data_1RD5
#
_model_server_result.job_id            DFS7lRntEnY_N7MKMLmRNQ 
_model_server_result.datetime_utc      '2024-11-23 08:49:03' 
_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          1rd5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    1RD5 
#
_exptl.entry_id    1RD5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              104.061 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MALONIC ACID' 
_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         90 
_cell.entry_id            1RD5 
_cell.length_a            91.094 
_cell.length_b            159.815 
_cell.length_c            162.877 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1RD5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        22 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'F 2 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
PISA,PQS octameric 8 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E 1 1 
B,D,F 2 1 
A,B,C,D,E,F 3 1,2,3,4 
#
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' 8_555 x,-y+1/2,-z+1/2 1 0 0 0 -1 0 0 0 -1 0 79.9075 81.4385 
3 'crystal symmetry operation' 11_555 -x+1/2,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 45.547 0 81.4385 
4 'crystal symmetry operation' 14_555 -x+1/2,-y+1/2,z -1 0 0 0 -1 0 0 0 1 45.547 79.9075 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C3 H4 O4' 
_chem_comp.formula_weight    104.061 
_chem_comp.id                MLA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MALONIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'DICARBOXYLIC ACID C3;PROPANEDIOLIC ACID;METHANEDICARBOXYLIC ACID' 
#
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
C1 O1A MLA sing 237 n n 
C1 O1B MLA doub 238 n n 
C1 C2 MLA sing 239 n n 
O1A H1A MLA sing 240 n n 
C2 C3 MLA sing 241 n n 
C2 HC21 MLA sing 242 n n 
C2 HC22 MLA sing 243 n n 
C3 O3A MLA doub 244 n n 
C3 O3B MLA sing 245 n n 
O3B H3B MLA sing 246 n n 
#
_atom_sites.entry_id                     1RD5 
_atom_sites.fract_transf_matrix[1][1]    0.010978 
_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]    0.006257 
_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]    0.00614 
_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 MLA A 1 302 302 MLA MLA . 
D 2 MLA B 1 301 301 MLA MLA . 
E 3 HOH A 1 303 2 HOH HOH . 
E 3 HOH A 2 304 3 HOH HOH . 
E 3 HOH A 3 305 4 HOH HOH . 
E 3 HOH A 4 306 7 HOH HOH . 
E 3 HOH A 5 307 9 HOH HOH . 
E 3 HOH A 6 308 10 HOH HOH . 
E 3 HOH A 7 309 11 HOH HOH . 
E 3 HOH A 8 310 12 HOH HOH . 
E 3 HOH A 9 311 14 HOH HOH . 
E 3 HOH A 10 312 18 HOH HOH . 
E 3 HOH A 11 313 22 HOH HOH . 
E 3 HOH A 12 314 24 HOH HOH . 
E 3 HOH A 13 315 25 HOH HOH . 
E 3 HOH A 14 316 28 HOH HOH . 
E 3 HOH A 15 317 33 HOH HOH . 
E 3 HOH A 16 318 34 HOH HOH . 
E 3 HOH A 17 319 36 HOH HOH . 
E 3 HOH A 18 320 37 HOH HOH . 
E 3 HOH A 19 321 38 HOH HOH . 
E 3 HOH A 20 322 44 HOH HOH . 
E 3 HOH A 21 323 45 HOH HOH . 
E 3 HOH A 22 324 46 HOH HOH . 
E 3 HOH A 23 325 47 HOH HOH . 
E 3 HOH A 24 326 51 HOH HOH . 
E 3 HOH A 25 327 54 HOH HOH . 
E 3 HOH A 26 328 55 HOH HOH . 
E 3 HOH A 27 329 59 HOH HOH . 
E 3 HOH A 28 330 60 HOH HOH . 
E 3 HOH A 29 331 61 HOH HOH . 
E 3 HOH A 30 332 63 HOH HOH . 
E 3 HOH A 31 333 65 HOH HOH . 
E 3 HOH A 32 334 66 HOH HOH . 
E 3 HOH A 33 335 67 HOH HOH . 
E 3 HOH A 34 336 69 HOH HOH . 
E 3 HOH A 35 337 70 HOH HOH . 
E 3 HOH A 36 338 72 HOH HOH . 
E 3 HOH A 37 339 73 HOH HOH . 
E 3 HOH A 38 340 75 HOH HOH . 
E 3 HOH A 39 341 76 HOH HOH . 
E 3 HOH A 40 342 79 HOH HOH . 
