data_3U5Y
#
_model_server_result.job_id            lYS0qk-kBxErfPvYk1tEtA 
_model_server_result.datetime_utc      '2025-02-26 13:07:05' 
_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          3u5y 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1001}' 
#
_entry.id    3U5Y 
#
_exptl.entry_id    3U5Y 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              388.366 
_entity.id                          2 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            Secologanin 
_entity.pdbx_number_of_molecules    2 
_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            3U5Y 
_cell.length_a            104.927 
_cell.length_b            129.203 
_cell.length_c            216.798 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3U5Y 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA octameric 8 software_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H 1 1,2,3,4 
A,C,G 2 1 
B,D,E,F,H 3 1 
#
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' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 104.927 129.203 0 
3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 104.927 0 0 
4 'crystal symmetry operation' 4_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 129.203 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
#
_chem_comp.formula           'C17 H24 O10' 
_chem_comp.formula_weight    388.366 
_chem_comp.id                SCG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              Secologanin 
_chem_comp.type              d-saccharide 
_chem_comp.pdbx_synonyms     'METHYL (2S,3R,4S)-2-(BETA-D-GLUCOPYRANOSYLOXY)-4-(2-OXOETHYL)-3-VINYL-3,4-DIHYDRO-2H-PYRAN-5-CARBOXYLATE' 
#
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
O16 C10 SCG doub 277 n n 
C10 C9 SCG sing 278 n n 
C10 H10 SCG sing 279 n n 
C9 C3 SCG sing 280 n n 
C9 H91 SCG sing 281 n n 
C9 H92 SCG sing 282 n n 
C3 C2 SCG sing 283 n n 
C3 C4 SCG sing 284 n n 
C3 H3 SCG sing 285 n n 
C2 C7 SCG sing 286 n n 
C2 C1 SCG sing 287 n n 
C2 H2 SCG sing 288 n n 
C7 C8 SCG doub 289 n n 
C7 H7 SCG sing 290 n n 
C8 H81 SCG sing 291 n n 
C8 H82 SCG sing 292 n n 
C1 O5 SCG sing 293 n n 
C1 O1 SCG sing 294 n n 
C1 H1 SCG sing 295 n n 
O5 C5 SCG sing 296 n n 
C5 C4 SCG doub 297 n n 
C5 H5 SCG sing 298 n n 
C4 C12 SCG sing 299 n n 
C12 O14 SCG sing 300 n n 
C12 O13 SCG doub 301 n n 
O14 C15 SCG sing 302 n n 
C15 H151 SCG sing 303 n n 
C15 H152 SCG sing 304 n n 
C15 H153 SCG sing 305 n n 
O1 C17 SCG sing 306 n n 
C17 O22 SCG sing 307 n n 
C17 C18 SCG sing 308 n n 
C17 H17 SCG sing 309 n n 
O22 C21 SCG sing 310 n n 
C21 C23 SCG sing 311 n n 
C21 C20 SCG sing 312 n n 
C21 H21 SCG sing 313 n n 
C23 O24 SCG sing 314 n n 
C23 H231 SCG sing 315 n n 
C23 H232 SCG sing 316 n n 
O24 H24 SCG sing 317 n n 
C20 O25 SCG sing 318 n n 
C20 C19 SCG sing 319 n n 
C20 H20 SCG sing 320 n n 
O25 H25 SCG sing 321 n n 
C19 O26 SCG sing 322 n n 
C19 C18 SCG sing 323 n n 
C19 H19 SCG sing 324 n n 
O26 H26 SCG sing 325 n n 
C18 O27 SCG sing 326 n n 
C18 H18 SCG sing 327 n n 
O27 H27 SCG sing 328 n n 
#
_atom_sites.entry_id                     3U5Y 
_atom_sites.fract_transf_matrix[1][1]    0.00953 
_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]    0.00774 
_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]    0.004613 
_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 2 SCG A 1 1001 1001 SCG SCG . 
D 2 SCG B 1 1001 1001 SCG SCG . 
E 3 CL B 1 514 1 CL CL . 
F 3 CL B 1 515 2 CL CL . 
G 4 HOH A 1 514 1 HOH HOH . 
G 4 HOH A 2 515 2 HOH HOH . 
