 333 n n C5B C4B NDP sing 334 n n C5B H51A NDP sing 335 n n C5B H52A NDP sing 336 n n C4B O4B NDP sing 337 n n C4B C3B NDP sing 338 n n C4B H4B NDP sing 339 n n O4B C1B NDP sing 340 n n C3B O3B NDP sing 341 n n C3B C2B NDP sing 342 n n C3B H3B NDP sing 343 n n O3B HO3A NDP sing 344 n n C2B O2B NDP sing 345 n n C2B C1B NDP sing 346 n n C2B H2B NDP sing 347 n n O2B P2B NDP sing 348 n n C1B N9A NDP sing 349 n n C1B H1B NDP sing 350 n n N9A C8A NDP sing 351 n y N9A C4A NDP sing 352 n y C8A N7A NDP doub 353 n y C8A H8A NDP sing 354 n n N7A C5A NDP sing 355 n y C5A C6A NDP sing 356 n y C5A C4A NDP doub 357 n y C6A N6A NDP sing 358 n n C6A N1A NDP doub 359 n y N6A H61A NDP sing 360 n n N6A H62A NDP sing 361 n n N1A C2A NDP sing 362 n y C2A N3A NDP doub 363 n y C2A H2A NDP sing 364 n n N3A C4A NDP sing 365 n y O3 PN NDP sing 366 n n PN O1N NDP doub 367 n n PN O2N NDP sing 368 n n PN O5D NDP sing 369 n n O2N H21N NDP sing 370 n n O5D C5D NDP sing 371 n n C5D C4D NDP sing 372 n n C5D H51N NDP sing 373 n n C5D H52N NDP sing 374 n n C4D O4D NDP sing 375 n n C4D C3D NDP sing 376 n n C4D H4D NDP sing 377 n n O4D C1D NDP sing 378 n n C3D O3D NDP sing 379 n n C3D C2D NDP sing 380 n n C3D H3D NDP sing 381 n n O3D HO3N NDP sing 382 n n C2D O2D NDP sing 383 n n C2D C1D NDP sing 384 n n C2D H2D NDP sing 385 n n O2D HO2N NDP sing 386 n n C1D N1N NDP sing 387 n n C1D H1D NDP sing 388 n n N1N C2N NDP sing 389 n n N1N C6N NDP sing 390 n n C2N C3N NDP doub 391 n n C2N H2N NDP sing 392 n n C3N C7N NDP sing 393 n n C3N C4N NDP sing 394 n n C7N O7N NDP doub 395 n n C7N N7N NDP sing 396 n n N7N H71N NDP sing 397 n n N7N H72N NDP sing 398 n n C4N C5N NDP sing 399 n n C4N H41N NDP sing 400 n n C4N H42N NDP sing 401 n n C5N C6N NDP doub 402 n n C5N H5N NDP sing 403 n n C6N H6N NDP sing 404 n n P2B O1X NDP doub 405 n n P2B O2X NDP sing 406 n n P2B O3X NDP sing 407 n n O2X HOP2 NDP sing 408 n n O3X HOP3 NDP sing 409 n n # _atom_sites.entry_id 3D8X _atom_sites.fract_transf_matrix[1][1] 0.01844 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00827 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008 _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] 0.017976 _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 2 FAD A 1 1001 1001 FAD FAD . D 3 NDP A 1 481 481 NDP NDP . E 2 FAD B 1 1001 1001 FAD FAD . F 4 HOH A 1 1002 1 HOH HOH . F 4 HOH A 2 1003 2 HOH HOH . F 4 HOH A 3 1004 4 HOH HOH . F 4 HOH A 4 1005 5 HOH HOH . F 4 HOH A 5 