data_8K09
#
_model_server_result.job_id            dZCqpsb39iWi079BAxf0-g 
_model_server_result.datetime_utc      '2025-03-22 05:26:01' 
_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          8k09 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    8K09 
#
_exptl.entry_id    8K09 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              785.013 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[[(3~{S},5~{R},8~{R},9~{R},10~{R},12~{R},13~{R},14~{R},17~{S})-17-[(2~{S})-2-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-methyl-hept-5-en-2-yl]-4,4,8,10,14-pentamethyl-12-oxidanyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl]oxy]oxane-3,4,5-triol 
_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            8K09 
_cell.length_a            60.27 
_cell.length_b            88.18 
_cell.length_c            164.51 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8K09 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C 1 1 
B,D 2 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 
#
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           'C42 H72 O13' 
_chem_comp.formula_weight    785.013 
_chem_comp.id                VEI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[[(3~{S},5~{R},8~{R},9~{R},10~{R},12~{R},13~{R},14~{R},17~{S})-17-[(2~{S})-2-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-6-methyl-hept-5-en-2-yl]-4,4,8,10,14-pentamethyl-12-oxidanyl-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1~{H}-cyclopenta[a]phenanthren-3-yl]oxy]oxane-3,4,5-triol 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ginsenoside F2' 
#
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
C07 C06 VEI sing 374 n n 
C03 C04 VEI sing 375 n n 
C03 C02 VEI doub 376 n n 
C04 C05 VEI sing 377 n n 
C01 C02 VEI sing 378 n n 
C02 C55 VEI sing 379 n n 
C09 C10 VEI sing 380 n n 
C09 C08 VEI sing 381 n n 
C10 C11 VEI sing 382 n n 
C05 C06 VEI sing 383 n n 
C06 C08 VEI sing 384 n n 
C06 O43 VEI sing 385 n n 
O54 C45 VEI sing 386 n n 
C08 C12 VEI sing 387 n n 
C44 O49 VEI sing 388 n n 
C44 O43 VEI sing 389 n n 
C44 C45 VEI sing 390 n n 
O49 C48 VEI sing 391 n n 
C45 C46 VEI sing 392 n n 
C11 C42 VEI sing 393 n n 
C11 C12 VEI sing 394 n n 
C11 C16 VEI sing 395 n n 
C12 C13 VEI sing 396 n n 
C48 C47 VEI sing 397 n n 
C48 C50 VEI sing 398 n n 
C40 C16 VEI sing 399 n n 
C17 C16 VEI sing 400 n n 
C17 C18 VEI sing 401 n n 
C16 C15 VEI sing 402 n n 
C46 C47 VEI sing 403 n n 
C46 O53 VEI sing 404 n n 
O52 C47 VEI sing 405 n n 
C50 O51 VEI sing 406 n n 
C13 O41 VEI sing 407 n n 
C13 C14 VEI sing 408 n n 
C18 C19 VEI sing 409 n n 
C15 C14 VEI sing 410 n n 
C15 C20 VEI sing 411 n n 
C19 C20 VEI sing 412 n n 
C19 C24 VEI sing 413 n n 
