data_4Y9C
#
_model_server_result.job_id            uj9ZKkH7FdYHhakOA6u2vw 
_model_server_result.datetime_utc      '2025-08-31 21:48:18' 
_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          4y9c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":201}' 
#
_entry.id    4Y9C 
#
_exptl.entry_id    4Y9C 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              410.46 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            1,3,6-trihydroxy-7-methoxy-2,8-bis(3-methylbut-2-en-1-yl)-9H-xanthen-9-one 
_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            4Y9C 
_cell.length_a            43.089 
_cell.length_b            85.624 
_cell.length_c            63.552 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4Y9C 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L 1 1 
A,B,C,D,E,F,G,H,I,J,K,L 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' 2_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -43.089 0 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 I N N 
#
_chem_comp.formula           'C24 H26 O6' 
_chem_comp.formula_weight    410.46 
_chem_comp.id                MKS 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              1,3,6-trihydroxy-7-methoxy-2,8-bis(3-methylbut-2-en-1-yl)-9H-xanthen-9-one 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     alpha-Mangostin 
#
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
CAD CAS MKS sing 218 n n 
CAE CAS MKS sing 219 n n 
CAS CAK MKS doub 220 n n 
CAA OAP MKS sing 221 n n 
CAK CAO MKS sing 222 n n 
OAP CAY MKS sing 223 n n 
CAO CAX MKS sing 224 n n 
CAY CAX MKS doub 225 n y 
CAY CAU MKS sing 226 n y 
CAX CBD MKS sing 227 n y 
OAH CAU MKS sing 228 n n 
OAF CAZ MKS doub 229 n n 
CAU CAM MKS doub 230 n y 
CBD CAZ MKS sing 231 n n 
CBD CBB MKS doub 232 n y 
CAZ CBC MKS sing 233 n n 
CAM CBB MKS sing 234 n y 
CBB OAQ MKS sing 235 n n 
OAI CAV MKS sing 236 n n 
CBC CAV MKS sing 237 n y 
CBC CBA MKS doub 238 n y 
CAV CAW MKS doub 239 n y 
OAQ CBA MKS sing 240 n n 
CBA CAL MKS sing 241 n y 
CAW CAN MKS sing 242 n n 
CAW CAT MKS sing 243 n y 
CAN CAJ MKS sing 244 n n 
CAL CAT MKS doub 245 n y 
CAJ CAR MKS doub 246 n n 
CAT OAG MKS sing 247 n n 
CAR CAB MKS sing 248 n n 
CAR CAC MKS sing 249 n n 
CAD H1 MKS sing 250 n n 
CAD H2 MKS sing 251 n n 
CAD H3 MKS sing 252 n n 
CAE H4 MKS sing 253 n n 
CAE H5 MKS sing 254 n n 
CAE H6 MKS sing 255 n n 
CAK H7 MKS sing 256 n n 
CAO H8 MKS sing 257 n n 
CAO H9 MKS sing 258 n n 
OAI H10 MKS sing 259 n n 
CAN H11 MKS sing 260 n n 
CAN H12 MKS sing 261 n n 
CAJ H13 MKS sing 262 n n 
CAC H14 MKS sing 263 n n 
CAC H15 MKS sing 264 n n 
CAC H16 MKS sing 265 n n 
CAB H17 MKS sing 266 n n 
CAB H18 MKS sing 267 n n 
CAB H19 MKS sing 268 n n 
OAG H20 MKS sing 269 n n 
CAL H21 MKS sing 270 n n 
CAM H22 MKS sing 271 n n 
OAH H23 MKS sing 272 n n 
CAA H24 MKS sing 273 n n 
CAA H25 MKS sing 274 n n 
CAA H26 MKS sing 275 n n 
#
_atom_sites.entry_id                     4Y9C 
_atom_sites.fract_transf_matrix[1][1]    0.023208 
_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]    0.011679 
_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]    0.015735 
_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 MKS A 1 201 200 MKS DRG . 
D 3 BR A 1 202 201 BR BR . 
E 3 BR A 1 203 203 BR BR . 
F 3 BR A 1 204 204 BR BR . 
G 3 BR A 1 205 205 BR BR . 
H 3 BR B 1 201 202 BR BR . 
I 2 MKS B 1 202 200 MKS DRG . 
J 3 BR B 1 203 201 BR BR . 
K 4 HOH A 1 301 179 HOH HOH . 
K 4 HOH A 2 302 112 HOH HOH . 
K 4 HOH A 3 303 98 HOH HOH . 
K 4 HOH A 4 304 157 HOH HOH . 
K 4 HOH A 5 305 115 HOH HOH . 
K 4 HOH A 6 306 45 HOH HOH . 
K 4 HOH A 7 307 168 HOH HOH . 
K 4 HOH A 8 308 110 HOH HOH . 
