data_8RDO
#
_model_server_result.job_id            d14aNOx17q5-DdVmhgWP3w 
_model_server_result.datetime_utc      '2024-10-22 23:19:04' 
_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          8rdo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":402}' 
#
_entry.id    8RDO 
#
_exptl.entry_id    8RDO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              284.398 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ~{N}-(4-methyl-5-oxidanylidene-[1,2]dithiolo[4,3-b]pyrrol-6-yl)hexanamide 
_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            8RDO 
_cell.length_a            53.43 
_cell.length_b            53.43 
_cell.length_c            209.31 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8RDO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        91 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 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,D,E,F,G,H 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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' 8_665 -y+1,-x+1,-z+1/4 0 -1 0 -1 0 0 0 0 -1 53.43 53.43 52.3275 
#
_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           'C12 H16 N2 O2 S2' 
_chem_comp.formula_weight    284.398 
_chem_comp.id                YRD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              ~{N}-(4-methyl-5-oxidanylidene-[1,2]dithiolo[4,3-b]pyrrol-6-yl)hexanamide 
_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
C15 C14 YRD sing 451 n n 
C14 C13 YRD sing 452 n n 
C13 C12 YRD sing 453 n n 
C12 C11 YRD sing 454 n n 
O16 C10 YRD doub 455 n n 
C11 C10 YRD sing 456 n n 
C10 N9 YRD sing 457 n n 
S1 C17 YRD sing 458 n n 
S1 S2 YRD sing 459 n n 
N9 C8 YRD sing 460 n n 
C8 C17 YRD doub 461 n n 
C8 C6 YRD sing 462 n n 
C17 C4 YRD sing 463 n n 
S2 C3 YRD sing 464 n n 
C6 O7 YRD doub 465 n n 
C6 N5 YRD sing 466 n n 
C4 C3 YRD doub 467 n n 
C4 N5 YRD sing 468 n n 
N5 C18 YRD sing 469 n n 
C13 H2 YRD sing 470 n n 
C13 H3 YRD sing 471 n n 
C15 H4 YRD sing 472 n n 
C15 H5 YRD sing 473 n n 
C15 H6 YRD sing 474 n n 
C18 H7 YRD sing 475 n n 
C18 H8 YRD sing 476 n n 
C18 H9 YRD sing 477 n n 
C3 H10 YRD sing 478 n n 
N9 H11 YRD sing 479 n n 
C11 H12 YRD sing 480 n n 
C11 H13 YRD sing 481 n n 
C12 H14 YRD sing 482 n n 
C12 H15 YRD sing 483 n n 
C14 H16 YRD sing 484 n n 
C14 H17 YRD sing 485 n n 
#
_atom_sites.entry_id                     8RDO 
_atom_sites.fract_transf_matrix[1][1]    0.018716 
_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]    0.018716 
_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]    0.004778 
_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
B 2 SAH A 1 401 998 SAH SAH . 
C 3 YRD A 1 402 999 YRD LIG . 
D 4 GOL A 1 403 1 GOL GOL . 
E 4 GOL A 1 404 2 GOL GOL . 
F 4 GOL A 1 405 3 GOL GOL . 
G 5 MLT A 1 406 4 MLT MLT . 
H 6 HOH A 1 501 41 HOH HOH . 
H 6 HOH A 2 502 8 HOH HOH . 
H 6 HOH A 3 503 128 HOH HOH . 
H 6 HOH A 4 504 56 HOH HOH . 
H 6 HOH A 5 505 7 HOH HOH . 
H 6 HOH A 6 506 109 HOH HOH . 
H 6 HOH A 7 507 25 HOH HOH . 
H 6 HOH A 8 508 85 HOH HOH . 
H 6 HOH A 9 509 116 HOH HOH . 
H 6 HOH A 10 510 124 HOH HOH . 
H 6 HOH A 11 511 115 HOH HOH . 
H 6 HOH A 12 512 37 HOH HOH . 
H 6 HOH A 13 513 9 HOH HOH . 
H 6 HOH A 14 514 38 HOH HOH . 
H 6 HOH A 15 515 24 HOH HOH . 
H 6 HOH A 16 516 80 HOH HOH . 
H 6 HOH A 17 517 26 HOH HOH . 
H 6 HOH A 18 518 32 HOH HOH . 
H 6 HOH A 19 519 16 HOH HOH . 
H 6 HOH A 20 520 122 HOH HOH . 
H 6 HOH A 21 521 121 HOH HOH . 
H 6 HOH A 22 522 94 HOH HOH . 
H 6 HOH A 23 523 81 HOH HOH . 
H 6 HOH A 24 524 52 HOH HOH . 
H 6 HOH A 25 525 10 HOH HOH . 
H 6 HOH A 26 526 123 HOH HOH . 
H 6 HOH A 27 527 43 HOH HOH . 
H 6 HOH A 28 528 17 HOH HOH . 