1006 6 HOH HOH . F 4 HOH A 6 1007 10 HOH HOH . F 4 HOH A 7 1008 13 HOH HOH . F 4 HOH A 8 1009 14 HOH HOH . F 4 HOH A 9 1010 18 HOH HOH . F 4 HOH A 10 1011 19 HOH HOH . F 4 HOH A 11 1012 20 HOH HOH . F 4 HOH A 12 1013 26 HOH HOH . F 4 HOH A 13 1014 27 HOH HOH . F 4 HOH A 14 1015 28 HOH HOH . F 4 HOH A 15 1016 30 HOH HOH . F 4 HOH A 16 1017 31 HOH HOH . F 4 HOH A 17 1018 39 HOH HOH . F 4 HOH A 18 1019 41 HOH HOH . F 4 HOH A 19 1020 45 HOH HOH . F 4 HOH A 20 1021 47 HOH HOH . F 4 HOH A 21 1022 49 HOH HOH . F 4 HOH A 22 1023 50 HOH HOH . F 4 HOH A 23 1024 53 HOH HOH . F 4 HOH A 24 1025 56 HOH HOH . F 4 HOH A 25 1026 58 HOH HOH . F 4 HOH A 26 1027 61 HOH HOH . F 4 HOH A 27 1028 62 HOH HOH . F 4 HOH A 28 1029 63 HOH HOH . F 4 HOH A 29 1030 66 HOH HOH . F 4 HOH A 30 1031 68 HOH HOH . F 4 HOH A 31 1032 71 HOH HOH . F 4 HOH A 32 1033 72 HOH HOH . F 4 HOH A 33 1034 73 HOH HOH . F 4 HOH A 34 1035 74 HOH HOH . F 4 HOH A 35 1036 75 HOH HOH . F 4 HOH A 36 1037 80 HOH HOH . F 4 HOH A 37 1038 81 HOH HOH . F 4 HOH A 38 1039 82 HOH HOH . F 4 HOH A 39 1040 83 HOH HOH . F 4 HOH A 40 1041 84 HOH HOH . F 4 HOH A 41 1042 88 HOH HOH . F 4 HOH A 42 1043 89 HOH HOH . F 4 HOH A 43 1044 90 HOH HOH . F 4 HOH A 44 1045 91 HOH HOH . F 4 HOH A 45 1046 92 HOH HOH . F 4 HOH A 46 1047 94 HOH HOH . F 4 HOH A 47 1048 97 HOH HOH . G 4 HOH B 1 1049 99 HOH HOH . G 4 HOH B 2 1050 3 HOH HOH . G 4 HOH B 3 1051 7 HOH HOH . G 4 HOH B 4 1052 8 HOH HOH . G 4 HOH B 5 1053 9 HOH HOH . G 4 HOH B 6 1054 11 HOH HOH . G 4 HOH B 7 1055 12 HOH HOH . G 4 HOH B 8 1056 15 HOH HOH . G 4 HOH B 9 1057 16 HOH HOH . G 4 HOH B 10 1058 17 HOH HOH . G 4 HOH B 11 1059 21 HOH HOH . G 4 HOH B 12 1060 22 HOH HOH . G 4 HOH B 13 1061 23 HOH HOH . G 4 HOH B 14 1062 24 HOH HOH . G 4 HOH B 15 1063 25 HOH HOH . G 4 HOH B 16 1064 29 HOH HOH . G 4 HOH B 17 1065 32 HOH HOH . G 4 HOH B 18 1066 33 HOH HOH . G 4 HOH B 19 1067 34 HOH HOH . G 4 HOH B 20 1068 35 HOH HOH . G 4 HOH B 21 1069 36 HOH HOH . G 4 HOH B 22 1070 37 HOH HOH . G 4 HOH B 23 1071 38 HOH HOH . G 4 HOH B 24 1072 40 HOH HOH . G 4 HOH B 25 1073 42 HOH HOH . G 4 HOH B 26 1074 43 HOH HOH . G 4 HOH B 27 1075 44 HOH HOH . G 4 HOH B 28 1076 46 HOH HOH . G 4 HOH B 29 1077 48 HOH HOH . G 4 HOH B 30 1078 51 HOH HOH . G 4 HOH B 31 1079 52 HOH HOH . G 4 HOH B 32 1080 54 HOH HOH . G 4 HOH B 33 1081 55 HOH HOH . G 4 HOH B 34 1082 57 HOH HOH . G 4 HOH B 35 1083 59 HOH HOH . G 4 HOH B 36 1084 60 HOH HOH . G 4 HOH B 37 1085 64 HOH HOH . G 