data_8F2Z
#
_model_server_result.job_id            SfEVFfxXa9GwYaX1LLJ3rg 
_model_server_result.datetime_utc      '2025-07-17 06:36:06' 
_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          8f2z 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":901}' 
#
_entry.id    8F2Z 
#
_exptl.entry_id    8F2Z 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              995.821 
_entity.id                          3 
_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-[(1R,3S,3aS,13R)-3-([1,1'-biphenyl]-4-yl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-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            8F2Z 
_cell.length_a            119.474 
_cell.length_b            179.246 
_cell.length_c            234.683 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8F2Z 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C 
_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                      3 
_struct_asym.id                             C 
_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                XB3 
_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-[(1R,3S,3aS,13R)-3-([1,1'-biphenyl]-4-yl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-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 XB3 sing 374 n n 
C7 C6 XB3 doub 375 n y 
C7 C2 XB3 sing 376 n y 
C6 C5 XB3 sing 377 n y 
O1 C9 XB3 sing 378 n n 
C9 C10 XB3 sing 379 n n 
C9 N1 XB3 sing 380 n n 
C10 C11 XB3 sing 381 n n 
C1 C2 XB3 sing 382 n n 
C2 C3 XB3 doub 383 n y 
C5 N1 XB3 sing 384 n n 
C5 C4 XB3 doub 385 n y 
N1 C24 XB3 sing 386 n n 
O2 C25 XB3 doub 387 n n 
C11 C24 XB3 sing 388 n n 
C11 C12 XB3 sing 389 n n 
C3 C4 XB3 sing 390 n y 
C4 N4 XB3 sing 391 n n 
C23 C12 XB3 doub 392 n y 
C23 C22 XB3 sing 393 n y 
C24 C25 XB3 sing 394 n n 
C24 C27 XB3 sing 395 n n 
C12 C13 XB3 sing 396 n y 
C25 N2 XB3 sing 397 n n 
C22 C15 XB3 doub 398 n y 
N4 C27 XB3 sing 399 n n 
N4 C28 XB3 sing 400 n n 
C13 C14 XB3 doub 401 n y 
C27 N3 XB3 doub 402 n n 
C15 C14 XB3 sing 403 n y 
C15 C16 XB3 sing 404 n n 
N2 C26 XB3 sing 405 n n 
O4 C29 XB3 sing 406 n n 
C17 C16 XB3 doub 407 n y 
C17 C18 XB3 sing 408 n y 
C16 C21 XB3 sing 409 n y 
C28 C29 XB3 sing 410 n n 
N3 C26 XB3 sing 411 n n 
C18 C19 XB3 doub 412 n y 
C26 O3 XB3 doub 413 n n 
C21 C20 XB3 doub 414 n y 
C29 C30 XB3 sing 415 n n 
O15 C41 XB3 sing 416 n n 
C19 C20 XB3 sing 417 n y 
C30 O5 XB3 sing 418 n n 
C30 C31 XB3 sing 419 n n 
C41 C42 XB3 sing 420 n n 
C41 C35 XB3 sing 421 n n 
O6 C31 XB3 sing 422 n n 
O11 P2 XB3 doub 423 n n 
C42 O16 XB3 sing 424 n n 
C42 C34 XB3 sing 425 n n 
