data_3EU5
#
_model_server_result.job_id            KCPk6GH67wwOY285oZA8hw 
_model_server_result.datetime_utc      '2024-11-29 12:07:29' 
_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          3eu5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":429}' 
#
_entry.id    3EU5 
#
_exptl.entry_id    3EU5 
_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            3EU5 
_cell.length_a            175.065 
_cell.length_b            175.065 
_cell.length_c            70.618 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3EU5 
_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 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc2 B SG CYS 299 B CYS 299 1_555 C ZN ZN . B ZN 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
metalc ? metalc3 B NE2 HIS 362 B HIS 362 1_555 C ZN ZN . B ZN 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
#
_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                     3EU5 
_atom_sites.fract_transf_matrix[1][1]    0.005712 
_atom_sites.fract_transf_matrix[1][2]    0.003298 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006596 
_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]    0.014161 
_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 1 ZN ZN . 
D 4 GBO B 1 429 1 GBO BIO . 
E 5 HOH B 1 430 1 HOH HOH . 
E 5 HOH B 2 431 4 HOH HOH . 
E 5 HOH B 3 432 6 HOH HOH . 
E 5 HOH B 4 433 7 HOH HOH . 
E 5 HOH B 5 434 8 HOH HOH . 
E 5 HOH B 6 435 9 HOH HOH . 
E 5 HOH B 7 436 10 HOH HOH . 
E 5 HOH B 8 437 11 HOH HOH . 
E 5 HOH B 9 438 12 HOH HOH . 
E 5 HOH B 10 439 13 HOH HOH . 
E 5 HOH B 11 440 15 HOH HOH . 
E 5 HOH B 12 441 16 HOH HOH . 
E 5 HOH B 13 442 18 HOH HOH . 
E 5 HOH B 14 443 19 HOH HOH . 
E 5 HOH B 15 444 20 HOH HOH . 
E 5 HOH B 16 445 21 HOH HOH . 
E 5 HOH B 17 446 22 HOH HOH . 
E 5 HOH B 18 447 23 HOH HOH . 
E 5 HOH B 19 448 24 HOH HOH . 
E 5 HOH B 20 449 25 HOH HOH . 
E 5 HOH B 21 450 26 HOH HOH . 
E 5 HOH B 22 451 28 HOH HOH . 
E 5 HOH B 23 452 30 HOH HOH . 
E 5 HOH B 24 453 31 HOH HOH . 
E 5 HOH B 25 454 32 HOH HOH . 
E 5 HOH B 26 455 33 HOH HOH . 
E 5 HOH B 27 456 34 HOH HOH . 
E 5 HOH B 28 457 35 HOH HOH . 
E 5 HOH B 29 458 38 HOH HOH . 
E 5 HOH B 30 459 40 HOH HOH . 
E 5 HOH B 31 460 41 HOH HOH . 
E 5 HOH B 32 461 43 HOH HOH . 
E 5 HOH B 33 462 44 HOH HOH . 
E 5 HOH B 34 463 45 HOH HOH . 
E 5 HOH B 35 464 46 HOH HOH . 
E 5 HOH B 36 465 49 HOH HOH . 
E 5 HOH B 37 466 50 HOH HOH . 
E 5 HOH B 38 467 52 HOH HOH . 
E 5 HOH B 39 468 54 HOH HOH . 
E 5 HOH B 40 469 55 HOH HOH . 
E 5 HOH B 41 470 56 HOH HOH . 
E 5 HOH B 42 471 57 HOH HOH . 
E 5 HOH B 43 472 58 HOH HOH . 
E 5 HOH B 44 473 59 HOH HOH . 
E 5 HOH B 45 474 60 HOH HOH . 
E 5 HOH B 46 475 62 HOH HOH . 
E 5 HOH B 47 476 63 HOH HOH . 
E 5 HOH B 48 477 64 HOH HOH . 
E 5 HOH B 49 478 66 HOH HOH . 
E 5 HOH B 50 479 67 HOH HOH . 
E 5 HOH B 51 480 70 HOH HOH . 
E 5 HOH B 52 481 72 HOH HOH . 
E 5 HOH B 53 482 74 HOH HOH . 
E 5 HOH B 54 483 75 HOH HOH . 
E 5 HOH B 55 484 76 HOH HOH . 
E 5 HOH B 56 485 78 HOH HOH . 
E 5 HOH B 57 486 79 HOH HOH . 
E 5 HOH B 58 487 80 HOH HOH . 
E 5 HOH B 59 488 82 HOH HOH . 
E 5 HOH B 60 489 83 HOH HOH . 
E 5 HOH B 61 490 84 HOH HOH . 
