data_8F59
#
_model_server_result.job_id            rS_LB_fBj5hcIycacHHZ6Q 
_model_server_result.datetime_utc      '2025-07-13 23:13:53' 
_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          8f59 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":901}' 
#
_entry.id    8F59 
#
_exptl.entry_id    8F59 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              995.821 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-{5-[3-([1,1'-biphenyl]-4-yl)propanoyl]-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)" 
_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         90 
_cell.entry_id            8F59 
_cell.length_a            120.206 
_cell.length_b            179.201 
_cell.length_c            236.155 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8F59 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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           'C42 H47 N9 O16 P2' 
_chem_comp.formula_weight    995.821 
_chem_comp.id                XB6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-{5-[3-([1,1'-biphenyl]-4-yl)propanoyl]-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name)" 
_chem_comp.type              non-polymer 
_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
C8 C7 XB6 sing 374 n n 
O1 C9 XB6 doub 375 n n 
C7 C6 XB6 doub 376 n y 
C7 C2 XB6 sing 377 n y 
C6 C5 XB6 sing 378 n y 
C9 C10 XB6 sing 379 n n 
C9 N1 XB6 sing 380 n n 
C10 C11 XB6 sing 381 n n 
C1 C2 XB6 sing 382 n n 
C2 C3 XB6 doub 383 n y 
C5 N1 XB6 sing 384 n n 
C5 C4 XB6 doub 385 n y 
N1 C24 XB6 sing 386 n n 
O3 C27 XB6 doub 387 n n 
C11 C12 XB6 sing 388 n n 
C3 C4 XB6 sing 389 n y 
C4 N4 XB6 sing 390 n n 
C24 C27 XB6 sing 391 n n 
C24 C25 XB6 doub 392 n n 
C12 C23 XB6 doub 393 n y 
C12 C13 XB6 sing 394 n y 
C27 N3 XB6 sing 395 n n 
C23 C22 XB6 sing 396 n y 
C13 C14 XB6 doub 397 n y 
C22 C15 XB6 doub 398 n y 
N4 C25 XB6 sing 399 n n 
N4 C28 XB6 sing 400 n n 
C25 N2 XB6 sing 401 n n 
N3 C26 XB6 sing 402 n n 
C14 C15 XB6 sing 403 n y 
O4 C29 XB6 sing 404 n n 
C15 C16 XB6 sing 405 n n 
C28 C29 XB6 sing 406 n n 
C21 C16 XB6 doub 407 n y 
C21 C20 XB6 sing 408 n y 
N2 C26 XB6 sing 409 n n 
C26 O2 XB6 doub 410 n n 
C16 C17 XB6 sing 411 n y 
C29 C30 XB6 sing 412 n n 
C20 C19 XB6 doub 413 n y 
O15 C41 XB6 sing 414 n n 
C17 C18 XB6 doub 415 n y 
C30 O5 XB6 sing 416 n n 
C30 C31 XB6 sing 417 n n 
C41 C42 XB6 sing 418 n n 
C41 C35 XB6 sing 419 n n 
O12 P2 XB6 doub 420 n n 
C19 C18 XB6 sing 421 n y 
O6 C31 XB6 sing 422 n n 
C42 O16 XB6 sing 423 n n 
C42 C34 XB6 sing 424 n n 
C36 N6 XB6 doub 425 n y 