G 4 HOH A 3 516 7 HOH HOH . 
G 4 HOH A 4 517 8 HOH HOH . 
G 4 HOH A 5 518 11 HOH HOH . 
G 4 HOH A 6 519 13 HOH HOH . 
G 4 HOH A 7 520 15 HOH HOH . 
G 4 HOH A 8 521 16 HOH HOH . 
G 4 HOH A 9 522 19 HOH HOH . 
G 4 HOH A 10 523 20 HOH HOH . 
G 4 HOH A 11 524 21 HOH HOH . 
G 4 HOH A 12 525 25 HOH HOH . 
G 4 HOH A 13 526 27 HOH HOH . 
G 4 HOH A 14 527 30 HOH HOH . 
G 4 HOH A 15 528 31 HOH HOH . 
G 4 HOH A 16 529 33 HOH HOH . 
G 4 HOH A 17 530 35 HOH HOH . 
G 4 HOH A 18 531 39 HOH HOH . 
G 4 HOH A 19 532 41 HOH HOH . 
G 4 HOH A 20 533 42 HOH HOH . 
G 4 HOH A 21 534 45 HOH HOH . 
G 4 HOH A 22 535 47 HOH HOH . 
G 4 HOH A 23 536 49 HOH HOH . 
G 4 HOH A 24 537 50 HOH HOH . 
G 4 HOH A 25 538 51 HOH HOH . 
G 4 HOH A 26 539 54 HOH HOH . 
G 4 HOH A 27 540 57 HOH HOH . 
G 4 HOH A 28 541 58 HOH HOH . 
G 4 HOH A 29 542 59 HOH HOH . 
G 4 HOH A 30 543 63 HOH HOH . 
G 4 HOH A 31 544 64 HOH HOH . 
G 4 HOH A 32 545 65 HOH HOH . 
G 4 HOH A 33 546 67 HOH HOH . 
G 4 HOH A 34 547 69 HOH HOH . 
G 4 HOH A 35 548 73 HOH HOH . 
G 4 HOH A 36 549 74 HOH HOH . 
G 4 HOH A 37 550 75 HOH HOH . 
G 4 HOH A 38 551 78 HOH HOH . 
G 4 HOH A 39 552 79 HOH HOH . 
G 4 HOH A 40 553 81 HOH HOH . 
G 4 HOH A 41 554 82 HOH HOH . 
G 4 HOH A 42 555 83 HOH HOH . 
G 4 HOH A 43 556 85 HOH HOH . 
G 4 HOH A 44 557 87 HOH HOH . 
G 4 HOH A 45 558 88 HOH HOH . 
G 4 HOH A 46 559 90 HOH HOH . 
G 4 HOH A 47 560 91 HOH HOH . 
G 4 HOH A 48 561 95 HOH HOH . 
G 4 HOH A 49 562 96 HOH HOH . 
G 4 HOH A 50 563 97 HOH HOH . 
G 4 HOH A 51 564 102 HOH HOH . 
G 4 HOH A 52 565 104 HOH HOH . 
G 4 HOH A 53 566 107 HOH HOH . 
G 4 HOH A 54 567 109 HOH HOH . 
G 4 HOH A 55 568 110 HOH HOH . 
G 4 HOH A 56 569 114 HOH HOH . 
G 4 HOH A 57 570 115 HOH HOH . 
G 4 HOH A 58 571 117 HOH HOH . 
G 4 HOH A 59 572 118 HOH HOH . 
G 4 HOH A 60 573 119 HOH HOH . 
G 4 HOH A 61 574 120 HOH HOH . 
G 4 HOH A 62 575 122 HOH HOH . 
G 4 HOH A 63 576 124 HOH HOH . 
G 4 HOH A 64 577 125 HOH HOH . 
G 4 HOH A 65 578 126 HOH HOH . 
G 4 HOH A 66 579 128 HOH HOH . 
G 4 HOH A 67 580 136 HOH HOH . 
G 4 HOH A 68 581 137 HOH HOH . 
G 4 HOH A 69 582 138 HOH HOH . 
G 4 HOH A 70 583 147 HOH HOH . 
G 4 HOH A 71 584 148 HOH HOH . 