E 5 HOH B 62 491 86 HOH HOH . 
E 5 HOH B 63 492 87 HOH HOH . 
E 5 HOH B 64 493 90 HOH HOH . 
E 5 HOH B 65 494 91 HOH HOH . 
E 5 HOH B 66 495 92 HOH HOH . 
E 5 HOH B 67 496 94 HOH HOH . 
E 5 HOH B 68 497 95 HOH HOH . 
E 5 HOH B 69 498 96 HOH HOH . 
E 5 HOH B 70 499 97 HOH HOH . 
E 5 HOH B 71 500 98 HOH HOH . 
E 5 HOH B 72 501 99 HOH HOH . 
E 5 HOH B 73 502 100 HOH HOH . 
E 5 HOH B 74 503 101 HOH HOH . 
E 5 HOH B 75 504 102 HOH HOH . 
E 5 HOH B 76 505 103 HOH HOH . 
E 5 HOH B 77 506 105 HOH HOH . 
E 5 HOH B 78 507 106 HOH HOH . 
E 5 HOH B 79 508 108 HOH HOH . 
E 5 HOH B 80 509 109 HOH HOH . 
E 5 HOH B 81 510 110 HOH HOH . 
E 5 HOH B 82 511 111 HOH HOH . 
E 5 HOH B 83 512 116 HOH HOH . 
E 5 HOH B 84 513 117 HOH HOH . 
E 5 HOH B 85 514 118 HOH HOH . 
E 5 HOH B 86 515 120 HOH HOH . 
E 5 HOH B 87 516 122 HOH HOH . 
E 5 HOH B 88 517 125 HOH HOH . 
E 5 HOH B 89 518 126 HOH HOH . 
E 5 HOH B 90 519 127 HOH HOH . 
E 5 HOH B 91 520 128 HOH HOH . 
E 5 HOH B 92 521 129 HOH HOH . 
E 5 HOH B 93 522 130 HOH HOH . 
E 5 HOH B 94 523 132 HOH HOH . 
E 5 HOH B 95 524 136 HOH HOH . 
E 5 HOH B 96 525 137 HOH HOH . 
E 5 HOH B 97 526 138 HOH HOH . 
E 5 HOH B 98 527 139 HOH HOH . 
E 5 HOH B 99 528 142 HOH HOH . 
E 5 HOH B 100 529 146 HOH HOH . 
E 5 HOH B 101 530 147 HOH HOH . 
E 5 HOH B 102 531 149 HOH HOH . 
E 5 HOH B 103 532 150 HOH HOH . 
E 5 HOH B 104 533 152 HOH HOH . 
E 5 HOH B 105 534 153 HOH HOH . 
E 5 HOH B 106 535 154 HOH HOH . 
E 5 HOH B 107 536 155 HOH HOH . 
E 5 HOH B 108 537 160 HOH HOH . 
E 5 HOH B 109 538 161 HOH HOH . 
E 5 HOH B 110 539 163 HOH HOH . 
E 5 HOH B 111 540 164 HOH HOH . 
E 5 HOH B 112 541 165 HOH HOH . 
E 5 HOH B 113 542 166 HOH HOH . 
E 5 HOH B 114 543 168 HOH HOH . 
E 5 HOH B 115 544 169 HOH HOH . 
E 5 HOH B 116 545 170 HOH HOH . 
E 5 HOH B 117 546 171 HOH HOH . 
E 5 HOH B 118 547 172 HOH HOH . 
E 5 HOH B 119 548 174 HOH HOH . 
E 5 HOH B 120 549 176 HOH HOH . 
E 5 HOH B 121 550 177 HOH HOH . 
E 5 HOH B 122 551 178 HOH HOH . 
E 5 HOH B 123 552 179 HOH HOH . 
E 5 HOH B 124 553 180 HOH HOH . 
E 5 HOH B 125 554 181 HOH HOH . 
E 5 HOH B 126 555 183 HOH HOH . 
E 5 HOH B 127 556 185 HOH HOH . 
E 5 HOH B 128 557 186 HOH HOH . 
E 5 HOH B 129 558 187 HOH HOH . 
E 5 HOH B 130 559 188 HOH HOH . 
E 5 HOH B 131 560 189 HOH HOH . 