K 4 HOH A 9 309 44 HOH HOH . 
K 4 HOH A 10 310 184 HOH HOH . 
K 4 HOH A 11 311 66 HOH HOH . 
K 4 HOH A 12 312 108 HOH HOH . 
K 4 HOH A 13 313 92 HOH HOH . 
K 4 HOH A 14 314 76 HOH HOH . 
K 4 HOH A 15 315 154 HOH HOH . 
K 4 HOH A 16 316 119 HOH HOH . 
K 4 HOH A 17 317 81 HOH HOH . 
K 4 HOH A 18 318 14 HOH HOH . 
K 4 HOH A 19 319 188 HOH HOH . 
K 4 HOH A 20 320 59 HOH HOH . 
K 4 HOH A 21 321 150 HOH HOH . 
K 4 HOH A 22 322 33 HOH HOH . 
K 4 HOH A 23 323 187 HOH HOH . 
K 4 HOH A 24 324 194 HOH HOH . 
K 4 HOH A 25 325 25 HOH HOH . 
K 4 HOH A 26 326 117 HOH HOH . 
K 4 HOH A 27 327 20 HOH HOH . 
K 4 HOH A 28 328 166 HOH HOH . 
K 4 HOH A 29 329 169 HOH HOH . 
K 4 HOH A 30 330 86 HOH HOH . 
K 4 HOH A 31 331 11 HOH HOH . 
K 4 HOH A 32 332 153 HOH HOH . 
K 4 HOH A 33 333 164 HOH HOH . 
K 4 HOH A 34 334 96 HOH HOH . 
K 4 HOH A 35 335 22 HOH HOH . 
K 4 HOH A 36 336 93 HOH HOH . 
K 4 HOH A 37 337 133 HOH HOH . 
K 4 HOH A 38 338 114 HOH HOH . 
K 4 HOH A 39 339 19 HOH HOH . 
K 4 HOH A 40 340 67 HOH HOH . 
K 4 HOH A 41 341 146 HOH HOH . 
K 4 HOH A 42 342 181 HOH HOH . 
K 4 HOH A 43 343 126 HOH HOH . 
K 4 HOH A 44 344 185 HOH HOH . 
K 4 HOH A 45 345 180 HOH HOH . 
K 4 HOH A 46 346 186 HOH HOH . 
K 4 HOH A 47 347 193 HOH HOH . 
K 4 HOH A 48 348 192 HOH HOH . 
K 4 HOH A 49 349 3 HOH HOH . 
K 4 HOH A 50 350 7 HOH HOH . 
K 4 HOH A 51 351 8 HOH HOH . 
K 4 HOH A 52 352 10 HOH HOH . 
K 4 HOH A 53 353 15 HOH HOH . 
K 4 HOH A 54 354 16 HOH HOH . 
K 4 HOH A 55 355 21 HOH HOH . 
K 4 HOH A 56 356 23 HOH HOH . 
K 4 HOH A 57 357 28 HOH HOH . 
K 4 HOH A 58 358 30 HOH HOH . 
K 4 HOH A 59 359 31 HOH HOH . 
K 4 HOH A 60 360 32 HOH HOH . 
K 4 HOH A 61 361 34 HOH HOH . 
K 4 HOH A 62 362 35 HOH HOH . 
K 4 HOH A 63 363 37 HOH HOH . 
K 4 HOH A 64 364 41 HOH HOH . 
K 4 HOH A 65 365 46 HOH HOH . 
K 4 HOH A 66 366 47 HOH HOH . 
K 4 HOH A 67 367 49 HOH HOH . 
K 4 HOH A 68 368 51 HOH HOH . 
K 4 HOH A 69 369 70 HOH HOH . 
K 4 HOH A 70 370 71 HOH HOH . 
K 4 HOH A 71 371 73 HOH HOH . 
K 4 HOH A 72 372 78 HOH HOH . 
K 4 HOH A 73 373 79 HOH HOH . 
K 4 HOH A 74 374 80 HOH HOH . 
K 4 HOH A 75 375 83 HOH HOH . 
K 4 HOH A 76 376 85 HOH HOH . 
K 4 HOH A 77 377 99 HOH HOH . 
K 4 HOH A 78 378 104 HOH HOH . 
K 4 HOH A 79 379 111 HOH HOH . 
K 4 HOH A 80 380 116 HOH HOH . 
K 4 HOH A 81 381 124 HOH HOH . 
K 4 HOH A 82 382 127 HOH HOH . 
K 4 HOH A 83 383 128 HOH HOH . 
K 4 HOH A 84 384 130 HOH HOH . 
K 4 HOH A 85 385 131 HOH HOH . 
K 4 HOH A 86 386 134 HOH HOH . 
K 4 HOH A 87 387 147 HOH HOH . 
K 4 HOH A 88 388 156 HOH HOH . 
