data_2DFN
#
_model_server_result.job_id            '_JaaeYahIIZyXfdzXcKO7Q' 
_model_server_result.datetime_utc      '2024-10-20 19:41:42' 
_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          2dfn 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":500}' 
#
_entry.id    2DFN 
#
_exptl.entry_id    2DFN 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              174.151 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID' 
_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         120 
_cell.entry_id            2DFN 
_cell.length_a            63.296 
_cell.length_b            63.296 
_cell.length_c            91.61 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2DFN 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C7 H10 O5' 
_chem_comp.formula_weight    174.151 
_chem_comp.id                SKM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     SHIKIMATE 
#
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
O12 C8 SKM sing 321 n n 
O12 H12 SKM sing 322 n n 
C8 C6 SKM sing 323 n n 
C8 C9 SKM sing 324 n n 
C8 H8 SKM sing 325 n n 
C6 O7 SKM sing 326 n n 
C6 C5 SKM sing 327 n n 
C6 H6 SKM sing 328 n n 
O7 HO7 SKM sing 329 n n 
C5 C4 SKM sing 330 n n 
C5 H51 SKM sing 331 n n 
C5 H52 SKM sing 332 n n 
C4 C1 SKM sing 333 n n 
C4 C10 SKM doub 334 n n 
C1 O2 SKM sing 335 n n 
C1 O3 SKM doub 336 n n 
O2 HO2 SKM sing 337 n n 
C10 C9 SKM sing 338 n n 
C10 H10 SKM sing 339 n n 
C9 O11 SKM sing 340 n n 
C9 H9 SKM sing 341 n n 
O11 H11 SKM sing 342 n n 
#
_atom_sites.entry_id                     2DFN 
_atom_sites.fract_transf_matrix[1][1]    0.015799 
_atom_sites.fract_transf_matrix[1][2]    0.009121 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018243 
_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]    0.010916 
_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 CL A 1 1180 180 CL CL . 
C 3 ADP A 1 177 177 ADP ADP . 
D 4 SKM A 1 500 500 SKM SHI . 
E 5 HOH A 1 178 178 HOH HOH . 
E 5 HOH A 2 179 179 HOH HOH . 
E 5 HOH A 3 180 180 HOH HOH . 
E 5 HOH A 4 181 181 HOH HOH . 
E 5 HOH A 5 182 182 HOH HOH . 
E 5 HOH A 6 183 183 HOH HOH . 
E 5 HOH A 7 184 184 HOH HOH . 
E 5 HOH A 8 185 185 HOH HOH . 
E 5 HOH A 9 186 186 HOH HOH . 
E 5 HOH A 10 187 187 HOH HOH . 
E 5 HOH A 11 188 188 HOH HOH . 
E 5 HOH A 12 189 189 HOH HOH . 
E 5 HOH A 13 190 190 HOH HOH . 
E 5 HOH A 14 191 191 HOH HOH . 
E 5 HOH A 15 192 192 HOH HOH . 
E 5 HOH A 16 193 193 HOH HOH . 
E 5 HOH A 17 194 194 HOH HOH . 
E 5 HOH A 18 195 195 HOH HOH . 
E 5 HOH A 19 196 196 HOH HOH . 
E 5 HOH A 20 197 197 HOH HOH . 
E 5 HOH A 21 198 198 HOH HOH . 
E 5 HOH A 22 199 199 HOH HOH . 
E 5 HOH A 23 200 200 HOH HOH . 
E 5 HOH A 24 201 201 HOH HOH . 
E 5 HOH A 25 202 202 HOH HOH . 
E 5 HOH A 26 203 203 HOH HOH . 
E 5 HOH A 27 204 204 HOH HOH . 
E 5 HOH A 28 205 205 HOH HOH . 
E 5 HOH A 29 206 206 HOH HOH . 
E 5 HOH A 30 208 208 HOH HOH . 
E 5 HOH A 31 209 209 HOH HOH . 
E 5 HOH A 32 210 210 HOH HOH . 
E 5 HOH A 33 211 211 HOH HOH . 
E 5 HOH A 34 212 212 HOH HOH . 
E 5 HOH A 35 213 213 HOH HOH . 
E 5 HOH A 36 214 214 HOH HOH . 
E 5 HOH A 37 215 215 HOH HOH . 
E 5 HOH A 38 216 216 HOH HOH . 
E 5 HOH A 39 218 218 HOH HOH . 
E 5 HOH A 40 219 219 HOH HOH . 
E 5 HOH A 41 220 220 HOH HOH . 
E 5 HOH A 42 221 221 HOH HOH . 
E 5 HOH A 43 222 222 HOH HOH . 
E 5 HOH A 44 223 223 HOH HOH . 
E 5 HOH A 45 224 224 HOH HOH . 
E 5 HOH A 46 225 225 HOH HOH . 
E 5 HOH A 47 226 226 HOH HOH . 
E 5 HOH A 48 227 227 HOH HOH . 
E 5 HOH A 49 228 228 HOH HOH . 
E 5 HOH A 50 229 229 HOH HOH . 
E 5 HOH A 51 230 230 HOH HOH . 