C20 C39 VEI sing 414 n n 
C20 C21 VEI sing 415 n n 
C26 C24 VEI sing 416 n n 
C24 C25 VEI sing 417 n n 
C24 C23 VEI sing 418 n n 
C21 C22 VEI sing 419 n n 
C23 C22 VEI sing 420 n n 
C23 O27 VEI sing 421 n n 
O27 C28 VEI sing 422 n n 
C28 O33 VEI sing 423 n n 
C28 C29 VEI sing 424 n n 
O38 C29 VEI sing 425 n n 
O33 C32 VEI sing 426 n n 
C29 C30 VEI sing 427 n n 
C32 C34 VEI sing 428 n n 
C32 C31 VEI sing 429 n n 
C30 O37 VEI sing 430 n n 
C30 C31 VEI sing 431 n n 
O35 C34 VEI sing 432 n n 
C31 O36 VEI sing 433 n n 
C10 H1 VEI sing 434 n n 
C10 H2 VEI sing 435 n n 
C13 H3 VEI sing 436 n n 
C15 H4 VEI sing 437 n n 
C17 H5 VEI sing 438 n n 
C17 H6 VEI sing 439 n n 
C21 H7 VEI sing 440 n n 
C21 H8 VEI sing 441 n n 
C22 H9 VEI sing 442 n n 
C22 H10 VEI sing 443 n n 
C26 H11 VEI sing 444 n n 
C26 H12 VEI sing 445 n n 
C26 H13 VEI sing 446 n n 
C28 H14 VEI sing 447 n n 
C01 H15 VEI sing 448 n n 
C01 H16 VEI sing 449 n n 
C01 H17 VEI sing 450 n n 
C03 H18 VEI sing 451 n n 
C04 H19 VEI sing 452 n n 
C04 H20 VEI sing 453 n n 
C05 H21 VEI sing 454 n n 
C05 H22 VEI sing 455 n n 
C07 H23 VEI sing 456 n n 
C07 H24 VEI sing 457 n n 
C07 H25 VEI sing 458 n n 
C08 H26 VEI sing 459 n n 
C09 H27 VEI sing 460 n n 
C09 H28 VEI sing 461 n n 
C12 H29 VEI sing 462 n n 
C14 H30 VEI sing 463 n n 
C14 H31 VEI sing 464 n n 
C18 H32 VEI sing 465 n n 
C18 H33 VEI sing 466 n n 
C19 H34 VEI sing 467 n n 
C23 H35 VEI sing 468 n n 
C25 H36 VEI sing 469 n n 
C25 H37 VEI sing 470 n n 
C25 H38 VEI sing 471 n n 
C29 H39 VEI sing 472 n n 
C30 H40 VEI sing 473 n n 
C31 H41 VEI sing 474 n n 
C32 H42 VEI sing 475 n n 
C34 H43 VEI sing 476 n n 
C34 H44 VEI sing 477 n n 
C39 H45 VEI sing 478 n n 
C39 H46 VEI sing 479 n n 
C39 H47 VEI sing 480 n n 
C40 H48 VEI sing 481 n n 
C40 H49 VEI sing 482 n n 
C40 H50 VEI sing 483 n n 
C42 H51 VEI sing 484 n n 
C42 H52 VEI sing 485 n n 
C42 H53 VEI sing 486 n n 
C44 H54 VEI sing 487 n n 
C45 H55 VEI sing 488 n n 
C46 H56 VEI sing 489 n n 
C47 H57 VEI sing 490 n n 
C48 H58 VEI sing 491 n n 
C50 H59 VEI sing 492 n n 
C50 H60 VEI sing 493 n n 
C55 H61 VEI sing 494 n n 
C55 H62 VEI sing 495 n n 
C55 H63 VEI sing 496 n n 
O35 H64 VEI sing 497 n n 
O36 H65 VEI sing 498 n n 
O37 H66 VEI sing 499 n n 
O38 H67 VEI sing 500 n n 
O41 H68 VEI sing 501 n n 
O51 H69 VEI sing 502 n n 
O52 H70 VEI sing 503 n n 
O53 H71 VEI sing 504 n n 
O54 H72 VEI sing 505 n n 
#
_atom_sites.entry_id                     8K09 
_atom_sites.fract_transf_matrix[1][1]    0.016592 
_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]    0.01134 
_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]    0.006079 
_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 VEI C 1 501 501 VEI LIG . 
D 2 VEI A 1 501 501 VEI LIG . 
