data_8FRI
#
_model_server_result.job_id            6IOU0182iYZn1Ny9y1uLng 
_model_server_result.datetime_utc      '2024-12-23 06:19:44' 
_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          8fri 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":901}' 
#
_entry.id    8FRI 
#
_exptl.entry_id    8FRI 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              1071.917 
_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)-2,3,4-trihydroxy-5-[(1R,3S,3aS,13R)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-([1~1~,2~1~:2~3~,3~1~-terphenyl]-1~4~-yl)-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl 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            8FRI 
_cell.length_a            118.427 
_cell.length_b            178.992 
_cell.length_c            233.98 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8FRI 
_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           'C48 H51 N9 O16 P2' 
_chem_comp.formula_weight    1071.917 
_chem_comp.id                Y9K 
_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)-2,3,4-trihydroxy-5-[(1R,3S,3aS,13R)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-([1~1~,2~1~:2~3~,3~1~-terphenyl]-1~4~-yl)-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl 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 Y9K sing 374 n n 
C7 C6 Y9K doub 375 n y 
C7 C2 Y9K sing 376 n y 
C6 C5 Y9K sing 377 n y 
O1 C9 Y9K sing 378 n n 
C9 C10 Y9K sing 379 n n 
C9 N1 Y9K sing 380 n n 
C1 C2 Y9K sing 381 n n 
C10 C11 Y9K sing 382 n n 
C2 C3 Y9K doub 383 n y 
C5 N1 Y9K sing 384 n n 
C5 C4 Y9K doub 385 n y 
N1 C30 Y9K sing 386 n n 
O2 C31 Y9K doub 387 n n 
C3 C4 Y9K sing 388 n y 
C11 C30 Y9K sing 389 n n 
C11 C12 Y9K sing 390 n n 
C4 N4 Y9K sing 391 n n 
C30 C31 Y9K sing 392 n n 
C30 C33 Y9K sing 393 n n 
C13 C12 Y9K doub 394 n y 
C13 C14 Y9K sing 395 n y 
C31 N2 Y9K sing 396 n n 
C12 C29 Y9K sing 397 n y 
C14 C15 Y9K doub 398 n y 
N4 C33 Y9K sing 399 n n 
N4 C34 Y9K sing 400 n n 
C33 N3 Y9K doub 401 n n 
C29 C28 Y9K doub 402 n y 
N2 C32 Y9K sing 403 n n 
C15 C28 Y9K sing 404 n y 
C15 C16 Y9K sing 405 n n 
O4 C35 Y9K sing 406 n n 
C16 C27 Y9K doub 407 n y 
C16 C17 Y9K sing 408 n y 
C34 C35 Y9K sing 409 n n 
C27 C20 Y9K sing 410 n y 
N3 C32 Y9K sing 411 n n 
C17 C18 Y9K doub 412 n y 
C32 O3 Y9K doub 413 n n 
C20 C21 Y9K sing 414 n n 
C20 C19 Y9K doub 415 n y 
C26 C21 Y9K doub 416 n y 
C26 C25 Y9K sing 417 n y 
C35 C36 Y9K sing 418 n n 
C21 C22 Y9K sing 419 n y 
C18 C19 Y9K sing 420 n y 
C25 C24 Y9K doub 421 n y 
C22 C23 Y9K doub 422 n y 
C24 C23 Y9K sing 423 n y 
O15 C47 Y9K sing 424 n n 
C36 O5 Y9K sing 425 n n 
C36 C37 Y9K sing 426 n n 
C47 C48 Y9K sing 427 n n 
C47 C41 Y9K sing 428 n n 
O11 P2 Y9K doub 429 n n 
O6 C37 Y9K sing 430 n n 