G 4 HOH A 72 585 149 HOH HOH . 
G 4 HOH A 73 586 150 HOH HOH . 
G 4 HOH A 74 587 151 HOH HOH . 
G 4 HOH A 75 588 152 HOH HOH . 
H 4 HOH B 1 516 3 HOH HOH . 
H 4 HOH B 2 517 4 HOH HOH . 
H 4 HOH B 3 518 5 HOH HOH . 
H 4 HOH B 4 519 6 HOH HOH . 
H 4 HOH B 5 520 9 HOH HOH . 
H 4 HOH B 6 521 10 HOH HOH . 
H 4 HOH B 7 522 12 HOH HOH . 
H 4 HOH B 8 523 14 HOH HOH . 
H 4 HOH B 9 524 17 HOH HOH . 
H 4 HOH B 10 525 18 HOH HOH . 
H 4 HOH B 11 526 23 HOH HOH . 
H 4 HOH B 12 527 24 HOH HOH . 
H 4 HOH B 13 528 26 HOH HOH . 
H 4 HOH B 14 529 28 HOH HOH . 
H 4 HOH B 15 530 29 HOH HOH . 
H 4 HOH B 16 531 32 HOH HOH . 
H 4 HOH B 17 532 34 HOH HOH . 
H 4 HOH B 18 533 36 HOH HOH . 
H 4 HOH B 19 534 37 HOH HOH . 
H 4 HOH B 20 535 38 HOH HOH . 
H 4 HOH B 21 536 40 HOH HOH . 
H 4 HOH B 22 537 43 HOH HOH . 
H 4 HOH B 23 538 44 HOH HOH . 
H 4 HOH B 24 539 48 HOH HOH . 
H 4 HOH B 25 540 52 HOH HOH . 
H 4 HOH B 26 541 53 HOH HOH . 
H 4 HOH B 27 542 55 HOH HOH . 
H 4 HOH B 28 543 56 HOH HOH . 
H 4 HOH B 29 544 61 HOH HOH . 
H 4 HOH B 30 545 62 HOH HOH . 
H 4 HOH B 31 546 66 HOH HOH . 
H 4 HOH B 32 547 68 HOH HOH . 
H 4 HOH B 33 548 70 HOH HOH . 
H 4 HOH B 34 549 71 HOH HOH . 
H 4 HOH B 35 550 72 HOH HOH . 
H 4 HOH B 36 551 76 HOH HOH . 
H 4 HOH B 37 552 77 HOH HOH . 
H 4 HOH B 38 553 80 HOH HOH . 
H 4 HOH B 39 554 84 HOH HOH . 
H 4 HOH B 40 555 86 HOH HOH . 
H 4 HOH B 41 556 89 HOH HOH . 
H 4 HOH B 42 557 92 HOH HOH . 
H 4 HOH B 43 558 93 HOH HOH . 
H 4 HOH B 44 559 94 HOH HOH . 
H 4 HOH B 45 560 98 HOH HOH . 
H 4 HOH B 46 561 100 HOH HOH . 
H 4 HOH B 47 562 101 HOH HOH . 
H 4 HOH B 48 563 103 HOH HOH . 
H 4 HOH B 49 564 105 HOH HOH . 
H 4 HOH B 50 565 106 HOH HOH . 
H 4 HOH B 51 566 108 HOH HOH . 
H 4 HOH B 52 567 111 HOH HOH . 
H 4 HOH B 53 568 112 HOH HOH . 
H 4 HOH B 54 569 113 HOH HOH . 
H 4 HOH B 55 570 116 HOH HOH . 
H 4 HOH B 56 571 121 HOH HOH . 
H 4 HOH B 57 572 123 HOH HOH . 
H 4 HOH B 58 573 127 HOH HOH . 
H 4 HOH B 59 574 129 HOH HOH . 
H 4 HOH B 60 575 130 HOH HOH . 
H 4 HOH B 61 576 131 HOH HOH . 
H 4 HOH B 62 577 132 HOH HOH . 
H 4 HOH B 63 578 133 HOH HOH . 
H 4 HOH B 64 579 134 HOH HOH . 
H 4 HOH B 65 580 139 HOH HOH . 