E 3 HOH A 41 343 80 HOH HOH . 
E 3 HOH A 42 344 81 HOH HOH . 
E 3 HOH A 43 345 82 HOH HOH . 
E 3 HOH A 44 346 85 HOH HOH . 
E 3 HOH A 45 347 86 HOH HOH . 
E 3 HOH A 46 348 87 HOH HOH . 
E 3 HOH A 47 349 89 HOH HOH . 
E 3 HOH A 48 350 90 HOH HOH . 
E 3 HOH A 49 351 91 HOH HOH . 
E 3 HOH A 50 352 92 HOH HOH . 
E 3 HOH A 51 353 94 HOH HOH . 
E 3 HOH A 52 354 98 HOH HOH . 
E 3 HOH A 53 355 102 HOH HOH . 
E 3 HOH A 54 356 105 HOH HOH . 
E 3 HOH A 55 357 108 HOH HOH . 
E 3 HOH A 56 358 113 HOH HOH . 
E 3 HOH A 57 359 114 HOH HOH . 
E 3 HOH A 58 360 116 HOH HOH . 
E 3 HOH A 59 361 117 HOH HOH . 
E 3 HOH A 60 362 118 HOH HOH . 
E 3 HOH A 61 363 119 HOH HOH . 
E 3 HOH A 62 364 121 HOH HOH . 
E 3 HOH A 63 365 123 HOH HOH . 
E 3 HOH A 64 366 125 HOH HOH . 
E 3 HOH A 65 367 127 HOH HOH . 
E 3 HOH A 66 368 131 HOH HOH . 
E 3 HOH A 67 369 135 HOH HOH . 
E 3 HOH A 68 370 136 HOH HOH . 
E 3 HOH A 69 371 139 HOH HOH . 
E 3 HOH A 70 372 140 HOH HOH . 
E 3 HOH A 71 373 141 HOH HOH . 
E 3 HOH A 72 374 142 HOH HOH . 
E 3 HOH A 73 375 144 HOH HOH . 
E 3 HOH A 74 376 145 HOH HOH . 
E 3 HOH A 75 377 147 HOH HOH . 
E 3 HOH A 76 378 151 HOH HOH . 
E 3 HOH A 77 379 153 HOH HOH . 
E 3 HOH A 78 380 155 HOH HOH . 
E 3 HOH A 79 381 156 HOH HOH . 
E 3 HOH A 80 382 157 HOH HOH . 
E 3 HOH A 81 383 160 HOH HOH . 
E 3 HOH A 82 384 162 HOH HOH . 
E 3 HOH A 83 385 163 HOH HOH . 
E 3 HOH A 84 386 164 HOH HOH . 
E 3 HOH A 85 387 165 HOH HOH . 
E 3 HOH A 86 388 166 HOH HOH . 
E 3 HOH A 87 389 172 HOH HOH . 
E 3 HOH A 88 390 173 HOH HOH . 
E 3 HOH A 89 391 176 HOH HOH . 
E 3 HOH A 90 392 178 HOH HOH . 
E 3 HOH A 91 393 179 HOH HOH . 
E 3 HOH A 92 394 182 HOH HOH . 
E 3 HOH A 93 395 186 HOH HOH . 
E 3 HOH A 94 396 187 HOH HOH . 
E 3 HOH A 95 397 188 HOH HOH . 
E 3 HOH A 96 398 189 HOH HOH . 
E 3 HOH A 97 399 191 HOH HOH . 
E 3 HOH A 98 400 192 HOH HOH . 
E 3 HOH A 99 401 193 HOH HOH . 
E 3 HOH A 100 402 196 HOH HOH . 
E 3 HOH A 101 403 197 HOH HOH . 
E 3 HOH A 102 404 199 HOH HOH . 
E 3 HOH A 103 405 202 HOH HOH . 
E 3 HOH A 104 406 208 HOH HOH . 
E 3 HOH A 105 407 209 HOH HOH . 
E 3 HOH A 106 408 212 HOH HOH . 
E 3 HOH A 107 409 215 HOH HOH . 
E 3 HOH A 108 410 217 HOH HOH . 
E 3 HOH A 109 411 218 HOH HOH . 
E 3 HOH A 110 412 219 HOH HOH . 
E 3 HOH A 111 413 220 HOH HOH . 
E 3 HOH A 112 414 222 HOH HOH . 
E 3 HOH A 113 415 223 HOH HOH . 
E 3 HOH A 114 416 225 HOH HOH . 
E 3 HOH A 115 417 226 HOH HOH . 
