data_3EUV
#
_model_server_result.job_id            k06MkEAmfOM86oac1mQv3A 
_model_server_result.datetime_utc      '2024-11-17 02:55:48' 
_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          3euv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":429}' 
#
_entry.id    3EUV 
#
_exptl.entry_id    3EUV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              555.519 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2E,6E)-3,7-dimethyl-8-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)octa-2,6-dien-1-yl trihydrogen diphosphate' 
_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         120 
_cell.entry_id            3EUV 
_cell.length_a            174.783 
_cell.length_b            174.783 
_cell.length_c            70.377 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EUV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61' 
#
_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 
_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 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc ? metalc1 B OD2 ASP 297 B ASP 297 1_555 C ZN ZN . B ZN 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
metalc ? metalc2 B SG CYS 299 B CYS 299 1_555 C ZN ZN . B ZN 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc3 B NE2 HIS 362 B HIS 362 1_555 C ZN ZN . B ZN 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
#
_chem_comp.formula           'C20 H35 N3 O9 P2 S' 
_chem_comp.formula_weight    555.519 
_chem_comp.id                GBO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2E,6E)-3,7-dimethyl-8-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)octa-2,6-dien-1-yl trihydrogen diphosphate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Biotin-GPP 
#
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
P1 O2 GBO sing 83 n n 
O2 HO2 GBO sing 84 n n 
O1 P1 GBO doub 85 n n 
O3 P1 GBO sing 86 n n 
P1 O8 GBO sing 87 n n 
O8 HO8 GBO sing 88 n n 
P2 O3 GBO sing 89 n n 
O9 P2 GBO doub 90 n n 
O5 P2 GBO sing 91 n n 
P2 O4 GBO sing 92 n n 
O4 HO4 GBO sing 93 n n 
C1 O5 GBO sing 94 n n 
C1 C2 GBO sing 95 n n 
C1 H1 GBO sing 96 n n 
C1 H1A GBO sing 97 n n 
C3 C2 GBO doub 98 n n 
C2 H2 GBO sing 99 e n 
C4 C3 GBO sing 100 n n 
C3 C5 GBO sing 101 n n 
C4 H4 GBO sing 102 n n 
C4 H4A GBO sing 103 n n 
C4 H4B GBO sing 104 n n 
C5 C6 GBO sing 105 n n 
C5 H5 GBO sing 106 n n 
C5 H5A GBO sing 107 n n 
C7 C6 GBO sing 108 n n 
C6 H6 GBO sing 109 n n 
C6 H6A GBO sing 110 n n 
C7 C8 GBO doub 111 e n 
C7 H7 GBO sing 112 n n 
C10 C8 GBO sing 113 n n 
C8 C9 GBO sing 114 n n 
C9 H9 GBO sing 115 n n 
C9 H9A GBO sing 116 n n 
C9 H9B GBO sing 117 n n 
N1 C10 GBO sing 118 n n 
C10 H10 GBO sing 119 n n 
C10 H10A GBO sing 120 n n 
C11 N1 GBO sing 121 n n 
N1 HN1 GBO sing 122 n n 
C12 C11 GBO sing 123 n n 
O6 C11 GBO doub 124 n n 
C12 C13 GBO sing 125 n n 
C12 H12 GBO sing 126 n n 
C12 H12A GBO sing 127 n n 
C14 C13 GBO sing 128 n n 
C13 H13 GBO sing 129 n n 
C13 H13A GBO sing 130 n n 
C14 C15 GBO sing 131 n n 
C14 H14 GBO sing 132 n n 
C14 H14A GBO sing 133 n n 
C16 C15 GBO sing 134 n n 
C15 H15 GBO sing 135 n n 
C15 H15A GBO sing 136 n n 
S1 C16 GBO sing 137 n n 
C19 C16 GBO sing 138 n n 
C16 H16 GBO sing 139 n n 
C17 S1 GBO sing 140 n n 
C18 C17 GBO sing 141 n n 
C17 H17 GBO sing 142 n n 
C17 H17A GBO sing 143 n n 
N3 C18 GBO sing 144 n n 
C18 C19 GBO sing 145 n n 
C18 H18 GBO sing 146 n n 
N2 C19 GBO sing 147 n n 
C19 H19 GBO sing 148 n n 
C20 N2 GBO sing 149 n n 
N2 HN2 GBO sing 150 n n 
O7 C20 GBO doub 151 n n 
C20 N3 GBO sing 152 n n 
N3 HN3 GBO sing 153 n n 
#
_atom_sites.entry_id                     3EUV 
_atom_sites.fract_transf_matrix[1][1]    0.005721 
_atom_sites.fract_transf_matrix[1][2]    0.003303 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006606 
_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]    0.014209 
_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 3 ZN B 1 428 428 ZN ZN . 
D 4 GBO B 1 429 429 GBO GBO . 
E 5 HOH A 1 430 430 HOH HOH . 
E 5 HOH A 2 432 432 HOH HOH . 