C42 N6 Y9K doub 431 n y 
C42 N5 Y9K sing 432 n y 
N6 C43 Y9K sing 433 n y 
C48 O16 Y9K sing 434 n n 
C48 C40 Y9K sing 435 n n 
O12 P2 Y9K sing 436 n n 
C37 C38 Y9K sing 437 n n 
N5 C41 Y9K sing 438 n n 
N5 C46 Y9K sing 439 n y 
P2 O13 Y9K sing 440 n n 
P2 O10 Y9K sing 441 n n 
C41 O14 Y9K sing 442 n n 
C43 C46 Y9K doub 443 n y 
C43 C44 Y9K sing 444 n y 
N7 C44 Y9K sing 445 n n 
C46 N9 Y9K sing 446 n y 
C38 O7 Y9K sing 447 n n 
C44 N8 Y9K doub 448 n y 
C40 O14 Y9K sing 449 n n 
C40 C39 Y9K sing 450 n n 
O13 C39 Y9K sing 451 n n 
O7 P1 Y9K sing 452 n n 
O10 P1 Y9K sing 453 n n 
N9 C45 Y9K doub 454 n y 
N8 C45 Y9K sing 455 n y 
P1 O8 Y9K doub 456 n n 
P1 O9 Y9K sing 457 n n 
C14 H1 Y9K sing 458 n n 
C6 H2 Y9K sing 459 n n 
C11 H3 Y9K sing 460 n n 
C8 H4 Y9K sing 461 n n 
C8 H5 Y9K sing 462 n n 
C8 H6 Y9K sing 463 n n 
C9 H7 Y9K sing 464 n n 
C10 H8 Y9K sing 465 n n 
C10 H9 Y9K sing 466 n n 
C13 H10 Y9K sing 467 n n 
N2 H11 Y9K sing 468 n n 
C3 H12 Y9K sing 469 n n 
C1 H14 Y9K sing 470 n n 
C1 H15 Y9K sing 471 n n 
C1 H16 Y9K sing 472 n n 
C17 H17 Y9K sing 473 n n 
C18 H18 Y9K sing 474 n n 
C19 H19 Y9K sing 475 n n 
C22 H20 Y9K sing 476 n n 
C23 H21 Y9K sing 477 n n 
C24 H22 Y9K sing 478 n n 
C25 H23 Y9K sing 479 n n 
C26 H24 Y9K sing 480 n n 
C27 H25 Y9K sing 481 n n 
C28 H26 Y9K sing 482 n n 
C29 H27 Y9K sing 483 n n 
C34 H29 Y9K sing 484 n n 
C34 H30 Y9K sing 485 n n 
C35 H31 Y9K sing 486 n n 
C36 H32 Y9K sing 487 n n 
C37 H33 Y9K sing 488 n n 
C38 H34 Y9K sing 489 n n 
C38 H35 Y9K sing 490 n n 
C39 H36 Y9K sing 491 n n 
C39 H37 Y9K sing 492 n n 
C40 H38 Y9K sing 493 n n 
C41 H39 Y9K sing 494 n n 
C42 H40 Y9K sing 495 n n 
C45 H41 Y9K sing 496 n n 
C47 H42 Y9K sing 497 n n 
C48 H43 Y9K sing 498 n n 
N7 H44 Y9K sing 499 n n 
N7 H45 Y9K sing 500 n n 
O1 H46 Y9K sing 501 n n 
O12 H47 Y9K sing 502 n n 
O15 H48 Y9K sing 503 n n 
O16 H49 Y9K sing 504 n n 
O4 H50 Y9K sing 505 n n 
O5 H51 Y9K sing 506 n n 
O6 H52 Y9K sing 507 n n 
O9 H53 Y9K sing 508 n n 
#
_atom_sites.entry_id                     8FRI 
_atom_sites.fract_transf_matrix[1][1]    0.008444 
_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]    0.005587 
_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]    0.004274 
_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           Y9K 
_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       Y9K 
_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 Y9K . . . C 3 -7.161 59.894 82.892 1 79.89 ? C4 Y9K 901 A 1 
HETATM 2 C C14 Y9K . . . C 3 -4.101 55.086 83.794 1 90.94 ? C14 Y9K 901 A 1 
HETATM 3 C C5 Y9K . . . C 3 -7.585 59.193 81.802 1 79.5 ? C5 Y9K 901 A 1 
HETATM 4 C C6 Y9K . . . C 3 -7.467 59.696 80.529 1 74.24 ? C6 Y9K 901 A 1 
HETATM 5 C C11 Y9K . . . C 3 -7.606 55.866 82.84 1 88.43 ? C11 Y9K 901 A 1 
