data_8JFI # _model_server_result.job_id ZqlhCCAxuIEId1NwOgXfDw _model_server_result.datetime_utc '2024-10-19 11:48:16' _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 8jfi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":301}' # _entry.id 8JFI # _exptl.entry_id 8JFI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _entity.pdbx_number_of_molecules 6 _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 8JFI _cell.length_a 85.843 _cell.length_b 252.65 _cell.length_c 166.44 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JFI _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,J,K,L,Q,R,W 1 1 A,B,G,J,K,L,Q,R,W 1 2 C,D,E,F,H,I,M,N,O,P,S,T,U,V 2 1 # 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_455 -x-1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 -85.843 0 83.22 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 J N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id E _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 160 _struct_conn.ptnr1_auth_asym_id E _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 159 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id O _struct_conn.ptnr2_label_atom_id O2D _struct_conn.ptnr2_label_comp_id NAP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id E _struct_conn.ptnr2_auth_comp_id NAP _struct_conn.ptnr2_auth_seq_id 301 _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 1.302 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C21 H28 N7 O17 P3' _chem_comp.formula_weight 743.405 _chem_comp.id NAP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" # 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 NAP doub 237 n n PA O2A NAP sing 238 n n PA O5B NAP sing 239 n n PA O3 NAP sing 240 n n O2A HOA2 NAP sing 241 n n O5B C5B NAP sing 242 n n C5B C4B NAP sing 243 n n C5B H51A NAP sing 244 n n C5B H52A NAP sing 245 n n C4B O4B NAP sing 246 n n C4B C3B NAP sing 247 n n C4B H4B NAP sing 248 n n O4B C1B NAP sing 249 n n C3B O3B NAP sing 250 n n C3B C2B NAP sing 251 n n C3B H3B NAP sing 252 n n O3B HO3A NAP sing 253 n n C2B O2B NAP sing 254 n n C2B C1B NAP sing 255 n n C2B H2B NAP sing 256 n n O2B P2B NAP sing 257 n n C1B N9A NAP sing 258 n n C1B H1B NAP sing 259 n n N9A C8A NAP sing 260 n y N9A C4A NAP sing 261 n y C8A N7A NAP doub 262 n y C8A H8A NAP sing 263 n n N7A C5A NAP sing 264 n y C5A C6A NAP sing 265 n y C5A C4A NAP doub 266 n y C6A N6A NAP sing 267 n n C6A N1A NAP doub 268 n y N6A H61A NAP sing 269 n n N6A H62A NAP sing 270 n n N1A C2A NAP sing 271 n y C2A N3A NAP doub 272 n y C2A H2A NAP sing 273 n n N3A C4A NAP sing 274 n y O3 PN NAP sing 275 n n PN O1N NAP