E 3 HOH A 116 418 227 HOH HOH . 
E 3 HOH A 117 419 228 HOH HOH . 
E 3 HOH A 118 420 229 HOH HOH . 
E 3 HOH A 119 421 231 HOH HOH . 
E 3 HOH A 120 422 232 HOH HOH . 
E 3 HOH A 121 423 233 HOH HOH . 
E 3 HOH A 122 424 234 HOH HOH . 
E 3 HOH A 123 425 235 HOH HOH . 
E 3 HOH A 124 426 236 HOH HOH . 
E 3 HOH A 125 427 237 HOH HOH . 
E 3 HOH A 126 428 240 HOH HOH . 
E 3 HOH A 127 429 242 HOH HOH . 
E 3 HOH A 128 430 243 HOH HOH . 
E 3 HOH A 129 431 245 HOH HOH . 
E 3 HOH A 130 432 247 HOH HOH . 
F 3 HOH B 1 302 1 HOH HOH . 
F 3 HOH B 2 303 5 HOH HOH . 
F 3 HOH B 3 304 6 HOH HOH . 
F 3 HOH B 4 305 8 HOH HOH . 
F 3 HOH B 5 306 13 HOH HOH . 
F 3 HOH B 6 307 15 HOH HOH . 
F 3 HOH B 7 308 16 HOH HOH . 
F 3 HOH B 8 309 17 HOH HOH . 
F 3 HOH B 9 310 19 HOH HOH . 
F 3 HOH B 10 311 20 HOH HOH . 
F 3 HOH B 11 312 21 HOH HOH . 
F 3 HOH B 12 313 23 HOH HOH . 
F 3 HOH B 13 314 26 HOH HOH . 
F 3 HOH B 14 315 27 HOH HOH . 
F 3 HOH B 15 316 29 HOH HOH . 
F 3 HOH B 16 317 30 HOH HOH . 
F 3 HOH B 17 318 31 HOH HOH . 
F 3 HOH B 18 319 32 HOH HOH . 
F 3 HOH B 19 320 35 HOH HOH . 
F 3 HOH B 20 321 39 HOH HOH . 
F 3 HOH B 21 322 40 HOH HOH . 
F 3 HOH B 22 323 41 HOH HOH . 
F 3 HOH B 23 324 42 HOH HOH . 
F 3 HOH B 24 325 43 HOH HOH . 
F 3 HOH B 25 326 48 HOH HOH . 
F 3 HOH B 26 327 49 HOH HOH . 
F 3 HOH B 27 328 50 HOH HOH . 
F 3 HOH B 28 329 52 HOH HOH . 
F 3 HOH B 29 330 53 HOH HOH . 
F 3 HOH B 30 331 56 HOH HOH . 
F 3 HOH B 31 332 57 HOH HOH . 
F 3 HOH B 32 333 58 HOH HOH . 
F 3 HOH B 33 334 62 HOH HOH . 
F 3 HOH B 34 335 64 HOH HOH . 
F 3 HOH B 35 336 68 HOH HOH . 
F 3 HOH B 36 337 71 HOH HOH . 
F 3 HOH B 37 338 74 HOH HOH . 
F 3 HOH B 38 339 77 HOH HOH . 
F 3 HOH B 39 340 78 HOH HOH . 
F 3 HOH B 40 341 83 HOH HOH . 
F 3 HOH B 41 342 84 HOH HOH . 
F 3 HOH B 42 343 88 HOH HOH . 
F 3 HOH B 43 344 93 HOH HOH . 
F 3 HOH B 44 345 95 HOH HOH . 
F 3 HOH B 45 346 96 HOH HOH . 
F 3 HOH B 46 347 97 HOH HOH . 
F 3 HOH B 47 348 99 HOH HOH . 
F 3 HOH B 48 349 100 HOH HOH . 
F 3 HOH B 49 350 101 HOH HOH . 
F 3 HOH B 50 351 103 HOH HOH . 
F 3 HOH B 51 352 104 HOH HOH . 
F 3 HOH B 52 353 106 HOH HOH . 
F 3 HOH B 53 354 107 HOH HOH . 
F 3 HOH B 54 355 109 HOH HOH . 
F 3 HOH B 55 356 110 HOH HOH . 
F 3 HOH B 56 357 111 HOH HOH . 
F 3 HOH B 57 358 112 HOH HOH . 
F 3 HOH B 58 359 115 HOH HOH . 
F 3 HOH B 59 360 120 HOH HOH . 