#
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 C10 VEI . . . D 2 26.931 -3.495 -64.984 1 123.59 ? C10 VEI 501 A 1 
HETATM 2 C C13 VEI . . . D 2 28.339 -6.594 -66.87 1 122.65 ? C13 VEI 501 A 1 
HETATM 3 C C15 VEI . . . D 2 27.594 -7.537 -64.642 1 115.56 ? C15 VEI 501 A 1 
HETATM 4 C C17 VEI . . . D 2 26.772 -5.981 -62.671 1 118.56 ? C17 VEI 501 A 1 
HETATM 5 C C20 VEI . . . D 2 27.348 -8.869 -63.712 1 112.2 ? C20 VEI 501 A 1 
HETATM 6 C C21 VEI . . . D 2 28.358 -9.998 -64.095 1 118.22 ? C21 VEI 501 A 1 
HETATM 7 C C22 VEI . . . D 2 29.663 -10.095 -63.244 1 131.76 ? C22 VEI 501 A 1 
HETATM 8 C C24 VEI . . . D 2 28.113 -9.575 -61.171 1 113.92 ? C24 VEI 501 A 1 
HETATM 9 C C26 VEI . . . D 2 28.522 -8.864 -59.898 1 122.62 ? C26 VEI 501 A 1 
HETATM 10 C C28 VEI . . . D 2 30.918 -12.101 -60.979 1 135.01 ? C28 VEI 501 A 1 
HETATM 11 C C01 VEI . . . D 2 25.225 -2.154 -73.313 1 147.6 ? C01 VEI 501 A 1 
HETATM 12 C C02 VEI . . . D 2 25.019 -2.578 -71.857 1 147.77 ? C02 VEI 501 A 1 
HETATM 13 C C03 VEI . . . D 2 25.58 -2.004 -70.808 1 140.5 ? C03 VEI 501 A 1 
HETATM 14 C C04 VEI . . . D 2 25.46 -2.347 -69.306 1 129.77 ? C04 VEI 501 A 1 
HETATM 15 C C05 VEI . . . D 2 26.301 -3.492 -68.625 1 127.47 ? C05 VEI 501 A 1 
HETATM 16 C C06 VEI . . . D 2 27.897 -3.303 -68.47 1 130.62 ? C06 VEI 501 A 1 
HETATM 17 C C07 VEI . . . D 2 28.287 -1.842 -68.424 1 129.12 ? C07 VEI 501 A 1 
HETATM 18 C C08 VEI . . . D 2 28.36 -3.772 -67.009 1 129.27 ? C08 VEI 501 A 1 
HETATM 19 C C09 VEI . . . D 2 27.842 -2.711 -65.954 1 129.39 ? C09 VEI 501 A 1 
HETATM 20 C C11 VEI . . . D 2 27.54 -4.924 -64.978 1 118.55 ? C11 VEI 501 A 1 
HETATM 21 C C12 VEI . . . D 2 27.677 -5.156 -66.554 1 124.49 ? C12 VEI 501 A 1 
HETATM 22 C C14 VEI . . . D 2 27.543 -7.779 -66.162 1 123.78 ? C14 VEI 501 A 1 
HETATM 23 C C16 VEI . . . D 2 26.78 -6.149 -64.245 1 119.74 ? C16 VEI 501 A 1 
HETATM 24 C C18 VEI . . . D 2 26.577 -7.305 -61.822 1 116.89 ? C18 VEI 501 A 1 
HETATM 25 C C19 VEI . . . D 2 27.643 -8.394 -62.24 1 113.81 ? C19 VEI 501 A 1 
HETATM 26 C C23 VEI . . . D 2 29.453 -10.291 -61.697 1 124.78 ? C23 VEI 501 A 1 
HETATM 27 C C25 VEI . . . D 2 27.051 -10.616 -60.763 1 118.19 ? C25 VEI 501 A 1 
HETATM 28 C C29 VEI . . . D 2 30.982 -12.971 -59.684 1 129.14 ? C29 VEI 501 A 1 