doub 276 n n PN O2N NAP sing 277 n n PN O5D NAP sing 278 n n O5D C5D NAP sing 279 n n C5D C4D NAP sing 280 n n C5D H51N NAP sing 281 n n C5D H52N NAP sing 282 n n C4D O4D NAP sing 283 n n C4D C3D NAP sing 284 n n C4D H4D NAP sing 285 n n O4D C1D NAP sing 286 n n C3D O3D NAP sing 287 n n C3D C2D NAP sing 288 n n C3D H3D NAP sing 289 n n O3D HO3N NAP sing 290 n n C2D O2D NAP sing 291 n n C2D C1D NAP sing 292 n n C2D H2D NAP sing 293 n n O2D HO2N NAP sing 294 n n C1D N1N NAP sing 295 n n C1D H1D NAP sing 296 n n N1N C2N NAP sing 297 n y N1N C6N NAP doub 298 n y C2N C3N NAP doub 299 n y C2N H2N NAP sing 300 n n C3N C7N NAP sing 301 n n C3N C4N NAP sing 302 n y C7N O7N NAP doub 303 n n C7N N7N NAP sing 304 n n N7N H71N NAP sing 305 n n N7N H72N NAP sing 306 n n C4N C5N NAP doub 307 n y C4N H4N NAP sing 308 n n C5N C6N NAP sing 309 n y C5N H5N NAP sing 310 n n C6N H6N NAP sing 311 n n P2B O1X NAP doub 312 n n P2B O2X NAP sing 313 n n P2B O3X NAP sing 314 n n O2X HOP2 NAP sing 315 n n O3X HOP3 NAP sing 316 n n # _atom_sites.entry_id 8JFI _atom_sites.fract_transf_matrix[1][1] 0.011649 _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] 0.003958 _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] 0.006008 _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 J 3 NAP A 1 301 301 NAP NAP . K 4 UHC A 1 302 101 UHC SHW . L 3 NAP B 1 301 301 NAP NAP . M 3 NAP C 1 301 301 NAP NAP . N 3 NAP D 1 301 301 NAP NAP . O 3 NAP E 1 301 301 NAP NAP . P 3 NAP F 1 301 301 NAP NAP . Q 5 HOH A 1 401 401 HOH HOH . Q 5 HOH A 2 402 402 HOH HOH . Q 5 HOH A 3 403 403 HOH HOH . Q 5 HOH A 4 404 404 HOH HOH . Q 5 HOH A 5 405 405 HOH HOH . Q 5 HOH A 6 406 406 HOH HOH . Q 5 HOH A 7 407 407 HOH HOH . Q 5 HOH A 8 408 408 HOH HOH . Q 5 HOH A 9 409 409 HOH HOH . Q 5 HOH A 10 410 410 HOH HOH . Q 5 HOH A 11 411 411 HOH HOH . Q 5 HOH A 12 412 412 HOH HOH . Q 5 HOH A 13 413 413 HOH HOH . Q 5 HOH A 14 414 414 HOH HOH . Q 5 HOH A 15 415 415 HOH HOH . Q 5 HOH A 16 416 416 HOH HOH . Q 5 HOH A 17 417 417 HOH HOH . Q 5 HOH A 18 418 418 HOH HOH . Q 5 HOH A 19 419 419 HOH HOH . Q 5 HOH A 20 420 420 HOH HOH . Q 5 HOH A 21 421 421 HOH HOH . Q 5 HOH A 22 422 422 HOH HOH . Q 5 HOH A 23 423 423 HOH HOH . R 5 HOH B 1 401 401 HOH HOH . R 5 HOH B 2 402 402 HOH HOH . R 5 HOH B 3 403 403 HOH HOH . R 5 HOH B 4 404 404 HOH HOH . R 5 HOH B 5 405 405 HOH HOH . R 5 HOH B 6 406 406 HOH HOH . R 5 HOH B 7 407 407 HOH HOH . R 5 HOH B 8 408 408 HOH HOH . R 5 HOH B 9 409 409 HOH HOH . R 5 HOH B 10 410 410 HOH HOH . R 5 HOH B 11 411 411 HOH HOH . R 5 HOH B 12 412 412 HOH HOH . R 5 HOH B 13 413 413 HOH HOH . R 5 HOH B 14 414 414 