H 4 HOH B 66 581 141 HOH HOH . 
H 4 HOH B 67 582 142 HOH HOH . 
H 4 HOH B 68 583 143 HOH HOH . 
H 4 HOH B 69 584 144 HOH HOH . 
H 4 HOH B 70 585 145 HOH HOH . 
H 4 HOH B 71 586 146 HOH HOH . 
H 4 HOH B 72 587 153 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 O16 SCG . . . C 2 36.03 40.444 41.952 1 83.76 ? O16 SCG 1001 A 1 
HETATM 2 C C10 SCG . . . C 2 35.021 40.945 41.422 1 83.61 ? C10 SCG 1001 A 1 
HETATM 3 C C9 SCG . . . C 2 35.098 41.512 39.99 1 83.38 ? C9 SCG 1001 A 1 
HETATM 4 C C3 SCG . . . C 2 34.316 42.837 39.868 1 82.69 ? C3 SCG 1001 A 1 
HETATM 5 C C2 SCG . . . C 2 35.013 43.818 38.907 1 80.9 ? C2 SCG 1001 A 1 
HETATM 6 C C7 SCG . . . C 2 36.478 43.385 38.701 1 80.33 ? C7 SCG 1001 A 1 
HETATM 7 C C8 SCG . . . C 2 36.903 42.114 39.092 1 80.3 ? C8 SCG 1001 A 1 
HETATM 8 C C1 SCG . . . C 2 34.267 43.938 37.557 1 79.56 ? C1 SCG 1001 A 1 
HETATM 9 O O5 SCG . . . C 2 32.897 44.277 37.731 1 80.83 ? O5 SCG 1001 A 1 
HETATM 10 C C5 SCG . . . C 2 32.25 43.306 38.414 1 82.81 ? C5 SCG 1001 A 1 
HETATM 11 C C4 SCG . . . C 2 32.859 42.579 39.428 1 83.69 ? C4 SCG 1001 A 1 
HETATM 12 C C12 SCG . . . C 2 32.005 41.513 40.122 1 85.55 ? C12 SCG 1001 A 1 
HETATM 13 O O14 SCG . . . C 2 30.716 41.326 39.708 1 86.31 ? O14 SCG 1001 A 1 
HETATM 14 C C15 SCG . . . C 2 29.824 42.141 40.526 1 86.73 ? C15 SCG 1001 A 1 
HETATM 15 O O13 SCG . . . C 2 32.466 40.821 41.032 1 87.06 ? O13 SCG 1001 A 1 
HETATM 16 O O1 SCG . . . C 2 34.721 45.054 36.775 1 76.3 ? O1 SCG 1001 A 1 
HETATM 17 C C17 SCG . . . C 2 34.453 44.843 35.376 1 71.95 ? C17 SCG 1001 A 1 
HETATM 18 O O22 SCG . . . C 2 35.387 43.799 35.054 1 70.04 ? O22 SCG 1001 A 1 
HETATM 19 C C21 SCG . . . C 2 35.506 43.615 33.66 1 68.16 ? C21 SCG 1001 A 1 
HETATM 20 C C23 SCG . . . C 2 36.374 42.355 33.449 1 66.52 ? C23 SCG 1001 A 1 
HETATM 21 O O24 SCG . . . C 2 37.725 42.551 33.904 1 64.23 ? O24 SCG 1001 A 1 
HETATM 22 C C20 SCG . . . C 2 36.135 44.878 33.058 1 67.65 ? C20 SCG 1001 A 1 
HETATM 23 O O25 SCG . . . C 2 36.369 44.664 31.663 1 66.12 ? O25 SCG 1001 A 1 
HETATM 24 C C19 SCG . . . C 2 35.273 46.145 33.272 1 68.1 ? C19 SCG 1001 A 1 
HETATM 25 O O26 SCG . . . C 2 36.092 47.321 33.093 1 64.94 ? O26 SCG 1001 A 1 
HETATM 26 C C18 SCG . . . C 2 34.643 46.217 34.678 1 70.03 ? C18 SCG 1001 A 1 
HETATM 27 O O27 SCG . . . C 2 33.397 46.944 34.616 1 70.28 ? O27 SCG 1001 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           275 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#