C36 N5 XB6 sing 426 n y 
C31 C32 XB6 sing 427 n n 
N6 C37 XB6 sing 428 n y 
O11 P2 XB6 sing 429 n n 
P2 O13 XB6 sing 430 n n 
P2 O10 XB6 sing 431 n n 
N5 C35 XB6 sing 432 n n 
N5 C40 XB6 sing 433 n y 
C35 O14 XB6 sing 434 n n 
C37 C40 XB6 doub 435 n y 
C37 C38 XB6 sing 436 n y 
C32 O7 XB6 sing 437 n n 
N7 C38 XB6 sing 438 n n 
C40 N9 XB6 sing 439 n y 
C33 O13 XB6 sing 440 n n 
C33 C34 XB6 sing 441 n n 
C34 O14 XB6 sing 442 n n 
C38 N8 XB6 doub 443 n y 
O7 P1 XB6 sing 444 n n 
O10 P1 XB6 sing 445 n n 
N9 C39 XB6 doub 446 n y 
N8 C39 XB6 sing 447 n y 
P1 O8 XB6 doub 448 n n 
P1 O9 XB6 sing 449 n n 
C14 H1 XB6 sing 450 n n 
C6 H2 XB6 sing 451 n n 
C11 H3 XB6 sing 452 n n 
C11 H4 XB6 sing 453 n n 
C8 H5 XB6 sing 454 n n 
C8 H6 XB6 sing 455 n n 
C8 H7 XB6 sing 456 n n 
C10 H8 XB6 sing 457 n n 
C10 H9 XB6 sing 458 n n 
C13 H10 XB6 sing 459 n n 
N2 H11 XB6 sing 460 n n 
C3 H12 XB6 sing 461 n n 
N3 H13 XB6 sing 462 n n 
C1 H14 XB6 sing 463 n n 
C1 H15 XB6 sing 464 n n 
C1 H16 XB6 sing 465 n n 
C17 H17 XB6 sing 466 n n 
C18 H18 XB6 sing 467 n n 
C19 H19 XB6 sing 468 n n 
C20 H20 XB6 sing 469 n n 
C21 H21 XB6 sing 470 n n 
C22 H22 XB6 sing 471 n n 
C23 H23 XB6 sing 472 n n 
C28 H24 XB6 sing 473 n n 
C28 H25 XB6 sing 474 n n 
C29 H26 XB6 sing 475 n n 
C30 H27 XB6 sing 476 n n 
C31 H28 XB6 sing 477 n n 
C32 H29 XB6 sing 478 n n 
C32 H30 XB6 sing 479 n n 
C33 H31 XB6 sing 480 n n 
C33 H32 XB6 sing 481 n n 
C34 H33 XB6 sing 482 n n 
C35 H34 XB6 sing 483 n n 
C36 H35 XB6 sing 484 n n 
C39 H36 XB6 sing 485 n n 
C41 H37 XB6 sing 486 n n 
C42 H38 XB6 sing 487 n n 
N7 H39 XB6 sing 488 n n 
N7 H40 XB6 sing 489 n n 
O11 H41 XB6 sing 490 n n 
O15 H42 XB6 sing 491 n n 
O16 H43 XB6 sing 492 n n 
O4 H44 XB6 sing 493 n n 
O5 H45 XB6 sing 494 n n 
O6 H46 XB6 sing 495 n n 
O9 H47 XB6 sing 496 n n 
#
_atom_sites.entry_id                     8F59 
_atom_sites.fract_transf_matrix[1][1]    0.008319 
_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]    0.00558 
_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]    0.004235 
_atom_sites.fract_transf_vector[1]       0 
_atom_sites.fract_transf_vector[2]       0 
_atom_sites.fract_transf_vector[3]       0 
#
_pdbx_nonpoly_scheme.asym_id          D 
_pdbx_nonpoly_scheme.entity_id        4 
_pdbx_nonpoly_scheme.mon_id           XB6 
_pdbx_nonpoly_scheme.pdb_strand_id    A 
_pdbx_nonpoly_scheme.ndb_seq_num      1 
_pdbx_nonpoly_scheme.pdb_seq_num      901 
_pdbx_nonpoly_scheme.auth_seq_num     901 
_pdbx_nonpoly_scheme.pdb_mon_id       XB6 
_pdbx_nonpoly_scheme.auth_mon_id      DRG 
_pdbx_nonpoly_scheme.pdb_ins_code     . 