C36 N6 XB3 doub 426 n y 
C36 N5 XB3 sing 427 n y 
O12 P2 XB3 sing 428 n n 
N6 C37 XB3 sing 429 n y 
C31 C32 XB3 sing 430 n n 
P2 O13 XB3 sing 431 n n 
P2 O10 XB3 sing 432 n n 
N5 C35 XB3 sing 433 n n 
N5 C40 XB3 sing 434 n y 
C35 O14 XB3 sing 435 n n 
C37 C40 XB3 doub 436 n y 
C37 C38 XB3 sing 437 n y 
C33 O13 XB3 sing 438 n n 
C33 C34 XB3 sing 439 n n 
N7 C38 XB3 sing 440 n n 
C32 O7 XB3 sing 441 n n 
C40 N9 XB3 sing 442 n y 
C34 O14 XB3 sing 443 n n 
C38 N8 XB3 doub 444 n y 
O7 P1 XB3 sing 445 n n 
N9 C39 XB3 doub 446 n y 
N8 C39 XB3 sing 447 n y 
O10 P1 XB3 sing 448 n n 
P1 O9 XB3 doub 449 n n 
P1 O8 XB3 sing 450 n n 
C14 H1 XB3 sing 451 n n 
C6 H2 XB3 sing 452 n n 
C11 H3 XB3 sing 453 n n 
C8 H4 XB3 sing 454 n n 
C8 H5 XB3 sing 455 n n 
C8 H6 XB3 sing 456 n n 
C9 H7 XB3 sing 457 n n 
C10 H8 XB3 sing 458 n n 
C10 H9 XB3 sing 459 n n 
C13 H10 XB3 sing 460 n n 
N2 H11 XB3 sing 461 n n 
C3 H12 XB3 sing 462 n n 
C1 H14 XB3 sing 463 n n 
C1 H15 XB3 sing 464 n n 
C1 H16 XB3 sing 465 n n 
C17 H17 XB3 sing 466 n n 
C18 H18 XB3 sing 467 n n 
C19 H19 XB3 sing 468 n n 
C20 H20 XB3 sing 469 n n 
C21 H21 XB3 sing 470 n n 
C22 H22 XB3 sing 471 n n 
C23 H23 XB3 sing 472 n n 
C28 H25 XB3 sing 473 n n 
C28 H26 XB3 sing 474 n n 
C29 H27 XB3 sing 475 n n 
C30 H28 XB3 sing 476 n n 
C31 H29 XB3 sing 477 n n 
C32 H30 XB3 sing 478 n n 
C32 H31 XB3 sing 479 n n 
C33 H32 XB3 sing 480 n n 
C33 H33 XB3 sing 481 n n 
C34 H34 XB3 sing 482 n n 
C35 H35 XB3 sing 483 n n 
C36 H36 XB3 sing 484 n n 
C39 H37 XB3 sing 485 n n 
C41 H38 XB3 sing 486 n n 
C42 H39 XB3 sing 487 n n 
N7 H40 XB3 sing 488 n n 
N7 H41 XB3 sing 489 n n 
O1 H42 XB3 sing 490 n n 
O12 H43 XB3 sing 491 n n 
O15 H44 XB3 sing 492 n n 
O16 H45 XB3 sing 493 n n 
O4 H46 XB3 sing 494 n n 
O5 H47 XB3 sing 495 n n 
O6 H48 XB3 sing 496 n n 
O8 H49 XB3 sing 497 n n 
#
_atom_sites.entry_id                     8F2Z 
_atom_sites.fract_transf_matrix[1][1]    0.00837 
_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]    0.005579 
_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]    0.004261 
_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          C 
_pdbx_nonpoly_scheme.entity_id        3 
_pdbx_nonpoly_scheme.mon_id           XB3 
_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       XB3 
_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 XB3 . . . C 3 -6.941 59.93 83.153 1 97.67 ? C4 XB3 901 A 1 
HETATM 2 C C14 XB3 . . . C 3 -5.441 53.664 85.113 1 101.6 ? C14 XB3 901 A 1 
HETATM 3 C C5 XB3 . . . C 3 -7.592 59.359 82.091 1 98.25 ? C5 XB3 901 A 1 