4 HOH B 38 1086 65 HOH HOH . G 4 HOH B 39 1087 67 HOH HOH . G 4 HOH B 40 1088 69 HOH HOH . G 4 HOH B 41 1089 70 HOH HOH . G 4 HOH B 42 1090 76 HOH HOH . G 4 HOH B 43 1091 77 HOH HOH . G 4 HOH B 44 1092 78 HOH HOH . G 4 HOH B 45 1093 79 HOH HOH . G 4 HOH B 46 1094 85 HOH HOH . G 4 HOH B 47 1095 86 HOH HOH . G 4 HOH B 48 1096 87 HOH HOH . G 4 HOH B 49 1097 93 HOH HOH . G 4 HOH B 50 1098 95 HOH HOH . G 4 HOH B 51 1099 96 HOH HOH . G 4 HOH B 52 1100 98 HOH HOH . G 4 HOH B 53 1101 100 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 . . . D 3 -9.614 14.568 30.557 0.5 18.07 ? PA NDP 481 A 1 HETATM 2 O O1A NDP . . . D 3 -8.964 15.864 30.129 0.5 18.2 ? O1A NDP 481 A 1 HETATM 3 O O2A NDP . . . D 3 -9.501 14.098 31.986 0.5 17.54 ? O2A NDP 481 A 1 HETATM 4 O O2B NDP . . . D 3 -14.408 17.49 33.229 0.5 16.26 ? O2B NDP 481 A 1 HETATM 5 C C1B NDP . . . D 3 -17.856 17.267 31.402 0.5 6.62 ? C1B NDP 481 A 1 HETATM 6 N N9A NDP . . . D 3 -17.464 16.115 32.261 0.5 6.87 ? N9A NDP 481 A 1 HETATM 7 C C8A NDP . . . D 3 -16.22 15.649 32.448 0.5 6.37 ? C8A NDP 481 A 1 HETATM 8 N N7A NDP . . . D 3 -16.251 14.598 33.3 0.5 5.98 ? N7A NDP 481 A 1 HETATM 9 C C5A NDP . . . D 3 -17.536 14.402 33.649 0.5 6.24 ? C5A NDP 481 A 1 HETATM 10 C C6A NDP . . . D 3 -18.181 13.49 34.481 0.5 6.58 ? C6A NDP 481 A 1 HETATM 11 N N6A NDP . . . D 3 -17.487 12.528 35.146 0.5 6.71 ? N6A NDP 481 A 1 HETATM 12 N N1A NDP . . . D 3 -19.525 13.566 34.622 0.5 6.73 ? N1A NDP 481 A 1 HETATM 13 C C2A NDP . . . D 3 -20.239 14.505 33.974 0.5 6.9 ? C2A NDP 481 A 1 HETATM 14 N N3A NDP . . . D 3 -19.64 15.388 33.16 0.5 7.19 ? N3A NDP 481 A 1 HETATM 15 C C4A NDP . . . D 3 -18.294 15.36 32.987 0.5 6.53 ? C4A NDP 481 A 1 HETATM 16 O O3 NDP . . . D 3 -9.058 13.395 29.608 0.5 18.32 ? O3 NDP 481 A 1 HETATM 17 P PN NDP . . . D 3 -9.027 13.546 28.001 0.5 18.73 ? PN NDP 481 A 1 HETATM 18 O O1N NDP . . . D 3 -10.011 14.62 27.594 0.5 17.6 ? O1N NDP 481 A 1 HETATM 19 O O2N NDP . . . D 3 -7.583 13.645 27.544 0.5 18.58 ? O2N NDP 481 A 1 HETATM 20 O O5D NDP . . . D 3 -9.566 12.091 27.575 0.5 17.94 ? O5D NDP 481 A 1 HETATM 21 P P2B NDP . . . D 3 -15.002 18.709 34.096 0.5 16.61 ? P2B NDP 481 A 1 HETATM 22 O O1X NDP . . . D 3 -15.75 18.024 35.234 0.5 15.95 ? O1X NDP 481 A 1 HETATM 23 O O2X NDP . . . D 3 -15.875 19.425 33.083 0.5 16.64 ? O2X NDP 481 A 1 HETATM 24 O O3X NDP . . . D 3 -13.775 19.489 34.507 0.5 15.21 ? O3X NDP 481 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 24 #