data_8JFI # _model_server_result.job_id X4fVDOMfPA130sRxPRXECg _model_server_result.datetime_utc '2024-10-19 11:30:25' _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":"P","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 . . . P 3 0.127 -56.322 109.349 1 102.94 ? PA NAP 301 F 1 HETATM 2 O O1A NAP . . . P 3 0.105 -57.593 108.565 1 81.6 ? O1A NAP 301 F 1 HETATM 3 O O2A NAP . . . P 3 -1.079 -55.842 110.122 1 94.05 ? O2A NAP 301 F 1 HETATM 4 O O5B NAP . . . P 3 1.44 -56.101 110.247 1 85.32 ? O5B NAP 301 F 1 HETATM 5 C C5B NAP . . . P 3 1.383 -54.916 111.171 1 65.55 ? C5B NAP 301 F 1 HETATM 6 C C4B NAP . . . P 3 2.054 -55.225 112.493 1 71.52 ? C4B NAP 301 F 1 HETATM 7 O O4B NAP . . . P 3 2.377 -54.045 113.299 1 67.13 ? O4B NAP 301 F 1 HETATM 8 C C3B NAP . . . P 3 1.344 -56.222 113.436 1 80.99 ? C3B NAP 301 F 1 HETATM 9 O O3B NAP . . . P 3 2.22 -57.285 113.824 1 79.58 ? O3B NAP 301 F 1 HETATM 10 C C2B NAP . . . P 3 0.942 -55.287 114.571 1 74.12 ? C2B NAP 301 F 1 HETATM 11 O O2B NAP . . . P 3 0.016 -55.315 115.65 1 79.01 ? O2B NAP 301 F 1 HETATM 12 C C1B NAP . . . P 3 2.187 -54.437 114.659 1 65.03 ? C1B NAP 301 F 1 HETATM 13 N N9A NAP . . . P 3 2.089 -53.327 115.598 1 61.66 ? N9A NAP 301 F 1 HETATM 14 C C8A NAP . . . P 3 1.166 -52.313 115.602 1 64.09 ? C8A NAP 301 F 1 HETATM 15 N N7A NAP . . . P 3 1.317 -51.451 116.562 1 50.15 ? N7A NAP 301 F 1 HETATM 16 C C5A NAP . . . P 3 2.413 -51.921 117.236 1 58.07 ? C5A NAP 301 F 1 HETATM 17 C C6A NAP . . . P 3 3.085 -51.436 118.371 1 63.54 ? C6A NAP 301 F 1 HETATM 18 N N6A NAP . . . P 3 2.675 -50.337 118.987 1 68.29 ? N6A NAP 301 F 1 HETATM 19 N N1A NAP . . . P 3 4.164 -52.134 118.835 1 59.41 ? N1A NAP 301 F 1 HETATM 20 C C2A NAP . . . P 3 4.516 -53.234 118.176 1 61.62 ? C2A NAP 301 F 1 HETATM 21 N N3A NAP . . . P 3 3.95 -53.78 117.096 1 68.74 ? N3A NAP 301 F 1 HETATM 22 C C4A NAP . . . P 3 2.899 -53.079 116.666 1 62.47 ? C4A NAP 301 F 1 HETATM 23 O O3 NAP . . . P 3 0.437 -55.165 108.239 1 94.85 ? O3 NAP 301 F 1 HETATM 24 P PN NAP . . . P 3 1.099 -55.212 106.757 1 79.91 ? PN NAP 301 F 1 HETATM 25 O O1N NAP . . . P 3 0.154 -54.454 105.869 1 77.9 ? O1N NAP 301 F 1 HETATM 26 O O2N NAP . . . P 3 1.374 -56.611 106.296 1 87.61 ? O2N NAP 301 F 1 HETATM 27 O O5D NAP . . . P 3 2.476 -54.396 106.897 1 76.22 ? O5D NAP 301 F 1 HETATM 28 C C5D NAP . . . P 3 2.848 -53.604 108.05 1 71.59 ? C5D NAP 301 F 1 HETATM 29 C C4D NAP . . . P 3 3.526 -52.266 107.733 1 64.26 ? C4D NAP 301 F 1 HETATM 30 O O4D NAP . . . P 3 3.568 -52.047 106.34 1 58.69 ? O4D NAP 301 F 1 HETATM 31 C C3D NAP . . . P 3 2.893 -50.952 108.294 1 62.07 ? C3D NAP 301 F 1 HETATM 32 O O3D NAP . . . P 3 3.737 -49.807 108.469 1 58.6 ? O3D NAP 301 F 1 HETATM 33 C C2D NAP . . . P 3 1.8 -50.664 107.242 1 62.37 ? C2D NAP 301 F 1 HETATM 34 O O2D NAP . . . P 3 1.19 -49.446 107.756 1 58.41 ? O2D NAP 301 F 1 HETATM 35 C C1D NAP . . . P 3 2.825 -50.887 106.061 1 62.09 ? C1D NAP 301 F 1 HETATM 36 N N1N NAP . . . P 3 2.337 -50.985 104.651 1 57.95 ? N1N NAP 301 F 1 HETATM 37 C C2N NAP . . . P 3 1.29 -51.814 104.272 1 60.84 ? C2N NAP 301 F 1 HETATM 38 C C3N NAP . . . P 3 0.761 -51.626 102.969 1 66.84 ? C3N NAP 301 F 1 HETATM 39 C C7N NAP . . . P 3 -0.063 -52.725 102.266 1 66.97 ? C7N NAP 301 F 1 HETATM 40 O O7N NAP . . . P 3 -0.915 -52.45 101.431 1 60.71 ? O7N NAP 301 F 1 HETATM 41 N N7N NAP . . . P 3 0.18 -53.995 102.584 1 65.25 ? N7N NAP 301 F 1 HETATM 42 C C4N NAP . . . P 3 1.184 -50.521 102.279 1 64.15 ? C4N NAP 301 F 1 HETATM 43 C C5N NAP . . . P 3 2.201 -49.751 102.771 1 60.08 ? C5N NAP 301 F 1 HETATM 44 C C6N NAP . . . P 3 2.952 -50.307 103.782 1 52.94 ? C6N NAP 301 F 1 HETATM 45 P P2B NAP . . . P 3 -0.458 -56.493 116.61 1 78.72 ? P2B NAP 301 F 1 HETATM 46 O O1X NAP . . . P 3 0.292 -56.573 117.944 1 60.9 ? O1X NAP 301 F 1 HETATM 47 O O2X NAP . . . P 3 -1.859 -55.952 116.77 1 86.94 ? O2X NAP 301 F 1 HETATM 48 O O3X NAP . . . P 3 -0.427 -57.786 115.756 1 75.63 ? O3X NAP 301 F 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 48 #