HETATM 4 C C6 XB3 . . . C 3 -7.535 59.924 80.837 1 93.65 ? C6 XB3 901 A 1 
HETATM 5 C C11 XB3 . . . C 3 -7.329 56.134 82.87 1 101.84 ? C11 XB3 901 A 1 
HETATM 6 C C7 XB3 . . . C 3 -6.816 61.068 80.63 1 95.97 ? C7 XB3 901 A 1 
HETATM 7 C C8 XB3 . . . C 3 -6.737 61.69 79.27 1 88.69 ? C8 XB3 901 A 1 
HETATM 8 C C9 XB3 . . . C 3 -8.111 57.357 81.105 1 104.42 ? C9 XB3 901 A 1 
HETATM 9 C C10 XB3 . . . C 3 -6.869 56.602 81.504 1 98.85 ? C10 XB3 901 A 1 
HETATM 10 C C12 XB3 . . . C 3 -6.267 55.366 83.618 1 104.76 ? C12 XB3 901 A 1 
HETATM 11 C C13 XB3 . . . C 3 -6.497 54.338 84.519 1 101.97 ? C13 XB3 901 A 1 
HETATM 12 N N1 XB3 . . . C 3 -8.324 58.209 82.233 1 100.37 ? N1 XB3 901 A 1 
HETATM 13 N N2 XB3 . . . C 3 -9.818 56.562 84.905 1 92.6 ? N2 XB3 901 A 1 
HETATM 14 C C3 XB3 . . . C 3 -6.207 61.089 82.961 1 95.05 ? C3 XB3 901 A 1 
HETATM 15 N N3 XB3 . . . C 3 -8.014 57.797 85.745 1 103.17 ? N3 XB3 901 A 1 
HETATM 16 C C1 XB3 . . . C 3 -5.351 62.927 81.516 1 82.33 ? C1 XB3 901 A 1 
HETATM 17 C C15 XB3 . . . C 3 -4.124 53.982 84.812 1 111.22 ? C15 XB3 901 A 1 
HETATM 18 C C16 XB3 . . . C 3 -2.954 53.274 85.396 1 117.3 ? C16 XB3 901 A 1 
HETATM 19 C C17 XB3 . . . C 3 -1.682 53.824 85.303 1 111.55 ? C17 XB3 901 A 1 
HETATM 20 C C18 XB3 . . . C 3 -0.573 53.168 85.805 1 116.88 ? C18 XB3 901 A 1 
HETATM 21 C C19 XB3 . . . C 3 -0.708 51.939 86.392 1 118.17 ? C19 XB3 901 A 1 
HETATM 22 C C2 XB3 . . . C 3 -6.141 61.671 81.728 1 98.48 ? C2 XB3 901 A 1 
HETATM 23 C C20 XB3 . . . C 3 -1.951 51.367 86.48 1 127.2 ? C20 XB3 901 A 1 
HETATM 24 C C21 XB3 . . . C 3 -3.066 52.021 85.981 1 129.04 ? C21 XB3 901 A 1 
HETATM 25 C C22 XB3 . . . C 3 -3.919 54.975 83.872 1 109.78 ? C22 XB3 901 A 1 
HETATM 26 C C23 XB3 . . . C 3 -4.964 55.647 83.272 1 103.32 ? C23 XB3 901 A 1 
HETATM 27 C C24 XB3 . . . C 3 -8.137 57.353 83.393 1 102.92 ? C24 XB3 901 A 1 
HETATM 28 C C25 XB3 . . . C 3 -9.502 56.791 83.652 1 103.83 ? C25 XB3 901 A 1 
HETATM 29 C C26 XB3 . . . C 3 -9.037 57.018 85.901 1 103.06 ? C26 XB3 901 A 1 
HETATM 30 C C27 XB3 . . . C 3 -7.7 58.164 84.565 1 97.42 ? C27 XB3 901 A 1 
HETATM 31 C C28 XB3 . . . C 3 -6.47 60.029 85.582 1 92.61 ? C28 XB3 901 A 1 
HETATM 32 C C29 XB3 . . . C 3 -7.359 61.123 86.108 1 91.82 ? C29 XB3 901 A 1 
HETATM 33 C C30 XB3 . . . C 3 -6.615 62.137 86.969 1 87.3 ? C30 XB3 901 A 1 
HETATM 34 C C31 XB3 . . . C 3 -7.438 62.776 88.075 1 88.77 ? C31 XB3 901 A 1 
HETATM 35 C C32 XB3 . . . C 3 -6.581 63.618 88.985 1 87.1 ? C32 XB3 901 A 1 
HETATM 36 C C33 XB3 . . . C 3 -6.296 70.049 88.937 1 78.07 ? C33 XB3 901 A 1 