K 4 HOH A 89 389 158 HOH HOH . 
K 4 HOH A 90 390 162 HOH HOH . 
K 4 HOH A 91 391 167 HOH HOH . 
K 4 HOH A 92 392 172 HOH HOH . 
K 4 HOH A 93 393 173 HOH HOH . 
K 4 HOH A 94 394 176 HOH HOH . 
L 4 HOH B 1 301 139 HOH HOH . 
L 4 HOH B 2 302 84 HOH HOH . 
L 4 HOH B 3 303 64 HOH HOH . 
L 4 HOH B 4 304 100 HOH HOH . 
L 4 HOH B 5 305 82 HOH HOH . 
L 4 HOH B 6 306 60 HOH HOH . 
L 4 HOH B 7 307 122 HOH HOH . 
L 4 HOH B 8 308 144 HOH HOH . 
L 4 HOH B 9 309 141 HOH HOH . 
L 4 HOH B 10 310 57 HOH HOH . 
L 4 HOH B 11 311 195 HOH HOH . 
L 4 HOH B 12 312 189 HOH HOH . 
L 4 HOH B 13 313 140 HOH HOH . 
L 4 HOH B 14 314 63 HOH HOH . 
L 4 HOH B 15 315 38 HOH HOH . 
L 4 HOH B 16 316 50 HOH HOH . 
L 4 HOH B 17 317 125 HOH HOH . 
L 4 HOH B 18 318 75 HOH HOH . 
L 4 HOH B 19 319 87 HOH HOH . 
L 4 HOH B 20 320 58 HOH HOH . 
L 4 HOH B 21 321 26 HOH HOH . 
L 4 HOH B 22 322 152 HOH HOH . 
L 4 HOH B 23 323 91 HOH HOH . 
L 4 HOH B 24 324 56 HOH HOH . 
L 4 HOH B 25 325 42 HOH HOH . 
L 4 HOH B 26 326 171 HOH HOH . 
L 4 HOH B 27 327 190 HOH HOH . 
L 4 HOH B 28 328 123 HOH HOH . 
L 4 HOH B 29 329 149 HOH HOH . 
L 4 HOH B 30 330 142 HOH HOH . 
L 4 HOH B 31 331 97 HOH HOH . 
L 4 HOH B 32 332 143 HOH HOH . 
L 4 HOH B 33 333 174 HOH HOH . 
L 4 HOH B 34 334 191 HOH HOH . 
L 4 HOH B 35 335 182 HOH HOH . 
L 4 HOH B 36 336 4 HOH HOH . 
L 4 HOH B 37 337 5 HOH HOH . 
L 4 HOH B 38 338 6 HOH HOH . 
L 4 HOH B 39 339 12 HOH HOH . 
L 4 HOH B 40 340 13 HOH HOH . 
L 4 HOH B 41 341 17 HOH HOH . 
L 4 HOH B 42 342 18 HOH HOH . 
L 4 HOH B 43 343 24 HOH HOH . 
L 4 HOH B 44 344 29 HOH HOH . 
L 4 HOH B 45 345 36 HOH HOH . 
L 4 HOH B 46 346 39 HOH HOH . 
L 4 HOH B 47 347 43 HOH HOH . 
L 4 HOH B 48 348 48 HOH HOH . 
L 4 HOH B 49 349 52 HOH HOH . 
L 4 HOH B 50 350 53 HOH HOH . 
L 4 HOH B 51 351 61 HOH HOH . 
L 4 HOH B 52 352 62 HOH HOH . 
L 4 HOH B 53 353 68 HOH HOH . 
L 4 HOH B 54 354 69 HOH HOH . 
L 4 HOH B 55 355 72 HOH HOH . 
L 4 HOH B 56 356 74 HOH HOH . 
L 4 HOH B 57 357 89 HOH HOH . 
L 4 HOH B 58 358 90 HOH HOH . 
L 4 HOH B 59 359 94 HOH HOH . 
L 4 HOH B 60 360 101 HOH HOH . 
L 4 HOH B 61 361 102 HOH HOH . 
L 4 HOH B 62 362 103 HOH HOH . 
L 4 HOH B 63 363 106 HOH HOH . 
L 4 HOH B 64 364 107 HOH HOH . 
L 4 HOH B 65 365 109 HOH HOH . 
L 4 HOH B 66 366 113 HOH HOH . 
L 4 HOH B 67 367 120 HOH HOH . 
L 4 HOH B 68 368 129 HOH HOH . 
L 4 HOH B 69 369 132 HOH HOH . 
L 4 HOH B 70 370 137 HOH HOH . 
L 4 HOH B 71 371 155 HOH HOH . 
L 4 HOH B 72 372 159 HOH HOH . 
L 4 HOH B 73 373 161 HOH HOH . 