E 5 HOH A 52 231 231 HOH HOH . 
E 5 HOH A 53 232 232 HOH HOH . 
E 5 HOH A 54 233 233 HOH HOH . 
E 5 HOH A 55 234 234 HOH HOH . 
E 5 HOH A 56 235 235 HOH HOH . 
E 5 HOH A 57 237 237 HOH HOH . 
E 5 HOH A 58 238 238 HOH HOH . 
E 5 HOH A 59 239 239 HOH HOH . 
E 5 HOH A 60 240 240 HOH HOH . 
E 5 HOH A 61 241 241 HOH HOH . 
E 5 HOH A 62 242 242 HOH HOH . 
E 5 HOH A 63 243 243 HOH HOH . 
E 5 HOH A 64 244 244 HOH HOH . 
E 5 HOH A 65 245 245 HOH HOH . 
E 5 HOH A 66 246 246 HOH HOH . 
E 5 HOH A 67 247 247 HOH HOH . 
E 5 HOH A 68 248 248 HOH HOH . 
E 5 HOH A 69 249 249 HOH HOH . 
E 5 HOH A 70 250 250 HOH HOH . 
E 5 HOH A 71 251 251 HOH HOH . 
E 5 HOH A 72 252 252 HOH HOH . 
E 5 HOH A 73 253 253 HOH HOH . 
E 5 HOH A 74 254 254 HOH HOH . 
E 5 HOH A 75 255 255 HOH HOH . 
E 5 HOH A 76 256 256 HOH HOH . 
E 5 HOH A 77 257 257 HOH HOH . 
E 5 HOH A 78 258 258 HOH HOH . 
E 5 HOH A 79 259 259 HOH HOH . 
E 5 HOH A 80 260 260 HOH HOH . 
E 5 HOH A 81 261 261 HOH HOH . 
E 5 HOH A 82 262 262 HOH HOH . 
E 5 HOH A 83 263 263 HOH HOH . 
E 5 HOH A 84 264 264 HOH HOH . 
E 5 HOH A 85 265 265 HOH HOH . 
E 5 HOH A 86 266 266 HOH HOH . 
E 5 HOH A 87 267 267 HOH HOH . 
E 5 HOH A 88 268 268 HOH HOH . 
E 5 HOH A 89 269 269 HOH HOH . 
E 5 HOH A 90 271 271 HOH HOH . 
E 5 HOH A 91 272 272 HOH HOH . 
E 5 HOH A 92 273 273 HOH HOH . 
E 5 HOH A 93 274 274 HOH HOH . 
E 5 HOH A 94 275 275 HOH HOH . 
E 5 HOH A 95 276 276 HOH HOH . 
E 5 HOH A 96 277 277 HOH HOH . 
E 5 HOH A 97 278 278 HOH HOH . 
E 5 HOH A 98 279 279 HOH HOH . 
E 5 HOH A 99 280 280 HOH HOH . 
E 5 HOH A 100 281 281 HOH HOH . 
E 5 HOH A 101 282 282 HOH HOH . 
E 5 HOH A 102 283 283 HOH HOH . 
E 5 HOH A 103 284 284 HOH HOH . 
E 5 HOH A 104 285 285 HOH HOH . 
E 5 HOH A 105 286 286 HOH HOH . 
E 5 HOH A 106 287 287 HOH HOH . 
E 5 HOH A 107 288 288 HOH HOH . 
E 5 HOH A 108 289 289 HOH HOH . 
E 5 HOH A 109 290 290 HOH HOH . 
E 5 HOH A 110 291 291 HOH HOH . 
E 5 HOH A 111 292 292 HOH HOH . 
E 5 HOH A 112 293 293 HOH HOH . 
E 5 HOH A 113 294 294 HOH HOH . 
E 5 HOH A 114 295 295 HOH HOH . 
E 5 HOH A 115 296 296 HOH HOH . 
E 5 HOH A 116 297 297 HOH HOH . 
E 5 HOH A 117 300 300 HOH HOH . 
E 5 HOH A 118 301 301 HOH HOH . 
E 5 HOH A 119 302 302 HOH HOH . 
E 5 HOH A 120 303 303 HOH HOH . 
E 5 HOH A 121 304 304 HOH HOH . 
E 5 HOH A 122 305 305 HOH HOH . 
E 5 HOH A 123 306 306 HOH HOH . 
E 5 HOH A 124 307 307 HOH HOH . 
E 5 HOH A 125 308 308 HOH HOH . 
E 5 HOH A 126 309 309 HOH HOH . 
E 5 HOH A 127 310 310 HOH HOH . 
E 5 HOH A 128 311 311 HOH HOH . 
E 5 HOH A 129 312 312 HOH HOH . 
E 5 HOH A 130 313 313 HOH HOH . 
E 5 HOH A 131 314 314 HOH HOH . 
E 5 HOH A 132 315 315 HOH HOH . 
E 5 HOH A 133 316 316 HOH HOH . 
E 5 HOH A 134 317 317 HOH HOH . 
E 5 HOH A 135 318 318 HOH HOH . 
