data_3T8A # _model_server_result.job_id 0AHOwbq6cozkA70RjjDtTw _model_server_result.datetime_utc '2024-10-14 16:26:57' _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 3t8a # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 3T8A # _exptl.entry_id 3T8A _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 954.663 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'o-succinylbenzoyl-N-coenzyme A' _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 3T8A _cell.length_a 87.133 _cell.length_b 87.133 _cell.length_c 414.84 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3T8A _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 10_664 -y+1,-x+1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 43.5665 75.459392 -69.14 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 E N N # _chem_comp.formula 'C32 H45 N8 O20 P3' _chem_comp.formula_weight 954.663 _chem_comp.id S0N _chem_comp.mon_nstd_flag . _chem_comp.name 'o-succinylbenzoyl-N-coenzyme A' _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 C02 C01 S0N sing 277 n n C01 H01 S0N sing 278 n n C01 H01A S0N sing 279 n n C01 H01B S0N sing 280 n n C04 C02 S0N sing 281 n n C36 C02 S0N sing 282 n n C02 C03 S0N sing 283 n n C03 H03 S0N sing 284 n n C03 H03A S0N sing 285 n n C03 H03B S0N sing 286 n n O05 C04 S0N sing 287 n n C04 H04 S0N sing 288 n n C04 H04A S0N sing 289 n n P06 O05 S0N sing 290 n n O08 P06 S0N doub 291 n n O07 P06 S0N sing 292 n n O09 P06 S0N sing 293 n n O07 HO07 S0N sing 294 n n P10 O09 S0N sing 295 n n O11 P10 S0N doub 296 n n P10 O13 S0N sing 297 n n P10 O12 S0N sing 298 n n O12 HO12 S0N sing 299 n n C14 O13 S0N sing 300 n n C14 C15 S0N sing 301 n n C14 H14 S0N sing 302 n n C14 H14A S0N sing 303 n n C15 C30 S0N sing 304 n n C15 O16 S0N sing 305 n n C15 H15 S0N sing 306 n n O16 C17 S0N sing 307 n n C28 C17 S0N sing 308 n n C17 N18 S0N sing 309 n n C17 H17 S0N sing 310 n n N18 C19 S0N sing 311 n y N18 C27 S0N sing 312 n y C19 N20 S0N doub 313 n y C19 H19 S0N sing 314 n n N20 C21 S0N sing 315 n y C27 C21 S0N doub 316 n y C21 C22 S0N sing 317 n y C22 N24 S0N doub 318 n y C22 N23 S0N sing 319 n n N23 HN23 S0N sing 320 n n N23 HN2A S0N sing 321 n n C25 N24 S0N sing 322 n y N26 C25 S0N doub 323 n y C25 H25 S0N sing 324 n n C27 N26 S0N sing 325 n y C30 C28 S0N sing 326 n n C28 O29 S0N sing 327 n n C28 H28 S0N sing 328 n n O29 HO29 S0N sing 329 n n O31 C30 S0N sing 330 n n C30 H30 S0N sing 331 n n P32 O31 S0N sing 332 n n O35 P32 S0N doub 333 n n O33 P32 S0N sing 334 n n P32 O34 S0N sing 335 n n O33 HO33 S0N sing 336 n n O34 HO34 S0N sing 337 n n O37 C36 S0N sing 338 n n C36 C38 S0N sing 339 n n C36 H36 S0N sing 340 n n O37 HO37 S0N sing 341 n n C38 N40 S0N