data_8XKS
#
_model_server_result.job_id            AK3Al5Bn5GvBKo8T9uG8FA 
_model_server_result.datetime_utc      '2025-07-03 17:38:35' 
_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          8xks 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":401}' 
#
_entry.id    8XKS 
#
_exptl.entry_id    8XKS 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              949.299 
_entity.id                          22 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'DIGALACTOSYL DIACYL GLYCEROL (DGDG)' 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    eicosameric 
_pdbx_struct_assembly.oligomeric_count      20 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA 
_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    ? 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 22 X N N 
? 22 BA N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_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
_struct_conn.pdbx_value_order
disulf ? disulf1 P SG CYS 200 P CYS 136 1_555 P SG CYS 253 P CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
covale ? covale1 R C ASP 71 R ASP 43 1_555 R N SEP 72 R SEP 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 R C SEP 72 R SEP 44 1_555 R N LEU 73 R LEU 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
metalc ? metalc1 C SG CYS 58 C CYS 58 1_555 U ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc2 C SG CYS 61 C CYS 61 1_555 U ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc3 C SG CYS 69 C CYS 69 1_555 V ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc4 C SG CYS 72 C CYS 72 1_555 V ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc5 C SG CYS 113 C CYS 113 1_555 V ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc6 C SG CYS 116 C CYS 116 1_555 V ZN ZN . C ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc7 C SG CYS 306 C CYS 306 1_555 U ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? 
metalc ? metalc8 C SG CYS 309 C CYS 309 1_555 U ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
#
_chem_comp.formula           'C51 H96 O15' 
_chem_comp.formula_weight    949.299 
_chem_comp.id                DGD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'DIGALACTOSYL DIACYL GLYCEROL (DGDG)' 
_chem_comp.type              saccharide 
_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
C1A C2A DGD sing 255 n n 
C1A O1A DGD doub 256 n n 
C1A O1G DGD sing 257 n n 
C2A C3A DGD sing 258 n n 
C2A HA21 DGD sing 259 n n 
C2A HA22 DGD sing 260 n n 
C3A C4A DGD sing 261 n n 
C3A HA31 DGD sing 262 n n 
C3A HA32 DGD sing 263 n n 
C4A C5A DGD sing 264 n n 
C4A HA41 DGD sing 265 n n 
C4A HA42 DGD sing 266 n n 
C5A C6A DGD sing 267 n n 
C5A HA51 DGD sing 268 n n 
C5A HA52 DGD sing 269 n n 
C6A C7A DGD sing 270 n n 
C6A HA61 DGD sing 271 n n 