E 5 HOH A 136 319 319 HOH HOH . 
E 5 HOH A 137 320 320 HOH HOH . 
E 5 HOH A 138 321 321 HOH HOH . 
E 5 HOH A 139 322 322 HOH HOH . 
E 5 HOH A 140 323 323 HOH HOH . 
E 5 HOH A 141 324 324 HOH HOH . 
E 5 HOH A 142 325 325 HOH HOH . 
E 5 HOH A 143 326 326 HOH HOH . 
E 5 HOH A 144 327 327 HOH HOH . 
E 5 HOH A 145 328 328 HOH HOH . 
E 5 HOH A 146 329 329 HOH HOH . 
E 5 HOH A 147 330 330 HOH HOH . 
E 5 HOH A 148 331 331 HOH HOH . 
E 5 HOH A 149 332 332 HOH HOH . 
E 5 HOH A 150 333 333 HOH HOH . 
E 5 HOH A 151 334 334 HOH HOH . 
E 5 HOH A 152 335 335 HOH HOH . 
E 5 HOH A 153 336 336 HOH HOH . 
E 5 HOH A 154 337 337 HOH HOH . 
E 5 HOH A 155 338 338 HOH HOH . 
E 5 HOH A 156 339 339 HOH HOH . 
E 5 HOH A 157 340 340 HOH HOH . 
E 5 HOH A 158 341 341 HOH HOH . 
E 5 HOH A 159 342 342 HOH HOH . 
E 5 HOH A 160 343 343 HOH HOH . 
E 5 HOH A 161 344 344 HOH HOH . 
E 5 HOH A 162 345 345 HOH HOH . 
E 5 HOH A 163 346 346 HOH HOH . 
E 5 HOH A 164 347 347 HOH HOH . 
E 5 HOH A 165 348 348 HOH HOH . 
E 5 HOH A 166 349 349 HOH HOH . 
E 5 HOH A 167 350 350 HOH HOH . 
E 5 HOH A 168 351 351 HOH HOH . 
E 5 HOH A 169 352 352 HOH HOH . 
E 5 HOH A 170 353 353 HOH HOH . 
E 5 HOH A 171 354 354 HOH HOH . 
E 5 HOH A 172 355 355 HOH HOH . 
E 5 HOH A 173 356 356 HOH HOH . 
E 5 HOH A 174 357 357 HOH HOH . 
E 5 HOH A 175 358 358 HOH HOH . 
E 5 HOH A 176 359 359 HOH HOH . 
E 5 HOH A 177 360 360 HOH HOH . 
E 5 HOH A 178 361 361 HOH HOH . 
E 5 HOH A 179 362 362 HOH HOH . 
E 5 HOH A 180 363 363 HOH HOH . 
E 5 HOH A 181 364 364 HOH HOH . 
E 5 HOH A 182 365 365 HOH HOH . 
E 5 HOH A 183 366 366 HOH HOH . 
E 5 HOH A 184 367 367 HOH HOH . 
E 5 HOH A 185 368 368 HOH HOH . 
E 5 HOH A 186 369 369 HOH HOH . 
E 5 HOH A 187 370 370 HOH HOH . 
E 5 HOH A 188 371 371 HOH HOH . 
E 5 HOH A 189 372 372 HOH HOH . 
E 5 HOH A 190 373 373 HOH HOH . 
E 5 HOH A 191 398 398 HOH HOH . 
E 5 HOH A 192 399 399 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 O O12 SKM . . . D 4 -14.387 -14.309 17.068 1 28.84 ? O12 SKM 500 A 1 
HETATM 2 C C8 SKM . . . D 4 -14.494 -13.422 15.958 1 32.04 ? C8 SKM 500 A 1 
HETATM 3 C C6 SKM . . . D 4 -15.956 -13.09 15.62 1 39.85 ? C6 SKM 500 A 1 
HETATM 4 O O7 SKM . . . D 4 -16.859 -12.645 16.677 1 24.87 ? O7 SKM 500 A 1 
HETATM 5 C C5 SKM . . . D 4 -16.477 -13.937 14.461 1 27.22 ? C5 SKM 500 A 1 
HETATM 6 C C4 SKM . . . D 4 -15.979 -15.148 14.165 1 29.72 ? C4 SKM 500 A 1 
HETATM 7 C C1 SKM . . . D 4 -16.716 -16.1 13.562 1 28.22 ? C1 SKM 500 A 1 
HETATM 8 O O2 SKM . . . D 4 -16.187 -17.219 13.402 1 36.5 ? O2 SKM 500 A 1 
HETATM 9 O O3 SKM . . . D 4 -17.883 -15.898 13.165 1 30.22 ? O3 SKM 500 A 1 
HETATM 10 C C10 SKM . . . D 4 -14.702 -15.395 14.534 1 30.63 ? C10 SKM 500 A 1 
HETATM 11 C C9 SKM . . . D 4 -13.819 -14.191 14.814 1 40.69 ? C9 SKM 500 A 1 
HETATM 12 O O11 SKM . . . D 4 -13.617 -13.34 13.667 1 34.67 ? O11 SKM 500 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           12 
#