sing 342 n n C38 O39 S0N doub 343 n n N40 C41 S0N sing 344 n n N40 HN40 S0N sing 345 n n C41 C42 S0N sing 346 n n C41 H41 S0N sing 347 n n C41 H41A S0N sing 348 n n C42 C43 S0N sing 349 n n C42 H42 S0N sing 350 n n C42 H42A S0N sing 351 n n C43 O44 S0N doub 352 n n C43 N45 S0N sing 353 n n N45 C46 S0N sing 354 n n N45 HN45 S0N sing 355 n n C46 C47 S0N sing 356 n n C46 H46 S0N sing 357 n n C46 H46A S0N sing 358 n n C47 N48 S0N sing 359 n n C47 H47 S0N sing 360 n n C47 H47A S0N sing 361 n n N48 C49 S0N sing 362 n n N48 HN48 S0N sing 363 n n O50 C49 S0N doub 364 n n C49 C51 S0N sing 365 n n C51 C52 S0N sing 366 n n C51 H51 S0N sing 367 n n C51 H51A S0N sing 368 n n C52 C53 S0N sing 369 n n C52 H52 S0N sing 370 n n C52 H52A S0N sing 371 n n C53 O54 S0N doub 372 n n C53 C55 S0N sing 373 n n C60 C55 S0N doub 374 n y C55 C56 S0N sing 375 n y C56 C57 S0N doub 376 n y C56 H56 S0N sing 377 n n C58 C57 S0N sing 378 n y C57 H57 S0N sing 379 n n C59 C58 S0N doub 380 n y C58 H58 S0N sing 381 n n C60 C59 S0N sing 382 n y C59 H59 S0N sing 383 n n C61 C60 S0N sing 384 n n O62 C61 S0N doub 385 n n O63 C61 S0N sing 386 n n O63 HO63 S0N sing 387 n n # _atom_sites.entry_id 3T8A _atom_sites.fract_transf_matrix[1][1] 0.011477 _atom_sites.fract_transf_matrix[1][2] 0.006626 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013252 _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] 0.002411 _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 D 2 S0N B 1 500 500 S0N S0N . E 2 S0N C 1 600 600 S0N S0N . F 3 HOH A 1 315 10 HOH HOH . F 3 HOH A 2 316 12 HOH HOH . F 3 HOH A 3 317 13 HOH HOH . F 3 HOH A 4 318 15 HOH HOH . F 3 HOH A 5 319 17 HOH HOH . F 3 HOH A 6 320 27 HOH HOH . F 3 HOH A 7 321 28 HOH HOH . F 3 HOH A 8 322 29 HOH HOH . F 3 HOH A 9 323 35 HOH HOH . F 3 HOH A 10 324 44 HOH HOH . F 3 HOH A 11 325 50 HOH HOH . F 3 HOH A 12 326 54 HOH HOH . F 3 HOH A 13 327 63 HOH HOH . F 3 HOH A 14 328 70 HOH HOH . F 3 HOH A 15 329 75 HOH HOH . F 3 HOH A 16 330 89 HOH HOH . F 3 HOH A 17 331 92 HOH HOH . F 3 HOH A 18 332 94 HOH HOH . F 3 HOH A 19 333 97 HOH HOH . F 3 HOH A 20 334 98 HOH HOH . F 3 HOH A 21 335 99 HOH HOH . F 3 HOH A 22 336 102 HOH HOH . F 3 HOH A 23 337 105 HOH HOH . F 3 HOH A 24 338 110 HOH HOH . F 3 HOH A 25 339 113 HOH HOH . F 3 HOH A 26 340 116 HOH HOH . F 3 HOH A 27 341 120 HOH HOH . F 3 HOH A 28 342 124 HOH HOH . F 3 HOH A 29 343 141 HOH HOH . F 3 HOH A 30 344 146 HOH HOH . F 3 HOH A 31 345 152 HOH HOH . F 3 HOH A 32 346 188 HOH HOH . F 3 HOH A 33 347 192 HOH HOH . F 3 HOH A 34 348 209 HOH HOH . F 3 HOH A 35 349 211 HOH HOH . F 3 HOH A 36 350 232 HOH HOH . F 3 HOH A 37 351 256 HOH HOH . F 3 HOH A 38 352 279 HOH HOH . G 3 HOH B 1 315 1 HOH HOH . G 3 HOH B 2 316 2 HOH HOH . G 3 HOH B 3 317 5 HOH HOH . G 3 HOH B 4 318 7 HOH HOH . G 3 HOH B 5 319 8 HOH HOH . G 3 HOH B 6 320 9 HOH HOH . G 3 HOH B 7 321 14 HOH HOH . G 3 HOH B 8 322 18 HOH HOH . G 3 HOH B 9 323 21 HOH HOH . G 3 HOH B 10 324 22 HOH HOH . G 3 HOH B 11 325 24 HOH HOH . G 3 HOH B 12 326 26 HOH HOH . G 3 HOH B 13 327 30 HOH HOH . G 3 HOH B 14 328 33 HOH HOH . G 3 HOH B 15 329 36 HOH HOH . G 3 HOH B 16 330 37 HOH HOH . G 3 HOH B 17 331 38 HOH HOH . G 3 HOH B 18 332 39 HOH HOH . G 3 HOH B 19 333 40 HOH HOH . G 3 HOH B 20 334 41 HOH HOH . G 3 HOH B 21 335 47 HOH HOH . G 3 HOH B 22 336 48 HOH HOH . G 3 HOH B 23 337 57 HOH HOH . G 3 HOH B 24 338 58 HOH HOH . G 3 HOH B 25 339 64 HOH HOH . G 3 HOH B 26 340 71 HOH HOH . G 3 HOH B 27 341 78 HOH HOH . G 3 HOH B 28 342 82 HOH HOH . G 3 HOH B 29 343 90 HOH HOH . G 3 HOH B 30 344 96 HOH HOH . G 3 HOH B 31 345 109 HOH HOH . G 3 HOH B 32 346 130 HOH HOH . G 3 HOH B 33 347 144 HOH HOH . G 3 HOH B 34 348 148 HOH HOH . G 3 HOH B 35 349 156 HOH HOH . G 3 HOH B 36 350 158 HOH HOH . G 3 HOH B 37 351 170 HOH HOH . G 3 HOH B 38 352 182 HOH HOH . G 3 HOH B 39 353 184 HOH HOH . G 3 HOH B 40 354 189 HOH HOH . G 3 HOH B 41 355 218 HOH HOH . G 3 HOH B 42 356 310 HOH HOH . H 3 HOH C 1 315 6 HOH HOH . H 3 HOH C 2 316 11 HOH HOH . H 3 HOH C 3 317 16 HOH HOH . H 3 HOH C 4 318 19 HOH HOH . H 3 HOH C 5 319 23 HOH HOH . H 3 HOH C 6 320 25 HOH HOH . H 3 HOH C 7 321 31 HOH HOH . H 3 HOH C 8 322 43 HOH HOH . H 3 HOH C 9 323 49 HOH HOH . H 3 HOH C 10 324 53 HOH HOH . H 3 HOH C 11 325 61 HOH HOH . H 3 HOH C 12 326 62 HOH HOH . H 3 HOH C 13 327 66 HOH HOH . H 3 HOH C 14 328 76 HOH HOH . H 3 HOH C 15 329 84 HOH HOH . H 3 HOH C 16 330 87 HOH HOH . H 3 HOH C 17 331 88 HOH HOH . H 3 HOH C 18 332 101 HOH HOH . H 3 HOH C 19 333 106 HOH HOH . H 3 HOH C 20 334 127 HOH HOH . H 3 HOH C 21 335 128 HOH HOH . H 3 HOH C 22 336 129 HOH HOH . H 3 HOH C 23 337 161 HOH HOH . H 3 HOH C 24 338 187 HOH HOH . H 3 HOH C 25 339 200 HOH HOH . H 3 HOH C 26 340 204 HOH HOH . H 3 HOH C 27 341 210 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 C C01 S0N . . . D 2 17.87 52.742 -62.494 1 46.49 ? C01 S0N 500 B 1 HETATM 2 C C02 S0N . . . D 2 16.436 53.259 -62.311 0.79 51.21 ? C02 S0N 500 B 1 HETATM 3 C C03 S0N . . . D 2 15.733 52.441 -61.207 1 45.92 ? C03 S0N 500 B 1 HETATM 4 C C04 S0N . . . D 2 15.613 53.044 -63.642 0.89 48.39 ? C04 S0N 500 B 1 HETATM 5 O O05 S0N . . . D 2 15.811 54.206 -64.437 0.5 56.83 ? O05 S0N 500 B 1 HETATM 6 P P06 S0N . . . D 2 14.928 54.523 -65.789 0.86 52.55 ? P06 S0N 500 B 1 HETATM 7 O O07 S0N . . . D 2 14.374 53.214 -66.418 0.72 51.89 ? O07 S0N 500 B 1 HETATM 8 O O08 S0N . . . D 2 15.835 55.251 -66.812 