F 3 HOH B 60 361 122 HOH HOH . 
F 3 HOH B 61 362 124 HOH HOH . 
F 3 HOH B 62 363 126 HOH HOH . 
F 3 HOH B 63 364 128 HOH HOH . 
F 3 HOH B 64 365 129 HOH HOH . 
F 3 HOH B 65 366 130 HOH HOH . 
F 3 HOH B 66 367 132 HOH HOH . 
F 3 HOH B 67 368 133 HOH HOH . 
F 3 HOH B 68 369 134 HOH HOH . 
F 3 HOH B 69 370 137 HOH HOH . 
F 3 HOH B 70 371 138 HOH HOH . 
F 3 HOH B 71 372 143 HOH HOH . 
F 3 HOH B 72 373 146 HOH HOH . 
F 3 HOH B 73 374 148 HOH HOH . 
F 3 HOH B 74 375 149 HOH HOH . 
F 3 HOH B 75 376 150 HOH HOH . 
F 3 HOH B 76 377 152 HOH HOH . 
F 3 HOH B 77 378 154 HOH HOH . 
F 3 HOH B 78 379 158 HOH HOH . 
F 3 HOH B 79 380 159 HOH HOH . 
F 3 HOH B 80 381 161 HOH HOH . 
F 3 HOH B 81 382 167 HOH HOH . 
F 3 HOH B 82 383 168 HOH HOH . 
F 3 HOH B 83 384 169 HOH HOH . 
F 3 HOH B 84 385 170 HOH HOH . 
F 3 HOH B 85 386 171 HOH HOH . 
F 3 HOH B 86 387 174 HOH HOH . 
F 3 HOH B 87 388 175 HOH HOH . 
F 3 HOH B 88 389 177 HOH HOH . 
F 3 HOH B 89 390 180 HOH HOH . 
F 3 HOH B 90 391 181 HOH HOH . 
F 3 HOH B 91 392 183 HOH HOH . 
F 3 HOH B 92 393 184 HOH HOH . 
F 3 HOH B 93 394 185 HOH HOH . 
F 3 HOH B 94 395 190 HOH HOH . 
F 3 HOH B 95 396 194 HOH HOH . 
F 3 HOH B 96 397 195 HOH HOH . 
F 3 HOH B 97 398 198 HOH HOH . 
F 3 HOH B 98 399 200 HOH HOH . 
F 3 HOH B 99 400 201 HOH HOH . 
F 3 HOH B 100 401 203 HOH HOH . 
F 3 HOH B 101 402 204 HOH HOH . 
F 3 HOH B 102 403 205 HOH HOH . 
F 3 HOH B 103 404 206 HOH HOH . 
F 3 HOH B 104 405 207 HOH HOH . 
F 3 HOH B 105 406 210 HOH HOH . 
F 3 HOH B 106 407 211 HOH HOH . 
F 3 HOH B 107 408 213 HOH HOH . 
F 3 HOH B 108 409 214 HOH HOH . 
F 3 HOH B 109 410 216 HOH HOH . 
F 3 HOH B 110 411 221 HOH HOH . 
F 3 HOH B 111 412 224 HOH HOH . 
F 3 HOH B 112 413 230 HOH HOH . 
F 3 HOH B 113 414 238 HOH HOH . 
F 3 HOH B 114 415 239 HOH HOH . 
F 3 HOH B 115 416 241 HOH HOH . 
F 3 HOH B 116 417 244 HOH HOH . 
F 3 HOH B 117 418 246 HOH HOH . 
F 3 HOH B 118 419 248 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 C1 MLA . . . C 2 25.207 12.991 14.178 1 55.42 ? C1 MLA 302 A 1 
HETATM 2 O O1A MLA . . . C 2 24.796 13.117 15.415 1 50.8 ? O1A MLA 302 A 1 
HETATM 3 O O1B MLA . . . C 2 25.192 11.909 13.389 1 51.19 ? O1B MLA 302 A 1 
HETATM 4 C C2 MLA . . . C 2 25.659 14.325 13.592 1 50.68 ? C2 MLA 302 A 1 
HETATM 5 C C3 MLA . . . C 2 25.248 14.571 12.124 1 55.79 ? C3 MLA 302 A 1 
HETATM 6 O O3A MLA . . . C 2 25.276 13.41 11.573 1 66.09 ? O3A MLA 302 A 1 
HETATM 7 O O3B MLA . . . C 2 24.757 15.694 11.503 1 54.22 ? O3B MLA 302 A 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           7 
#