#
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 C4 XB6 . . . D 4 -6.781 59.827 83.737 1 83.11 ? C4 XB6 901 A 1 
HETATM 2 C C14 XB6 . . . D 4 -4.499 53.484 85.701 1 94.51 ? C14 XB6 901 A 1 
HETATM 3 C C5 XB6 . . . D 4 -7.311 59.18 82.637 1 82.48 ? C5 XB6 901 A 1 
HETATM 4 C C6 XB6 . . . D 4 -7.26 59.755 81.382 1 79.61 ? C6 XB6 901 A 1 
HETATM 5 C C11 XB6 . . . D 4 -5.88 56.033 83.254 1 86.91 ? C11 XB6 901 A 1 
HETATM 6 C C7 XB6 . . . D 4 -6.728 60.992 81.213 1 84.08 ? C7 XB6 901 A 1 
HETATM 7 C C8 XB6 . . . D 4 -6.694 61.618 79.855 1 77.03 ? C8 XB6 901 A 1 
HETATM 8 C C9 XB6 . . . D 4 -7.65 57 81.782 1 88.51 ? C9 XB6 901 A 1 
HETATM 9 C C10 XB6 . . . D 4 -6.815 55.795 82.099 1 85.34 ? C10 XB6 901 A 1 
HETATM 10 C C12 XB6 . . . D 4 -5.743 54.817 84.129 1 93.62 ? C12 XB6 901 A 1 
HETATM 11 C C13 XB6 . . . D 4 -4.624 54.606 84.906 1 91.94 ? C13 XB6 901 A 1 
HETATM 12 N N1 XB6 . . . D 4 -7.796 57.943 82.774 1 86.65 ? N1 XB6 901 A 1 
HETATM 13 N N2 XB6 . . . D 4 -8.151 57.822 86.377 1 80.47 ? N2 XB6 901 A 1 
HETATM 14 C C3 XB6 . . . D 4 -6.234 61.091 83.573 1 81.23 ? C3 XB6 901 A 1 
HETATM 15 N N3 XB6 . . . D 4 -9.584 56.272 85.441 1 87.64 ? N3 XB6 901 A 1 
HETATM 16 C C1 XB6 . . . D 4 -5.612 63.049 82.167 1 70.76 ? C1 XB6 901 A 1 
HETATM 17 C C15 XB6 . . . D 4 -5.507 52.538 85.755 1 100.98 ? C15 XB6 901 A 1 
HETATM 18 C C16 XB6 . . . D 4 -5.393 51.32 86.593 1 107.94 ? C16 XB6 901 A 1 
HETATM 19 C C17 XB6 . . . D 4 -4.491 51.243 87.642 1 102.11 ? C17 XB6 901 A 1 
HETATM 20 C C18 XB6 . . . D 4 -4.39 50.097 88.407 1 104.27 ? C18 XB6 901 A 1 
HETATM 21 C C19 XB6 . . . D 4 -5.179 49.014 88.136 1 106.83 ? C19 XB6 901 A 1 
HETATM 22 C C2 XB6 . . . D 4 -6.201 61.683 82.343 1 81.6 ? C2 XB6 901 A 1 
HETATM 23 C C20 XB6 . . . D 4 -6.071 49.065 87.103 1 96.83 ? C20 XB6 901 A 1 
HETATM 24 C C21 XB6 . . . D 4 -6.178 50.206 86.334 1 103.58 ? C21 XB6 901 A 1 
HETATM 25 C C22 XB6 . . . D 4 -6.628 52.754 84.977 1 98.07 ? C22 XB6 901 A 1 
HETATM 26 C C23 XB6 . . . D 4 -6.742 53.875 84.183 1 97.68 ? C23 XB6 901 A 1 
HETATM 27 C C24 XB6 . . . D 4 -8.296 57.587 84.047 1 80.86 ? C24 XB6 901 A 1 
HETATM 28 C C25 XB6 . . . D 4 -7.753 58.187 85.139 1 78.89 ? C25 XB6 901 A 1 
HETATM 29 C C26 XB6 . . . D 4 -9.083 56.848 86.559 1 83.63 ? C26 XB6 901 A 1 
HETATM 30 C C27 XB6 . . . D 4 -9.196 56.607 84.172 1 82.77 ? C27 XB6 901 A 1 
HETATM 31 C C28 XB6 . . . D 4 -6.383 59.947 86.176 1 80.07 ? C28 XB6 901 A 1 
HETATM 32 C C29 XB6 . . . D 4 -7.326 60.938 86.77 1 73.99 ? C29 XB6 901 A 1 
HETATM 33 C C30 XB6 . . . D 4 -6.595 61.918 87.677 1 73.14 ? C30 XB6 901 A 1 
HETATM 34 C C31 XB6 . . . D 4 -7.43 62.558 88.769 1 70.29 ? C31 XB6 901 A 1 
HETATM 35 C C32 XB6 . . . D 4 -6.574 63.377 89.698 1 69.7 ? C32 XB6 901 A 1 