E 5 HOH A 3 433 433 HOH HOH . 
E 5 HOH A 4 434 434 HOH HOH . 
E 5 HOH A 5 435 435 HOH HOH . 
E 5 HOH A 6 439 439 HOH HOH . 
E 5 HOH A 7 443 443 HOH HOH . 
E 5 HOH A 8 445 445 HOH HOH . 
E 5 HOH A 9 446 446 HOH HOH . 
E 5 HOH A 10 447 447 HOH HOH . 
E 5 HOH A 11 448 448 HOH HOH . 
E 5 HOH A 12 453 453 HOH HOH . 
E 5 HOH A 13 455 455 HOH HOH . 
E 5 HOH A 14 457 457 HOH HOH . 
E 5 HOH A 15 459 459 HOH HOH . 
E 5 HOH A 16 460 460 HOH HOH . 
E 5 HOH A 17 462 462 HOH HOH . 
E 5 HOH A 18 469 469 HOH HOH . 
E 5 HOH A 19 472 472 HOH HOH . 
E 5 HOH A 20 473 473 HOH HOH . 
E 5 HOH A 21 474 474 HOH HOH . 
E 5 HOH A 22 478 478 HOH HOH . 
E 5 HOH A 23 479 479 HOH HOH . 
E 5 HOH A 24 483 483 HOH HOH . 
E 5 HOH A 25 484 484 HOH HOH . 
E 5 HOH A 26 485 485 HOH HOH . 
E 5 HOH A 27 487 487 HOH HOH . 
E 5 HOH A 28 492 492 HOH HOH . 
E 5 HOH A 29 495 495 HOH HOH . 
E 5 HOH A 30 497 497 HOH HOH . 
E 5 HOH A 31 501 501 HOH HOH . 
E 5 HOH A 32 502 502 HOH HOH . 
E 5 HOH A 33 503 503 HOH HOH . 
F 5 HOH B 1 431 431 HOH HOH . 
F 5 HOH B 2 436 436 HOH HOH . 
F 5 HOH B 3 437 437 HOH HOH . 
F 5 HOH B 4 438 438 HOH HOH . 
F 5 HOH B 5 440 440 HOH HOH . 
F 5 HOH B 6 441 441 HOH HOH . 
F 5 HOH B 7 442 442 HOH HOH . 
F 5 HOH B 8 444 444 HOH HOH . 
F 5 HOH B 9 449 449 HOH HOH . 
F 5 HOH B 10 450 450 HOH HOH . 
F 5 HOH B 11 451 451 HOH HOH . 
F 5 HOH B 12 452 452 HOH HOH . 
F 5 HOH B 13 454 454 HOH HOH . 
F 5 HOH B 14 456 456 HOH HOH . 
F 5 HOH B 15 458 458 HOH HOH . 
F 5 HOH B 16 461 461 HOH HOH . 
F 5 HOH B 17 463 463 HOH HOH . 
F 5 HOH B 18 464 464 HOH HOH . 
F 5 HOH B 19 465 465 HOH HOH . 
F 5 HOH B 20 466 466 HOH HOH . 
F 5 HOH B 21 467 467 HOH HOH . 
F 5 HOH B 22 468 468 HOH HOH . 
F 5 HOH B 23 470 470 HOH HOH . 
F 5 HOH B 24 471 471 HOH HOH . 
F 5 HOH B 25 475 475 HOH HOH . 
F 5 HOH B 26 476 476 HOH HOH . 
F 5 HOH B 27 477 477 HOH HOH . 
F 5 HOH B 28 480 480 HOH HOH . 
F 5 HOH B 29 481 481 HOH HOH . 
F 5 HOH B 30 482 482 HOH HOH . 
F 5 HOH B 31 486 486 HOH HOH . 
F 5 HOH B 32 488 488 HOH HOH . 
F 5 HOH B 33 489 489 HOH HOH . 
F 5 HOH B 34 490 490 HOH HOH . 
F 5 HOH B 35 491 491 HOH HOH . 
F 5 HOH B 36 493 493 HOH HOH . 
F 5 HOH B 37 494 494 HOH HOH . 
F 5 HOH B 38 496 496 HOH HOH . 
F 5 HOH B 39 498 498 HOH HOH . 
F 5 HOH B 40 499 499 HOH HOH . 
F 5 HOH B 41 500 500 HOH HOH . 
F 5 HOH B 42 504 504 HOH HOH . 
F 5 HOH B 43 505 505 HOH HOH . 
F 5 HOH B 44 506 506 HOH HOH . 
F 5 HOH B 45 507 507 HOH HOH . 
F 5 HOH B 46 508 508 HOH HOH . 
F 5 HOH B 47 509 509 HOH HOH . 
F 5 HOH B 48 510 510 HOH HOH . 
F 5 HOH B 49 511 511 HOH HOH . 