HETATM 37 C C34 XB3 . . . C 3 -7.013 71.352 89.099 1 77.44 ? C34 XB3 901 A 1 
HETATM 38 C C35 XB3 . . . C 3 -6.197 73.396 88.525 1 83.99 ? C35 XB3 901 A 1 
HETATM 39 C C36 XB3 . . . C 3 -3.803 73.899 87.916 1 79.65 ? C36 XB3 901 A 1 
HETATM 40 C C37 XB3 . . . C 3 -3.593 75.828 88.739 1 80.01 ? C37 XB3 901 A 1 
HETATM 41 C C38 XB3 . . . C 3 -3.208 77.09 89.187 1 79.4 ? C38 XB3 901 A 1 
HETATM 42 C C39 XB3 . . . C 3 -5.331 77.308 90.042 1 78.52 ? C39 XB3 901 A 1 
HETATM 43 C C40 XB3 . . . C 3 -4.874 75.441 89.013 1 76.94 ? C40 XB3 901 A 1 
HETATM 44 C C41 XB3 . . . C 3 -6.569 72.694 87.242 1 86.14 ? C41 XB3 901 A 1 
HETATM 45 C C42 XB3 . . . C 3 -7.699 71.882 87.841 1 85.41 ? C42 XB3 901 A 1 
HETATM 46 N N4 XB3 . . . C 3 -7.049 59.333 84.412 1 91.98 ? N4 XB3 901 A 1 
HETATM 47 N N5 XB3 . . . C 3 -5 74.197 88.485 1 80.44 ? N5 XB3 901 A 1 
HETATM 48 N N6 XB3 . . . C 3 -2.928 74.852 88.038 1 80.11 ? N6 XB3 901 A 1 
HETATM 49 N N7 XB3 . . . C 3 -2.008 77.602 88.984 1 75.02 ? N7 XB3 901 A 1 
HETATM 50 N N8 XB3 . . . C 3 -4.117 77.82 89.851 1 76.27 ? N8 XB3 901 A 1 
HETATM 51 N N9 XB3 . . . C 3 -5.805 76.139 89.662 1 80.27 ? N9 XB3 901 A 1 
HETATM 52 O O1 XB3 . . . C 3 -9.189 56.486 81.005 1 109.85 ? O1 XB3 901 A 1 
HETATM 53 O O10 XB3 . . . C 3 -6.32 67.082 89.871 1 86.49 ? O10 XB3 901 A 1 
HETATM 54 O O11 XB3 . . . C 3 -5.487 67.858 87.716 1 71.22 ? O11 XB3 901 A 1 
HETATM 55 O O12 XB3 . . . C 3 -7.832 66.888 87.953 1 80.37 -1 O12 XB3 901 A 1 
HETATM 56 O O13 XB3 . . . C 3 -7.256 69.02 88.947 1 92.83 ? O13 XB3 901 A 1 
HETATM 57 O O14 XB3 . . . C 3 -6.016 72.34 89.413 1 78.61 ? O14 XB3 901 A 1 
HETATM 58 O O15 XB3 . . . C 3 -7.072 73.583 86.282 1 83.92 ? O15 XB3 901 A 1 
HETATM 59 O O16 XB3 . . . C 3 -8.731 72.803 88.162 1 88.97 ? O16 XB3 901 A 1 
HETATM 60 O O2 XB3 . . . C 3 -10.271 56.525 82.749 1 100.96 ? O2 XB3 901 A 1 
HETATM 61 O O3 XB3 . . . C 3 -9.318 56.694 87.016 1 109.12 ? O3 XB3 901 A 1 
HETATM 62 O O4 XB3 . . . C 3 -7.82 61.785 85.002 1 94.44 ? O4 XB3 901 A 1 
HETATM 63 O O5 XB3 . . . C 3 -5.609 61.467 87.622 1 83.72 ? O5 XB3 901 A 1 
HETATM 64 O O6 XB3 . . . C 3 -8.463 63.564 87.494 1 89.52 ? O6 XB3 901 A 1 
HETATM 65 O O7 XB3 . . . C 3 -7.157 64.883 89.357 1 86.83 ? O7 XB3 901 A 1 
HETATM 66 O O8 XB3 . . . C 3 -7.486 65.771 91.596 1 85.42 ? O8 XB3 901 A 1 
HETATM 67 O O9 XB3 . . . C 3 -5.126 65.251 90.829 1 77.58 -1 O9 XB3 901 A 1 
HETATM 68 P P1 XB3 . . . C 3 -6.489 65.685 90.524 1 84.32 ? P1 XB3 901 A 1 
HETATM 69 P P2 XB3 . . . C 3 -6.706 67.645 88.483 1 83.47 ? P2 XB3 901 A 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           69 
#