HOH HOH . R 5 HOH B 15 415 415 HOH HOH . R 5 HOH B 16 416 416 HOH HOH . R 5 HOH B 17 417 417 HOH HOH . R 5 HOH B 18 418 418 HOH HOH . R 5 HOH B 19 419 419 HOH HOH . R 5 HOH B 20 420 420 HOH HOH . R 5 HOH B 21 421 421 HOH HOH . S 5 HOH C 1 401 401 HOH HOH . S 5 HOH C 2 402 402 HOH HOH . S 5 HOH C 3 403 403 HOH HOH . S 5 HOH C 4 404 404 HOH HOH . S 5 HOH C 5 405 405 HOH HOH . S 5 HOH C 6 406 406 HOH HOH . S 5 HOH C 7 407 407 HOH HOH . T 5 HOH D 1 401 401 HOH HOH . T 5 HOH D 2 402 402 HOH HOH . T 5 HOH D 3 403 403 HOH HOH . T 5 HOH D 4 404 404 HOH HOH . T 5 HOH D 5 405 405 HOH HOH . T 5 HOH D 6 406 406 HOH HOH . T 5 HOH D 7 407 407 HOH HOH . T 5 HOH D 8 408 408 HOH HOH . T 5 HOH D 9 409 409 HOH HOH . U 5 HOH E 1 401 401 HOH HOH . U 5 HOH E 2 402 402 HOH HOH . U 5 HOH E 3 403 403 HOH HOH . U 5 HOH E 4 404 404 HOH HOH . U 5 HOH E 5 405 405 HOH HOH . U 5 HOH E 6 406 406 HOH HOH . U 5 HOH E 7 407 407 HOH HOH . U 5 HOH E 8 408 408 HOH HOH . U 5 HOH E 9 409 409 HOH HOH . U 5 HOH E 10 410 410 HOH HOH . V 5 HOH F 1 401 401 HOH HOH . V 5 HOH F 2 402 402 HOH HOH . V 5 HOH F 3 403 403 HOH HOH . V 5 HOH F 4 404 404 HOH HOH . V 5 HOH F 5 405 405 HOH HOH . V 5 HOH F 6 406 406 HOH HOH . V 5 HOH F 7 407 407 HOH HOH . V 5 HOH F 8 408 408 HOH HOH . V 5 HOH F 9 409 409 HOH HOH . V 5 HOH F 10 410 410 HOH HOH . V 5 HOH F 11 411 411 HOH HOH . W 5 HOH G 1 201 201 HOH HOH . W 5 HOH G 2 202 202 HOH HOH . W 5 HOH G 3 203 203 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 NAP . . . O 3 32.149 -37.667 82.193 1 57.85 ? PA NAP 301 E 1 HETATM 2 O O1A NAP . . . O 3 33.414 -37.76 82.983 1 61.2 ? O1A NAP 301 E 1 HETATM 3 O O2A NAP . . . O 3 31.931 -36.597 81.151 1 58.9 ? O2A NAP 301 E 1 HETATM 4 O O5B NAP . . . O 3 31.614 -39.067 81.64 1 56.99 ? O5B NAP 301 E 1 HETATM 5 C C5B NAP . . . O 3 30.525 -38.869 80.634 1 45.28 ? C5B NAP 301 E 1 HETATM 6 C C4B NAP . . . O 3 30.722 -39.779 79.458 1 43.39 ? C4B NAP 301 E 1 HETATM 7 O O4B NAP . . . O 3 29.609 -39.686 78.532 1 38.36 ? O4B NAP 301 E 1 HETATM 8 C C3B NAP . . . O 3 32.01 -39.582 78.645 1 50.45 ? C3B NAP 301 E 1 HETATM 9 O O3B NAP . . . O 3 32.723 -40.805 78.46 1 47.93 ? O3B NAP 301 E 1 HETATM 10 C C2B NAP . . . O 3 31.428 -38.959 77.379 1 52.53 ? C2B NAP 301 E 1 HETATM 11 O O2B NAP . . . O 3 31.932 -38.264 76.262 1 49.21 ? O2B NAP 301 E 1 HETATM 12 C C1B NAP . . . O 3 30.16 -39.741 77.227 1 46.2 ? C1B NAP 301 E 1 HETATM 13 N N9A NAP . . . O 3 29.223 -39.234 76.238 1 48.18 ? N9A NAP 301 E 1 HETATM 14 C C8A NAP . . . O 3 28.648 -37.987 76.176 1 51.49 ? C8A NAP 301 E 1 HETATM 15 N N7A NAP . . . O 3 27.822 -37.834 75.171 1 53.16 ? N7A NAP 301 E 1 