HETATM 6 C C7 Y9K . . . C 3 -6.891 60.916 80.331 1 77.24 ? C7 Y9K 901 A 1 
HETATM 7 C C8 Y9K . . . C 3 -6.737 61.48 78.953 1 75.61 ? C8 Y9K 901 A 1 
HETATM 8 C C9 Y9K . . . C 3 -8.127 57.101 80.835 1 92.53 ? C9 Y9K 901 A 1 
HETATM 9 C C10 Y9K . . . C 3 -7.284 55.953 81.353 1 90.56 ? C10 Y9K 901 A 1 
HETATM 10 C C12 Y9K . . . C 3 -6.474 55.202 83.581 1 87.08 ? C12 Y9K 901 A 1 
HETATM 11 C C13 Y9K . . . C 3 -5.223 55.643 83.226 1 89.57 ? C13 Y9K 901 A 1 
HETATM 12 N N1 Y9K . . . C 3 -8.179 57.993 81.938 1 81.01 ? N1 Y9K 901 A 1 
HETATM 13 N N2 Y9K . . . C 3 -9.995 56.512 84.576 1 81.37 ? N2 Y9K 901 A 1 
HETATM 14 C C3 Y9K . . . C 3 -6.57 61.134 82.711 1 76.83 ? C3 Y9K 901 A 1 
HETATM 15 N N3 Y9K . . . C 3 -8.301 57.796 85.503 1 75.09 ? N3 Y9K 901 A 1 
HETATM 16 C C1 Y9K . . . C 3 -5.807 62.995 81.236 1 68.13 ? C1 Y9K 901 A 1 
HETATM 17 C C15 Y9K . . . C 3 -4.173 54.041 84.69 1 91.99 ? C15 Y9K 901 A 1 
HETATM 18 C C16 Y9K . . . C 3 -2.907 53.489 85.227 1 94.64 ? C16 Y9K 901 A 1 
HETATM 19 C C17 Y9K . . . C 3 -1.86 54.349 85.504 1 90.8 ? C17 Y9K 901 A 1 
HETATM 20 C C18 Y9K . . . C 3 -0.643 53.892 85.952 1 94.86 ? C18 Y9K 901 A 1 
HETATM 21 C C19 Y9K . . . C 3 -0.437 52.545 86.093 1 102.89 ? C19 Y9K 901 A 1 
HETATM 22 C C2 Y9K . . . C 3 -6.441 61.658 81.456 1 76.14 ? C2 Y9K 901 A 1 
HETATM 23 C C20 Y9K . . . C 3 -1.438 51.642 85.787 1 108.08 ? C20 Y9K 901 A 1 
HETATM 24 C C21 Y9K . . . C 3 -1.174 50.192 85.941 1 110.29 ? C21 Y9K 901 A 1 
HETATM 25 C C22 Y9K . . . C 3 -2.2 49.287 86.183 1 113.06 ? C22 Y9K 901 A 1 
HETATM 26 C C23 Y9K . . . C 3 -1.927 47.938 86.326 1 114 ? C23 Y9K 901 A 1 
HETATM 27 C C24 Y9K . . . C 3 -0.633 47.482 86.236 1 107.11 ? C24 Y9K 901 A 1 
HETATM 28 C C25 Y9K . . . C 3 0.393 48.363 86.009 1 104.73 ? C25 Y9K 901 A 1 
HETATM 29 C C26 Y9K . . . C 3 0.128 49.712 85.87 1 102.69 ? C26 Y9K 901 A 1 
HETATM 30 C C27 Y9K . . . C 3 -2.662 52.125 85.329 1 105.32 ? C27 Y9K 901 A 1 
HETATM 31 C C28 Y9K . . . C 3 -5.437 53.567 85.007 1 92.11 ? C28 Y9K 901 A 1 
HETATM 32 C C29 Y9K . . . C 3 -6.574 54.125 84.443 1 84.65 ? C29 Y9K 901 A 1 
HETATM 33 C C30 Y9K . . . C 3 -8.236 57.25 83.176 1 82.84 ? C30 Y9K 901 A 1 
HETATM 34 C C31 Y9K . . . C 3 -9.648 56.81 83.348 1 83.83 ? C31 Y9K 901 A 1 
HETATM 35 C C32 Y9K . . . C 3 -9.25 56.93 85.611 1 78.56 ? C32 Y9K 901 A 1 
HETATM 36 C C33 Y9K . . . C 3 -7.929 58.137 84.333 1 78.05 ? C33 Y9K 901 A 1 
HETATM 37 C C34 Y9K . . . C 3 -6.681 60.001 85.317 1 74.59 ? C34 Y9K 901 A 1 
HETATM 38 C C35 Y9K . . . C 3 -7.529 61.062 85.939 1 69.26 ? C35 Y9K 901 A 1 
HETATM 39 C C36 Y9K . . . C 3 -6.717 61.91 86.907 1 69.93 ? C36 Y9K 901 A 1 
HETATM 40 C C37 Y9K . . . C 3 -7.53 62.617 87.975 1 69.22 ? C37 Y9K 901 A 1 
HETATM 41 C C38 Y9K . . . C 3 -6.676 63.54 88.804 1 71.28 ? C38 Y9K 901 A 1 