HETATM 36 C C33 XB6 . . . D 4 -6.117 69.76 89.86 1 63.03 ? C33 XB6 901 A 1 
HETATM 37 C C34 XB6 . . . D 4 -6.842 71.068 89.906 1 64.54 ? C34 XB6 901 A 1 
HETATM 38 C C35 XB6 . . . D 4 -6.217 73.191 89.362 1 69.5 ? C35 XB6 901 A 1 
HETATM 39 C C36 XB6 . . . D 4 -3.872 73.82 88.678 1 66.7 ? C36 XB6 901 A 1 
HETATM 40 C C37 XB6 . . . D 4 -3.715 75.737 89.54 1 67.42 ? C37 XB6 901 A 1 
HETATM 41 C C38 XB6 . . . D 4 -3.372 77.006 90.011 1 62.66 ? C38 XB6 901 A 1 
HETATM 42 C C39 XB6 . . . D 4 -5.47 77.099 90.937 1 62.54 ? C39 XB6 901 A 1 
HETATM 43 C C40 XB6 . . . D 4 -4.97 75.286 89.84 1 65.99 ? C40 XB6 901 A 1 
HETATM 44 C C41 XB6 . . . D 4 -6.646 72.563 88.061 1 69.45 ? C41 XB6 901 A 1 
HETATM 45 C C42 XB6 . . . D 4 -7.552 71.477 88.619 1 68.38 ? C42 XB6 901 A 1 
HETATM 46 N N4 XB6 . . . D 4 -6.826 59.204 84.991 1 82.72 ? N4 XB6 901 A 1 
HETATM 47 N N5 XB6 . . . D 4 -5.067 74.056 89.279 1 65.67 ? N5 XB6 901 A 1 
HETATM 48 N N6 XB6 . . . D 4 -3.03 74.803 88.798 1 65.55 ? N6 XB6 901 A 1 
HETATM 49 N N7 XB6 . . . D 4 -2.208 77.59 89.793 1 54.14 ? N7 XB6 901 A 1 
HETATM 50 N N8 XB6 . . . D 4 -4.292 77.674 90.719 1 57.56 ? N8 XB6 901 A 1 
HETATM 51 N N9 XB6 . . . D 4 -5.91 75.927 90.53 1 73.72 ? N9 XB6 901 A 1 
HETATM 52 O O1 XB6 . . . D 4 -8.194 57.133 80.713 1 87.16 ? O1 XB6 901 A 1 
HETATM 53 O O10 XB6 . . . D 4 -5.943 66.698 90.252 1 56.84 ? O10 XB6 901 A 1 
HETATM 54 O O11 XB6 . . . D 4 -7.933 66.723 88.843 1 58.84 ? O11 XB6 901 A 1 
HETATM 55 O O12 XB6 . . . D 4 -5.753 67.836 88.096 1 55.13 ? O12 XB6 901 A 1 
HETATM 56 O O13 XB6 . . . D 4 -7.084 68.734 89.906 1 77.77 ? O13 XB6 901 A 1 
HETATM 57 O O14 XB6 . . . D 4 -5.867 72.096 90.141 1 68.4 ? O14 XB6 901 A 1 
HETATM 58 O O15 XB6 . . . D 4 -7.381 73.517 87.346 1 72.65 ? O15 XB6 901 A 1 
HETATM 59 O O16 XB6 . . . D 4 -8.819 72.011 88.942 1 71.6 ? O16 XB6 901 A 1 
HETATM 60 O O2 XB6 . . . D 4 -9.46 56.524 87.662 1 78.19 ? O2 XB6 901 A 1 
HETATM 61 O O3 XB6 . . . D 4 -9.7 56.032 83.227 1 87.87 ? O3 XB6 901 A 1 
HETATM 62 O O4 XB6 . . . D 4 -7.773 61.666 85.708 1 74.68 ? O4 XB6 901 A 1 
HETATM 63 O O5 XB6 . . . D 4 -5.595 61.239 88.332 1 74.53 ? O5 XB6 901 A 1 
HETATM 64 O O6 XB6 . . . D 4 -8.419 63.372 88.163 1 72.52 ? O6 XB6 901 A 1 
HETATM 65 O O7 XB6 . . . D 4 -7.145 64.634 90.081 1 73.52 ? O7 XB6 901 A 1 
HETATM 66 O O8 XB6 . . . D 4 -5.216 64.855 91.682 1 59.83 ? O8 XB6 901 A 1 
HETATM 67 O O9 XB6 . . . D 4 -7.498 65.865 92.035 1 70.06 ? O9 XB6 901 A 1 
HETATM 68 P P1 XB6 . . . D 4 -6.405 65.502 91.142 1 67.98 ? P1 XB6 901 A 1 
HETATM 69 P P2 XB6 . . . D 4 -6.705 67.453 89.127 1 62.27 ? P2 XB6 901 A 1 
#
_model_server_stats.io_time_ms              50 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           69 
#