F 5 HOH B 50 512 512 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 O O2 GBO . . . D 4 54.062 -42.576 1.498 1 48.76 ? O2 GBO 429 B 1 
HETATM 2 P P1 GBO . . . D 4 53.338 -41.911 0.178 1 51.25 ? P1 GBO 429 B 1 
HETATM 3 O O8 GBO . . . D 4 52.225 -40.758 0.69 1 51.1 ? O8 GBO 429 B 1 
HETATM 4 O O1 GBO . . . D 4 54.361 -41.307 -0.747 1 49.6 ? O1 GBO 429 B 1 
HETATM 5 O O3 GBO . . . D 4 52.433 -43.111 -0.41 1 52.14 ? O3 GBO 429 B 1 
HETATM 6 P P2 GBO . . . D 4 52.064 -43.143 -1.919 1 57.75 ? P2 GBO 429 B 1 
HETATM 7 O O4 GBO . . . D 4 51.35 -44.381 -2.285 1 64.36 ? O4 GBO 429 B 1 
HETATM 8 O O9 GBO . . . D 4 51.401 -41.856 -2.254 1 61.15 ? O9 GBO 429 B 1 
HETATM 9 O O5 GBO . . . D 4 53.555 -43.285 -2.414 1 55.46 ? O5 GBO 429 B 1 
HETATM 10 C C1 GBO . . . D 4 53.797 -44.088 -3.46 1 59.32 ? C1 GBO 429 B 1 
HETATM 11 C C2 GBO . . . D 4 55.144 -44.288 -3.563 1 60.75 ? C2 GBO 429 B 1 
HETATM 12 C C3 GBO . . . D 4 55.761 -44.544 -4.777 1 68.03 ? C3 GBO 429 B 1 
HETATM 13 C C4 GBO . . . D 4 54.907 -44.593 -6.084 1 74.93 ? C4 GBO 429 B 1 
HETATM 14 C C5 GBO . . . D 4 57.298 -44.789 -4.844 1 66.53 ? C5 GBO 429 B 1 
HETATM 15 C C6 GBO . . . D 4 57.981 -45.283 -3.528 1 61.91 ? C6 GBO 429 B 1 
HETATM 16 C C7 GBO . . . D 4 58.696 -46.489 -3.595 1 58.34 ? C7 GBO 429 B 1 
HETATM 17 C C8 GBO . . . D 4 58.651 -47.355 -2.512 1 55.76 ? C8 GBO 429 B 1 
HETATM 18 C C9 GBO . . . D 4 57.768 -47.044 -1.303 1 53.63 ? C9 GBO 429 B 1 
HETATM 19 C C10 GBO . . . D 4 59.321 -48.678 -2.488 1 61.27 ? C10 GBO 429 B 1 
HETATM 20 N N1 GBO . . . D 4 60.711 -48.903 -2.929 1 66.3 ? N1 GBO 429 B 1 
HETATM 21 C C11 GBO . . . D 4 60.895 -50.179 -3.373 1 73.13 ? C11 GBO 429 B 1 
HETATM 22 O O6 GBO . . . D 4 59.936 -50.983 -3.417 1 72.32 ? O6 GBO 429 B 1 
HETATM 23 C C12 GBO . . . D 4 62.333 -50.646 -3.831 1 78.97 ? C12 GBO 429 B 1 
HETATM 24 C C13 GBO . . . D 4 62.373 -51.719 -4.96 1 89.8 ? C13 GBO 429 B 1 
HETATM 25 C C14 GBO . . . D 4 63.527 -52.695 -4.85 1 101.08 ? C14 GBO 429 B 1 
HETATM 26 C C15 GBO . . . D 4 62.986 -54.104 -5.057 1 113.31 ? C15 GBO 429 B 1 
HETATM 27 C C16 GBO . . . D 4 63.375 -55.015 -3.864 1 125.09 ? C16 GBO 429 B 1 
HETATM 28 S S1 GBO . . . D 4 62.839 -56.765 -3.961 1 132.67 ? S1 GBO 429 B 1 
HETATM 29 C C17 GBO . . . D 4 63.09 -57.166 -2.216 1 137.32 ? C17 GBO 429 B 1 
HETATM 30 C C18 GBO . . . D 4 62.65 -55.831 -1.54 1 135.71 ? C18 GBO 429 B 1 
HETATM 31 C C19 GBO . . . D 4 62.752 -54.59 -2.5 1 129.58 ? C19 GBO 429 B 1 
HETATM 32 N N2 GBO . . . D 4 61.338 -54.064 -2.521 1 129.43 ? N2 GBO 429 B 1 
HETATM 33 C C20 GBO . . . D 4 60.533 -54.793 -1.713 1 131.68 ? C20 GBO 429 B 1 
HETATM 34 O O7 GBO . . . D 4 59.328 -54.561 -1.533 1 129.93 ? O7 GBO 429 B 1 
HETATM 35 N N3 GBO . . . D 4 61.206 -55.82 -1.15 1 136.16 ? N3 GBO 429 B 1 
#
_model_server_stats.io_time_ms              69 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           35 
#