C6A HA62 DGD sing 272 n n 
C7A C8A DGD sing 273 n n 
C7A HA71 DGD sing 274 n n 
C7A HA72 DGD sing 275 n n 
C8A C9A DGD sing 276 n n 
C8A HA81 DGD sing 277 n n 
C8A HA82 DGD sing 278 n n 
C9A CAA DGD sing 279 n n 
C9A HA91 DGD sing 280 n n 
C9A HA92 DGD sing 281 n n 
CAA CBA DGD sing 282 n n 
CAA HAT1 DGD sing 283 n n 
CAA HAT2 DGD sing 284 n n 
CBA CCA DGD sing 285 n n 
CBA HAE1 DGD sing 286 n n 
CBA HAE2 DGD sing 287 n n 
CCA CDA DGD sing 288 n n 
CCA HAW1 DGD sing 289 n n 
CCA HAW2 DGD sing 290 n n 
CDA CEA DGD sing 291 n n 
CDA HAH1 DGD sing 292 n n 
CDA HAH2 DGD sing 293 n n 
CEA CFA DGD sing 294 n n 
CEA HAF1 DGD sing 295 n n 
CEA HAF2 DGD sing 296 n n 
CFA CGA DGD sing 297 n n 
CFA HAN1 DGD sing 298 n n 
CFA HAN2 DGD sing 299 n n 
CGA CHA DGD sing 300 n n 
CGA HAS1 DGD sing 301 n n 
CGA HAS2 DGD sing 302 n n 
CHA CIA DGD sing 303 n n 
CHA HAV1 DGD sing 304 n n 
CHA HAV2 DGD sing 305 n n 
CIA HAG1 DGD sing 306 n n 
CIA HAG2 DGD sing 307 n n 
CIA HAG3 DGD sing 308 n n 
C1B C2B DGD sing 309 n n 
C1B O1B DGD doub 310 n n 
C1B O2G DGD sing 311 n n 
C2B C3B DGD sing 312 n n 
C2B HB21 DGD sing 313 n n 
C2B HB22 DGD sing 314 n n 
C3B C4B DGD sing 315 n n 
C3B HB31 DGD sing 316 n n 
C3B HB32 DGD sing 317 n n 
C4B C5B DGD sing 318 n n 
C4B HB41 DGD sing 319 n n 
C4B HB42 DGD sing 320 n n 
C5B C6B DGD sing 321 n n 
C5B HB51 DGD sing 322 n n 
C5B HB52 DGD sing 323 n n 
C6B C7B DGD sing 324 n n 
C6B HB61 DGD sing 325 n n 
C6B HB62 DGD sing 326 n n 
C7B C8B DGD sing 327 n n 
C7B HB71 DGD sing 328 n n 
C7B HB72 DGD sing 329 n n 
C8B C9B DGD sing 330 n n 
C8B HB81 DGD sing 331 n n 
C8B HB82 DGD sing 332 n n 
C9B CAB DGD sing 333 n n 
C9B HB91 DGD sing 334 n n 
C9B HB92 DGD sing 335 n n 
CAB CBB DGD sing 336 n n 
CAB HBT1 DGD sing 337 n n 
CAB HBT2 DGD sing 338 n n 
CBB CCB DGD sing 339 n n 
CBB HBE1 DGD sing 340 n n 
CBB HBE2 DGD sing 341 n n 
CCB CDB DGD sing 342 n n 
CCB HBW1 DGD sing 343 n n 
CCB HBW2 DGD sing 344 n n 
CDB CEB DGD sing 345 n n 
CDB HBH1 DGD sing 346 n n 
CDB HBH2 DGD sing 347 n n 
CEB CFB DGD sing 348 n n 
CEB HBF1 DGD sing 349 n n 
CEB HBF2 DGD sing 350 n n 
CFB CGB DGD sing 351 n n 
CFB HBN1 DGD sing 352 n n 
CFB HBN2 DGD sing 353 n n 
CGB CHB DGD sing 354 n n 
CGB HBS1 DGD sing 355 n n 
CGB HBS2 DGD sing 356 n n 
CHB CIB DGD sing 357 n n 
CHB HBV1 DGD sing 358 n n 
CHB HBV2 DGD sing 359 n n 
CIB HBG1 DGD sing 360 n n 
CIB HBG2 DGD sing 361 n n 
CIB HBG3 DGD sing 362 n n 
O1G C1G DGD sing 363 n n 
C1G C2G DGD sing 364 n n 
C1G HG11 DGD sing 365 n n 
C1G HG12 DGD sing 366 n n 
C2G O2G DGD sing 367 n n 
C2G C3G DGD sing 368 n n 
C2G HG2 DGD sing 369 n n 
C3G O3G DGD sing 370 n n 
C3G HG31 DGD sing 371 n n 
C3G HG32 DGD sing 372 n n 
O3G C1D DGD sing 373 n n 
C1D C2D DGD sing 374 n n 
C1D O6D DGD sing 375 n n 
C1D HD1 DGD sing 376 n n 