HETATM 42 C C39 Y9K . . . C 3 -6.239 69.805 89.277 1 64.37 ? C39 Y9K 901 A 1 
HETATM 43 C C40 Y9K . . . C 3 -6.86 71.143 89.031 1 63.34 ? C40 Y9K 901 A 1 
HETATM 44 C C41 Y9K . . . C 3 -6.185 73.194 88.342 1 68.63 ? C41 Y9K 901 A 1 
HETATM 45 C C42 Y9K . . . C 3 -3.901 73.815 87.488 1 65.17 ? C42 Y9K 901 A 1 
HETATM 46 C C43 Y9K . . . C 3 -3.649 75.714 88.364 1 63.54 ? C43 Y9K 901 A 1 
HETATM 47 C C44 Y9K . . . C 3 -3.254 76.972 88.821 1 61.39 ? C44 Y9K 901 A 1 
HETATM 48 C C45 Y9K . . . C 3 -5.257 77.081 89.927 1 61.1 ? C45 Y9K 901 A 1 
HETATM 49 C C46 Y9K . . . C 3 -4.874 75.272 88.771 1 62.85 ? C46 Y9K 901 A 1 
HETATM 50 C C47 Y9K . . . C 3 -6.581 72.495 87.065 1 68.78 ? C47 Y9K 901 A 1 
HETATM 51 C C48 Y9K . . . C 3 -7.403 71.346 87.623 1 63.57 ? C48 Y9K 901 A 1 
HETATM 52 N N4 Y9K . . . C 3 -7.308 59.324 84.166 1 76.44 ? N4 Y9K 901 A 1 
HETATM 53 N N5 Y9K . . . C 3 -5.028 74.047 88.209 1 65.38 ? N5 Y9K 901 A 1 
HETATM 54 N N6 Y9K . . . C 3 -3.045 74.786 87.55 1 64.98 ? N6 Y9K 901 A 1 
HETATM 55 N N7 Y9K . . . C 3 -2.099 77.535 88.521 1 55.56 ? N7 Y9K 901 A 1 
HETATM 56 N N8 Y9K . . . C 3 -4.094 77.64 89.618 1 57 ? N8 Y9K 901 A 1 
HETATM 57 N N9 Y9K . . . C 3 -5.74 75.917 89.551 1 70.31 ? N9 Y9K 901 A 1 
HETATM 58 O O1 Y9K . . . C 3 -9.431 56.685 80.625 1 92.86 ? O1 Y9K 901 A 1 
HETATM 59 O O10 Y9K . . . C 3 -6.11 66.761 89.418 1 63.2 ? O10 Y9K 901 A 1 
HETATM 60 O O11 Y9K . . . C 3 -5.827 67.916 87.28 1 54.03 ? O11 Y9K 901 A 1 
HETATM 61 O O12 Y9K . . . C 3 -8.027 66.841 87.956 1 64.37 -1 O12 Y9K 901 A 1 
HETATM 62 O O13 Y9K . . . C 3 -7.234 68.826 89.055 1 78.51 ? O13 Y9K 901 A 1 
HETATM 63 O O14 Y9K . . . C 3 -5.849 72.145 89.185 1 67.35 ? O14 Y9K 901 A 1 
HETATM 64 O O15 Y9K . . . C 3 -7.349 73.348 86.261 1 67.63 ? O15 Y9K 901 A 1 
HETATM 65 O O16 Y9K . . . C 3 -8.765 71.687 87.71 1 70.66 ? O16 Y9K 901 A 1 
HETATM 66 O O2 Y9K . . . C 3 -10.41 56.695 82.424 1 82.56 ? O2 Y9K 901 A 1 
HETATM 67 O O3 Y9K . . . C 3 -9.506 56.493 86.692 1 74.93 ? O3 Y9K 901 A 1 
HETATM 68 O O4 Y9K . . . C 3 -7.905 61.898 84.932 1 70.08 ? O4 Y9K 901 A 1 
HETATM 69 O O5 Y9K . . . C 3 -5.838 61.093 87.566 1 69.54 ? O5 Y9K 901 A 1 
HETATM 70 O O6 Y9K . . . C 3 -8.529 63.372 87.318 1 71.98 ? O6 Y9K 901 A 1 
HETATM 71 O O7 Y9K . . . C 3 -7.367 64.694 89.297 1 74.95 ? O7 Y9K 901 A 1 
HETATM 72 O O8 Y9K . . . C 3 -5.454 64.863 90.791 1 66.46 ? O8 Y9K 901 A 1 
HETATM 73 O O9 Y9K . . . C 3 -7.557 66.037 91.321 1 71.39 -1 O9 Y9K 901 A 1 
HETATM 74 P P1 Y9K . . . C 3 -6.61 65.593 90.316 1 64.85 ? P1 Y9K 901 A 1 
HETATM 75 P P2 Y9K . . . C 3 -6.808 67.556 88.284 1 81.1 ? P2 Y9K 901 A 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           901 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           75 
#