0.61 64.46 ? O08 S0N 500 B 1 HETATM 9 O O09 S0N . . . D 2 13.677 55.458 -65.401 0.93 48.02 ? O09 S0N 500 B 1 HETATM 10 P P10 S0N . . . D 2 13.884 56.928 -64.815 0.75 55.71 ? P10 S0N 500 B 1 HETATM 11 O O11 S0N . . . D 2 13.616 58.005 -65.942 0.56 63.85 ? O11 S0N 500 B 1 HETATM 12 O O12 S0N . . . D 2 15.308 57.082 -64.197 1 53.97 ? O12 S0N 500 B 1 HETATM 13 O O13 S0N . . . D 2 12.814 57.107 -63.678 0.92 51.7 ? O13 S0N 500 B 1 HETATM 14 C C14 S0N . . . D 2 11.412 57.239 -63.975 1 49.04 ? C14 S0N 500 B 1 HETATM 15 C C15 S0N . . . D 2 10.724 58.431 -63.227 0.91 52.35 ? C15 S0N 500 B 1 HETATM 16 O O16 S0N . . . D 2 10.754 58.145 -61.773 0.85 47.29 ? O16 S0N 500 B 1 HETATM 17 C C17 S0N . . . D 2 11.764 59.03 -61.155 0.82 50.25 ? C17 S0N 500 B 1 HETATM 18 N N18 S0N . . . D 2 12.422 58.129 -60.17 0.66 51.9 ? N18 S0N 500 B 1 HETATM 19 C C19 S0N . . . D 2 12.912 56.892 -60.424 0.9 49.04 ? C19 S0N 500 B 1 HETATM 20 N N20 S0N . . . D 2 13.479 56.41 -59.241 0.98 45.65 ? N20 S0N 500 B 1 HETATM 21 C C21 S0N . . . D 2 13.332 57.384 -58.262 1 47 ? C21 S0N 500 B 1 HETATM 22 C C22 S0N . . . D 2 13.717 57.422 -56.89 0.72 50.22 ? C22 S0N 500 B 1 HETATM 23 N N23 S0N . . . D 2 14.398 56.282 -56.276 1 41.83 ? N23 S0N 500 B 1 HETATM 24 N N24 S0N . . . D 2 13.438 58.528 -56.147 0.57 52.18 ? N24 S0N 500 B 1 HETATM 25 C C25 S0N . . . D 2 12.793 59.59 -56.702 0.72 52.82 ? C25 S0N 500 B 1 HETATM 26 N N26 S0N . . . D 2 12.406 59.548 -58.071 0.78 50.99 ? N26 S0N 500 B 1 HETATM 27 C C27 S0N . . . D 2 12.685 58.443 -58.814 1 48.19 ? C27 S0N 500 B 1 HETATM 28 C C28 S0N . . . D 2 12.618 59.632 -62.267 0.92 55.68 ? C28 S0N 500 B 1 HETATM 29 O O29 S0N . . . D 2 13.06 60.995 -61.918 0.79 60 ? O29 S0N 500 B 1 HETATM 30 C C30 S0N . . . D 2 11.591 59.696 -63.399 0.91 57.14 ? C30 S0N 500 B 1 HETATM 31 O O31 S0N . . . D 2 10.813 60.907 -63.248 0.71 62.41 ? O31 S0N 500 B 1 HETATM 32 P P32 S0N . . . D 2 10.793 61.973 -64.441 0.73 67.97 ? P32 S0N 500 B 1 HETATM 33 O O33 S0N . . . D 2 11.65 63.21 -64.015 1 59.56 ? O33 S0N 500 B 1 HETATM 34 O O34 S0N . . . D 2 9.308 62.36 -64.61 0.81 66.3 ? O34 S0N 500 B 1 HETATM 35 O O35 S0N . . . D 2 11.346 61.325 -65.78 1 61.9 ? O35 S0N 500 B 1 HETATM 36 C C36 S0N . . . D 2 16.288 54.779 -61.875 0.79 56.57 ? C36 S0N 500 B 1 HETATM 37 O O37 S0N . . . D 2 14.904 55.024 -61.875 0.65 59.55 ? O37 S0N 500 B 1 HETATM 38 C C38 S0N . . . D 2 16.883 54.992 -60.472 1 53.64 ? C38 S0N 500 B 1 HETATM 39 O O39 S0N . . . D 2 17.818 54.357 -60.123 0.75 57.38 ? O39 S0N 500 B 1 HETATM 40 N N40 S0N . . . D 2 16.299 55.981 -59.555 1 54.99 ? N40 S0N 500 B 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 602 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 40 #