C2D O2D DGD sing 377 n n 
C2D C3D DGD sing 378 n n 
C2D HD2 DGD sing 379 n n 
O2D HO2D DGD sing 380 n n 
C3D O3D DGD sing 381 n n 
C3D C4D DGD sing 382 n n 
C3D HD3 DGD sing 383 n n 
O3D HO3D DGD sing 384 n n 
C4D O4D DGD sing 385 n n 
C4D C5D DGD sing 386 n n 
C4D HD4 DGD sing 387 n n 
O4D HO4D DGD sing 388 n n 
C5D C6D DGD sing 389 n n 
C5D O6D DGD sing 390 n n 
C5D HD5 DGD sing 391 n n 
O5D C6D DGD sing 392 n n 
O5D C1E DGD sing 393 n n 
C6D HD61 DGD sing 394 n n 
C6D HD62 DGD sing 395 n n 
C1E C2E DGD sing 396 n n 
C1E O6E DGD sing 397 n n 
C1E HE1 DGD sing 398 n n 
C2E O2E DGD sing 399 n n 
C2E C3E DGD sing 400 n n 
C2E HE2 DGD sing 401 n n 
O2E HO2E DGD sing 402 n n 
C3E O3E DGD sing 403 n n 
C3E C4E DGD sing 404 n n 
C3E HE3 DGD sing 405 n n 
O3E HO3E DGD sing 406 n n 
C4E O4E DGD sing 407 n n 
C4E C5E DGD sing 408 n n 
C4E HE4 DGD sing 409 n n 
O4E HO4E DGD sing 410 n n 
C5E O6E DGD sing 411 n n 
C5E C6E DGD sing 412 n n 
C5E HE5 DGD sing 413 n n 
C6E O5E DGD sing 414 n n 
C6E HE61 DGD sing 415 n n 
C6E HE62 DGD sing 416 n n 
O5E HO5E DGD sing 417 n n 
#
_atom_sites.entry_id                     8XKS 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
U 20 ZN C 1 501 501 ZN ZN . 
V 20 ZN C 1 502 502 ZN ZN . 
W 21 DGA H 1 701 701 DGA DGA . 
X 22 DGD J 1 401 401 DGD DGD . 
Y 23 LMG J 1 402 402 LMG LMG . 
Z 24 ACD K 1 501 501 ACD ACD . 
AA 23 LMG L 1 301 403 LMG LMG . 
BA 22 DGD L 1 302 301 DGD DGD . 
CA 25 SQD L 1 303 302 SQD SQD . 
#
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 C1A DGD . . . X 22 182.619 257.612 200.79 1 29.48 ? C1A DGD 401 J 1 
HETATM 2 C C2A DGD . . . X 22 182.955 256.405 199.925 1 23.29 ? C2A DGD 401 J 1 
HETATM 3 C C3A DGD . . . X 22 181.829 255.832 199.029 1 21.64 ? C3A DGD 401 J 1 
HETATM 4 C C4A DGD . . . X 22 180.871 254.862 199.765 1 26.71 ? C4A DGD 401 J 1 
HETATM 5 C C5A DGD . . . X 22 181.186 253.357 199.621 1 24.44 ? C5A DGD 401 J 1 
HETATM 6 C C6A DGD . . . X 22 180.96 252.551 200.927 1 24.02 ? C6A DGD 401 J 1 
HETATM 7 C C7A DGD . . . X 22 180.434 251.113 200.72 1 24.64 ? C7A DGD 401 J 1 
HETATM 8 C C8A DGD . . . X 22 181.476 250.14 200.119 1 28.79 ? C8A DGD 401 J 1 
HETATM 9 C C9A DGD . . . X 22 180.904 248.757 199.756 1 23.98 ? C9A DGD 401 J 1 
HETATM 10 C CAA DGD . . . X 22 180.718 247.784 200.948 1 28.7 ? CAA DGD 401 J 1 
HETATM 11 C CBA DGD . . . X 22 180.001 246.476 200.561 1 28.07 ? CBA DGD 401 J 1 
HETATM 12 O O1A DGD . . . X 22 181.527 257.829 201.274 1 31.84 ? O1A DGD 401 J 1 
HETATM 13 C C1B DGD . . . X 22 183.24 262.366 198.94 1 28.06 ? C1B DGD 401 J 1 
HETATM 14 C C2B DGD . . . X 22 183.301 261.625 197.606 1 21.81 ? C2B DGD 401 J 1 
HETATM 15 C C3B DGD . . . X 22 182.209 262.082 196.612 1 23.65 ? C3B DGD 401 J 1 
HETATM 16 C C4B DGD . . . X 22 182.635 263.142 195.567 1 27 ? C4B DGD 401 J 1 