E 5 HOH B 132 561 190 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 54.796 -43.036 7.611 1 41.16 ? O2 GBO 429 B 1 
HETATM 2 P P1 GBO . . . D 4 54.157 -42.406 6.279 1 42.1 ? P1 GBO 429 B 1 
HETATM 3 O O8 GBO . . . D 4 53.285 -41.235 6.897 1 45.54 ? O8 GBO 429 B 1 
HETATM 4 O O1 GBO . . . D 4 55.173 -42.042 5.272 1 41.07 ? O1 GBO 429 B 1 
HETATM 5 O O3 GBO . . . D 4 53.112 -43.485 5.749 1 43.86 ? O3 GBO 429 B 1 
HETATM 6 P P2 GBO . . . D 4 52.72 -43.748 4.195 1 42.54 ? P2 GBO 429 B 1 
HETATM 7 O O4 GBO . . . D 4 51.79 -44.876 4.277 1 43.14 ? O4 GBO 429 B 1 
HETATM 8 O O9 GBO . . . D 4 52.323 -42.537 3.401 1 46.95 ? O9 GBO 429 B 1 
HETATM 9 O O5 GBO . . . D 4 54.148 -44.31 3.811 1 37.21 ? O5 GBO 429 B 1 
HETATM 10 C C1 GBO . . . D 4 54.705 -44.39 2.531 1 37.83 ? C1 GBO 429 B 1 
HETATM 11 C C2 GBO . . . D 4 56.002 -44.864 2.654 1 36.46 ? C2 GBO 429 B 1 
HETATM 12 C C3 GBO . . . D 4 56.735 -45.211 1.548 1 43.82 ? C3 GBO 429 B 1 
HETATM 13 C C4 GBO . . . D 4 56.092 -45.046 0.144 1 50.68 ? C4 GBO 429 B 1 
HETATM 14 C C5 GBO . . . D 4 58.163 -45.742 1.61 1 42.54 ? C5 GBO 429 B 1 
HETATM 15 C C6 GBO . . . D 4 58.505 -46.6 2.819 1 37.23 ? C6 GBO 429 B 1 
HETATM 16 C C7 GBO . . . D 4 59.624 -47.362 2.502 1 35.66 ? C7 GBO 429 B 1 
HETATM 17 C C8 GBO . . . D 4 60.223 -48.336 3.269 1 34.89 ? C8 GBO 429 B 1 
HETATM 18 C C9 GBO . . . D 4 59.595 -48.674 4.619 1 28.96 ? C9 GBO 429 B 1 
HETATM 19 C C10 GBO . . . D 4 61.444 -49.126 2.757 1 42.6 ? C10 GBO 429 B 1 
HETATM 20 N N1 GBO . . . D 4 60.817 -50.398 2.467 1 50.42 ? N1 GBO 429 B 1 
HETATM 21 C C11 GBO . . . D 4 61.35 -51.575 2.192 1 61.94 ? C11 GBO 429 B 1 
HETATM 22 O O6 GBO . . . D 4 62.547 -51.844 2.093 1 65.8 ? O6 GBO 429 B 1 
HETATM 23 C C12 GBO . . . D 4 60.271 -52.676 1.932 1 67.51 ? C12 GBO 429 B 1 
HETATM 24 C C13 GBO . . . D 4 59.196 -52.897 3.051 1 66.94 ? C13 GBO 429 B 1 
HETATM 25 C C14 GBO . . . D 4 58.066 -53.791 2.523 1 70.12 ? C14 GBO 429 B 1 
HETATM 26 C C15 GBO . . . D 4 56.677 -53.264 2.898 1 72.74 ? C15 GBO 429 B 1 
HETATM 27 C C16 GBO . . . D 4 55.578 -54.266 2.423 1 81.85 ? C16 GBO 429 B 1 
HETATM 28 S S1 GBO . . . D 4 56.14 -55.706 1.387 1 88.86 ? S1 GBO 429 B 1 
HETATM 29 C C17 GBO . . . D 4 54.428 -56.118 0.878 1 90.35 ? C17 GBO 429 B 1 
HETATM 30 C C18 GBO . . . D 4 53.772 -54.723 0.654 1 89.73 ? C18 GBO 429 B 1 
HETATM 31 C C19 GBO . . . D 4 54.489 -53.606 1.5 1 86.03 ? C19 GBO 429 B 1 
HETATM 32 N N2 GBO . . . D 4 55.148 -52.759 0.465 1 87.87 ? N2 GBO 429 B 1 
HETATM 33 C C20 GBO . . . D 4 54.917 -53.245 -0.749 1 91.52 ? C20 GBO 429 B 1 
HETATM 34 O O7 GBO . . . D 4 55.364 -52.749 -1.785 1 94 ? O7 GBO 429 B 1 
HETATM 35 N N3 GBO . . . D 4 54.132 -54.329 -0.714 1 93.76 ? N3 GBO 429 B 1 
#
_model_server_stats.io_time_ms              129 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           35 
#