L 4 HOH B 74 374 163 HOH HOH . 
L 4 HOH B 75 375 165 HOH HOH . 
L 4 HOH B 76 376 170 HOH HOH . 
L 4 HOH B 77 377 175 HOH HOH . 
L 4 HOH B 78 378 177 HOH HOH . 
L 4 HOH B 79 379 178 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 CAD MKS . . . C 2 -21.931 0.185 -10.635 0.5 18.17 ? CAD MKS 201 A 1 
HETATM 2 C CAS MKS . . . C 2 -22.1 1.385 -9.653 0.5 18.01 ? CAS MKS 201 A 1 
HETATM 3 C CAE MKS . . . C 2 -22.007 2.819 -10.164 0.5 17.19 ? CAE MKS 201 A 1 
HETATM 4 C CAK MKS . . . C 2 -22.436 1.216 -8.167 0.5 18.89 ? CAK MKS 201 A 1 
HETATM 5 C CAO MKS . . . C 2 -22.506 -0.192 -7.638 0.5 19.96 ? CAO MKS 201 A 1 
HETATM 6 C CAX MKS . . . C 2 -21.655 -0.407 -6.563 0.5 19.42 ? CAX MKS 201 A 1 
HETATM 7 C CBD MKS . . . C 2 -22.035 -0.051 -5.25 0.5 20.22 ? CBD MKS 201 A 1 
HETATM 8 C CAZ MKS . . . C 2 -23.228 0.64 -4.836 0.5 21.41 ? CAZ MKS 201 A 1 
HETATM 9 O OAF MKS . . . C 2 -23.929 1.281 -5.612 0.5 21.28 ? OAF MKS 201 A 1 
HETATM 10 C CBC MKS . . . C 2 -23.553 0.769 -3.487 0.5 20.16 ? CBC MKS 201 A 1 
HETATM 11 C CAV MKS . . . C 2 -24.749 1.306 -3.052 0.5 19.78 ? CAV MKS 201 A 1 
HETATM 12 O OAI MKS . . . C 2 -25.681 1.646 -3.973 0.5 20.41 ? OAI MKS 201 A 1 
HETATM 13 C CAW MKS . . . C 2 -25.065 1.449 -1.694 0.5 19.45 ? CAW MKS 201 A 1 
HETATM 14 C CAN MKS . . . C 2 -26.337 1.914 -1.33 0.5 17.58 ? CAN MKS 201 A 1 
HETATM 15 C CAJ MKS . . . C 2 -27.29 0.744 -0.918 0.5 17.26 ? CAJ MKS 201 A 1 
HETATM 16 C CAR MKS . . . C 2 -28.195 1.082 0.246 0.5 15.81 ? CAR MKS 201 A 1 
HETATM 17 C CAC MKS . . . C 2 -28.101 2.498 0.868 0.5 15.32 ? CAC MKS 201 A 1 
HETATM 18 C CAB MKS . . . C 2 -29.221 0.05 0.816 0.5 16.04 ? CAB MKS 201 A 1 
HETATM 19 C CAT MKS . . . C 2 -24.096 1.071 -0.754 0.5 20.2 ? CAT MKS 201 A 1 
HETATM 20 O OAG MKS . . . C 2 -24.385 1.192 0.561 0.5 21.07 ? OAG MKS 201 A 1 
HETATM 21 C CAL MKS . . . C 2 -22.877 0.57 -1.164 0.5 21.11 ? CAL MKS 201 A 1 
HETATM 22 C CBA MKS . . . C 2 -22.646 0.421 -2.534 0.5 20.8 ? CBA MKS 201 A 1 
HETATM 23 O OAQ MKS . . . C 2 -21.458 -0.027 -2.974 0.5 20.23 ? OAQ MKS 201 A 1 
HETATM 24 C CBB MKS . . . C 2 -21.128 -0.391 -4.248 0.5 21.29 ? CBB MKS 201 A 1 
HETATM 25 C CAM MKS . . . C 2 -19.895 -1.047 -4.466 0.5 21.01 ? CAM MKS 201 A 1 
HETATM 26 C CAU MKS . . . C 2 -19.53 -1.412 -5.755 0.5 21.12 ? CAU MKS 201 A 1 
HETATM 27 O OAH MKS . . . C 2 -18.342 -2.057 -6.079 0.5 21.61 ? OAH MKS 201 A 1 
HETATM 28 C CAY MKS . . . C 2 -20.427 -1.088 -6.783 0.5 20.45 ? CAY MKS 201 A 1 
HETATM 29 O OAP MKS . . . C 2 -20.071 -1.451 -8.046 0.5 21.08 ? OAP MKS 201 A 1 
HETATM 30 C CAA MKS . . . C 2 -19.048 -0.568 -8.494 0.5 22.06 ? CAA MKS 201 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           689 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           30 
#