HETATM 16 C C5A NAP . . . O 3 27.841 -39.056 74.539 1 48.38 ? C5A NAP 301 E 1 HETATM 17 C C6A NAP . . . O 3 27.165 -39.528 73.41 1 45.11 ? C6A NAP 301 E 1 HETATM 18 N N6A NAP . . . O 3 26.32 -38.78 72.711 1 45.91 ? N6A NAP 301 E 1 HETATM 19 N N1A NAP . . . O 3 27.408 -40.807 73.042 1 46.75 ? N1A NAP 301 E 1 HETATM 20 C C2A NAP . . . O 3 28.26 -41.535 73.76 1 46.37 ? C2A NAP 301 E 1 HETATM 21 N N3A NAP . . . O 3 28.952 -41.198 74.836 1 43.04 ? N3A NAP 301 E 1 HETATM 22 C C4A NAP . . . O 3 28.697 -39.935 75.182 1 45.82 ? C4A NAP 301 E 1 HETATM 23 O O3 NAP . . . O 3 30.9 -37.435 83.237 1 71.14 ? O3 NAP 301 E 1 HETATM 24 P PN NAP . . . O 3 30.397 -38.06 84.661 1 55.34 ? PN NAP 301 E 1 HETATM 25 O O1N NAP . . . O 3 29.561 -36.947 85.238 1 60.2 ? O1N NAP 301 E 1 HETATM 26 O O2N NAP . . . O 3 31.527 -38.477 85.615 1 62.8 ? O2N NAP 301 E 1 HETATM 27 O O5D NAP . . . O 3 29.346 -39.204 84.234 1 52.94 ? O5D NAP 301 E 1 HETATM 28 C C5D NAP . . . O 3 28.348 -39.004 83.201 1 48.29 ? C5D NAP 301 E 1 HETATM 29 C C4D NAP . . . O 3 26.901 -38.775 83.629 1 44.52 ? C4D NAP 301 E 1 HETATM 30 O O4D NAP . . . O 3 26.896 -38.287 84.934 1 55.49 ? O4D NAP 301 E 1 HETATM 31 C C3D NAP . . . O 3 26.058 -37.708 82.856 1 46.8 ? C3D NAP 301 E 1 HETATM 32 O O3D NAP . . . O 3 24.942 -38.157 82.086 1 49.21 ? O3D NAP 301 E 1 HETATM 33 C C2D NAP . . . O 3 25.471 -36.716 83.883 1 47.21 ? C2D NAP 301 E 1 HETATM 34 O O2D NAP . . . O 3 24.219 -36.386 83.226 1 53.27 ? O2D NAP 301 E 1 HETATM 35 C C1D NAP . . . O 3 25.664 -37.648 85.122 1 49.9 ? C1D NAP 301 E 1 HETATM 36 N N1N NAP . . . O 3 25.664 -37.033 86.483 1 47.69 ? N1N NAP 301 E 1 HETATM 37 C C2N NAP . . . O 3 26.83 -36.427 86.896 1 51.86 ? C2N NAP 301 E 1 HETATM 38 C C3N NAP . . . O 3 26.865 -35.968 88.213 1 54.32 ? C3N NAP 301 E 1 HETATM 39 C C7N NAP . . . O 3 28.229 -35.59 88.789 1 59.17 ? C7N NAP 301 E 1 HETATM 40 O O7N NAP . . . O 3 28.365 -34.686 89.599 1 57.63 ? O7N NAP 301 E 1 HETATM 41 N N7N NAP . . . O 3 29.266 -36.295 88.351 1 52.52 ? N7N NAP 301 E 1 HETATM 42 C C4N NAP . . . O 3 25.722 -36.091 88.943 1 46.55 ? C4N NAP 301 E 1 HETATM 43 C C5N NAP . . . O 3 24.534 -36.175 88.278 1 39.7 ? C5N NAP 301 E 1 HETATM 44 C C6N NAP . . . O 3 24.568 -36.657 86.986 1 40.96 ? C6N NAP 301 E 1 HETATM 45 P P2B NAP . . . O 3 33.429 -38.174 75.743 1 68.65 ? P2B NAP 301 E 1 HETATM 46 O O1X NAP . . . O 3 33.71 -39.08 74.533 1 67.94 ? O1X NAP 301 E 1 HETATM 47 O O2X NAP . . . O 3 33.296 -36.705 75.411 1 62.89 ? O2X NAP 301 E 1 HETATM 48 O O3X NAP . . . O 3 34.389 -38.479 76.918 1 58.65 ? O3X NAP 301 E 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 48 #