HETATM 17 C C5B DGD . . . X 22 181.996 263.026 194.159 1 24.47 ? C5B DGD 401 J 1 
HETATM 18 C C6B DGD . . . X 22 182.903 262.513 193.019 1 22.26 ? C6B DGD 401 J 1 
HETATM 19 O O1B DGD . . . X 22 182.445 263.262 199.152 1 30.91 ? O1B DGD 401 J 1 
HETATM 20 O O1G DGD . . . X 22 183.641 258.507 201.033 1 24.94 ? O1G DGD 401 J 1 
HETATM 21 C C1G DGD . . . X 22 183.373 259.883 200.8 1 22 ? C1G DGD 401 J 1 
HETATM 22 C C2G DGD . . . X 22 184.553 260.672 200.122 1 22.68 ? C2G DGD 401 J 1 
HETATM 23 O O2G DGD . . . X 22 184.115 262.018 199.948 1 30.14 ? O2G DGD 401 J 1 
HETATM 24 C C3G DGD . . . X 22 185.805 260.656 201.088 1 18.78 ? C3G DGD 401 J 1 
HETATM 25 O O3G DGD . . . X 22 186.97 261.205 200.482 1 26.49 ? O3G DGD 401 J 1 
HETATM 26 C C1D DGD . . . X 22 188.172 260.931 201.173 1 24.04 ? C1D DGD 401 J 1 
HETATM 27 C C2D DGD . . . X 22 189.387 261.802 200.702 1 22.48 ? C2D DGD 401 J 1 
HETATM 28 O O2D DGD . . . X 22 190.205 261.01 199.911 1 34.96 ? O2D DGD 401 J 1 
HETATM 29 C C3D DGD . . . X 22 190.165 262.347 201.939 1 21.47 ? C3D DGD 401 J 1 
HETATM 30 O O3D DGD . . . X 22 189.565 263.479 202.472 1 34.86 ? O3D DGD 401 J 1 
HETATM 31 C C4D DGD . . . X 22 190.249 261.249 203.019 1 22.2 ? C4D DGD 401 J 1 
HETATM 32 O O4D DGD . . . X 22 190.853 261.779 204.145 1 33.28 ? O4D DGD 401 J 1 
HETATM 33 C C5D DGD . . . X 22 188.822 260.728 203.422 1 24.27 ? C5D DGD 401 J 1 
HETATM 34 O O5D DGD . . . X 22 186.983 260.728 205.014 1 19.64 ? O5D DGD 401 J 1 
HETATM 35 C C6D DGD . . . X 22 188.352 261.097 204.872 1 20.89 ? C6D DGD 401 J 1 
HETATM 36 O O6D DGD . . . X 22 187.889 261.282 202.507 1 20.85 ? O6D DGD 401 J 1 
HETATM 37 C C1E DGD . . . X 22 186.489 260.726 206.334 1 22.88 ? C1E DGD 401 J 1 
HETATM 38 C C2E DGD . . . X 22 185.516 259.525 206.57 1 23.08 ? C2E DGD 401 J 1 
HETATM 39 O O2E DGD . . . X 22 186.203 258.36 206.263 1 25.06 ? O2E DGD 401 J 1 
HETATM 40 C C3E DGD . . . X 22 184.304 259.69 205.593 1 21.48 ? C3E DGD 401 J 1 
HETATM 41 O O3E DGD . . . X 22 183.329 258.755 205.92 1 26.19 ? O3E DGD 401 J 1 
HETATM 42 C C4E DGD . . . X 22 183.633 261.068 205.78 1 20.6 ? C4E DGD 401 J 1 
HETATM 43 O O4E DGD . . . X 22 183.185 261.182 207.09 1 24.62 ? O4E DGD 401 J 1 
HETATM 44 C C5E DGD . . . X 22 184.707 262.156 205.576 1 29.19 ? C5E DGD 401 J 1 
HETATM 45 O O6E DGD . . . X 22 185.829 261.972 206.416 1 35.26 ? O6E DGD 401 J 1 
HETATM 46 C C6E DGD . . . X 22 184.08 263.526 205.921 1 30.71 ? C6E DGD 401 J 1 
HETATM 47 O O5E DGD . . . X 22 185.181 264.398 205.92 1 29.77 ? O5E DGD 401 J 1 
#
_model_server_stats.io_time_ms              397 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    147 
_model_server_stats.query_time_ms           485 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           47 
#