H 6 HOH A 29 529 113 HOH HOH . 
H 6 HOH A 30 530 103 HOH HOH . 
H 6 HOH A 31 531 79 HOH HOH . 
H 6 HOH A 32 532 6 HOH HOH . 
H 6 HOH A 33 533 35 HOH HOH . 
H 6 HOH A 34 534 66 HOH HOH . 
H 6 HOH A 35 535 83 HOH HOH . 
H 6 HOH A 36 536 31 HOH HOH . 
H 6 HOH A 37 537 48 HOH HOH . 
H 6 HOH A 38 538 98 HOH HOH . 
H 6 HOH A 39 539 50 HOH HOH . 
H 6 HOH A 40 540 47 HOH HOH . 
H 6 HOH A 41 541 29 HOH HOH . 
H 6 HOH A 42 542 20 HOH HOH . 
H 6 HOH A 43 543 75 HOH HOH . 
H 6 HOH A 44 544 5 HOH HOH . 
H 6 HOH A 45 545 104 HOH HOH . 
H 6 HOH A 46 546 74 HOH HOH . 
H 6 HOH A 47 547 36 HOH HOH . 
H 6 HOH A 48 548 112 HOH HOH . 
H 6 HOH A 49 549 49 HOH HOH . 
H 6 HOH A 50 550 126 HOH HOH . 
H 6 HOH A 51 551 23 HOH HOH . 
H 6 HOH A 52 552 55 HOH HOH . 
H 6 HOH A 53 553 102 HOH HOH . 
H 6 HOH A 54 554 108 HOH HOH . 
H 6 HOH A 55 555 130 HOH HOH . 
H 6 HOH A 56 556 84 HOH HOH . 
H 6 HOH A 57 557 77 HOH HOH . 
H 6 HOH A 58 558 129 HOH HOH . 
H 6 HOH A 59 559 100 HOH HOH . 
H 6 HOH A 60 560 54 HOH HOH . 
H 6 HOH A 61 561 127 HOH HOH . 
H 6 HOH A 62 562 125 HOH HOH . 
H 6 HOH A 63 563 11 HOH HOH . 
H 6 HOH A 64 564 114 HOH HOH . 
H 6 HOH A 65 565 120 HOH HOH . 
H 6 HOH A 66 566 105 HOH HOH . 
H 6 HOH A 67 567 131 HOH HOH . 
H 6 HOH A 68 568 117 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 C4 YRD . . . C 3 8.022 66.693 36.575 1 29.87 ? C4 YRD 402 A 1 
HETATM 2 C C6 YRD . . . C 3 9.742 65.377 36.557 1 28.67 ? C6 YRD 402 A 1 
HETATM 3 C C8 YRD . . . C 3 8.773 64.708 35.932 1 28.82 ? C8 YRD 402 A 1 
HETATM 4 C C10 YRD . . . C 3 8.327 62.974 34.379 1 29.24 ? C10 YRD 402 A 1 
HETATM 5 C C13 YRD . . . C 3 8.43 59.706 32.287 1 27.42 ? C13 YRD 402 A 1 
HETATM 6 C C15 YRD . . . C 3 8.351 58.035 30.398 1 27.32 ? C15 YRD 402 A 1 
HETATM 7 C C17 YRD . . . C 3 7.679 65.508 35.947 1 29.43 ? C17 YRD 402 A 1 
HETATM 8 O O7 YRD . . . C 3 10.891 64.975 36.756 1 27.35 ? O7 YRD 402 A 1 
HETATM 9 N N5 YRD . . . C 3 9.296 66.555 36.93 1 29.07 ? N5 YRD 402 A 1 
HETATM 10 C C18 YRD . . . C 3 10.085 67.521 37.659 1 29.22 ? C18 YRD 402 A 1 
HETATM 11 C C3 YRD . . . C 3 7.122 67.701 36.722 1 30.56 ? C3 YRD 402 A 1 
HETATM 12 S S2 YRD . . . C 3 5.595 67.423 36.098 1 32.21 ? S2 YRD 402 A 1 
HETATM 13 S S1 YRD . . . C 3 6.007 65.523 35.383 1 29.99 ? S1 YRD 402 A 1 
HETATM 14 N N9 YRD . . . C 3 8.949 63.448 35.484 1 29 ? N9 YRD 402 A 1 
HETATM 15 O O16 YRD . . . C 3 7.628 63.643 33.621 1 30.2 ? O16 YRD 402 A 1 
HETATM 16 C C11 YRD . . . C 3 8.612 61.492 34.069 1 28.29 ? C11 YRD 402 A 1 
HETATM 17 C C12 YRD . . . C 3 8.067 61.141 32.676 1 27.93 ? C12 YRD 402 A 1 
HETATM 18 C C14 YRD . . . C 3 8.017 59.465 30.836 1 27.35 ? C14 YRD 402 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           30 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           18 
#