HETATM 29 C C30 VEI . . . D 2 31.904 -14.192 -59.91 1 132.62 ? C30 VEI 501 A 1 
HETATM 30 C C31 VEI . . . D 2 31.405 -15.042 -61.099 1 142.19 ? C31 VEI 501 A 1 
HETATM 31 C C32 VEI . . . D 2 31.339 -14.143 -62.368 1 142.2 ? C32 VEI 501 A 1 
HETATM 32 C C34 VEI . . . D 2 30.005 -14.496 -63.154 1 138.59 ? C34 VEI 501 A 1 
HETATM 33 C C39 VEI . . . D 2 25.933 -9.477 -63.91 1 120.65 ? C39 VEI 501 A 1 
HETATM 34 C C40 VEI . . . D 2 25.338 -6.086 -64.773 1 125.67 ? C40 VEI 501 A 1 
HETATM 35 C C42 VEI . . . D 2 28.912 -4.758 -64.369 1 121.08 ? C42 VEI 501 A 1 
HETATM 36 C C44 VEI . . . D 2 28.27 -4.376 -70.718 1 136.29 ? C44 VEI 501 A 1 
HETATM 37 C C45 VEI . . . D 2 29.314 -4.197 -71.873 1 138.06 ? C45 VEI 501 A 1 
HETATM 38 C C46 VEI . . . D 2 28.645 -4.667 -73.199 1 145.12 ? C46 VEI 501 A 1 
HETATM 39 C C47 VEI . . . D 2 28.239 -6.139 -72.993 1 141.99 ? C47 VEI 501 A 1 
HETATM 40 C C48 VEI . . . D 2 27.149 -6.07 -71.922 1 139.55 ? C48 VEI 501 A 1 
HETATM 41 C C50 VEI . . . D 2 26.381 -7.379 -71.713 1 145.58 ? C50 VEI 501 A 1 
HETATM 42 C C55 VEI . . . D 2 24.066 -3.754 -71.698 1 156.13 ? C55 VEI 501 A 1 
HETATM 43 O O27 VEI . . . D 2 29.645 -11.644 -61.282 1 126.54 ? O27 VEI 501 A 1 
HETATM 44 O O33 VEI . . . D 2 31.537 -12.764 -62.066 1 142.07 ? O33 VEI 501 A 1 
HETATM 45 O O35 VEI . . . D 2 28.947 -14.626 -62.295 1 135.6 ? O35 VEI 501 A 1 
HETATM 46 O O36 VEI . . . D 2 32.233 -16.092 -61.289 1 136.46 ? O36 VEI 501 A 1 
HETATM 47 O O37 VEI . . . D 2 31.952 -14.979 -58.8 1 136.68 ? O37 VEI 501 A 1 
HETATM 48 O O38 VEI . . . D 2 31.469 -12.247 -58.648 1 124.92 ? O38 VEI 501 A 1 
HETATM 49 O O41 VEI . . . D 2 28.23 -6.867 -68.263 1 116.39 ? O41 VEI 501 A 1 
HETATM 50 O O43 VEI . . . D 2 28.665 -4.057 -69.422 1 132.2 ? O43 VEI 501 A 1 
HETATM 51 O O49 VEI . . . D 2 27.714 -5.625 -70.752 1 140.19 ? O49 VEI 501 A 1 
HETATM 52 O O51 VEI . . . D 2 25.301 -7.509 -72.515 1 158.08 ? O51 VEI 501 A 1 
HETATM 53 O O52 VEI . . . D 2 27.812 -6.703 -74.131 1 147.97 ? O52 VEI 501 A 1 
HETATM 54 O O53 VEI . . . D 2 29.441 -4.427 -74.249 1 145.61 ? O53 VEI 501 A 1 
HETATM 55 O O54 VEI . . . D 2 29.772 -2.93 -71.901 1 138.83 ? O54 VEI 501 A 1 
#
_model_server_stats.io_time_ms              75 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           55 
#