data_3U5Y # _model_server_result.job_id v3qerrtMBOer8hRZQJKNQQ _model_server_result.datetime_utc '2024-11-18 12:49:00' _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":"D","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 . . . D 2 69.285 22.411 24.143 1 84.9 ? O16 SCG 1001 B 1 HETATM 2 C C10 SCG . . . D 2 70.211 22.976 23.552 1 84.18 ? C10 SCG 1001 B 1 HETATM 3 C C9 SCG . . . D 2 70.049 24.423 23.024 1 83.43 ? C9 SCG 1001 B 1 HETATM 4 C C3 SCG . . . D 2 70.826 24.647 21.706 1 82.06 ? C3 SCG 1001 B 1 HETATM 5 C C2 SCG . . . D 2 70.14 25.703 20.796 1 80.4 ? C2 SCG 1001 B 1 HETATM 6 C C7 SCG . . . D 2 68.679 25.934 21.24 1 79.58 ? C7 SCG 1001 B 1 HETATM 7 C C8 SCG . . . D 2 68.206 25.431 22.46 1 79.8 ? C8 SCG 1001 B 1 HETATM 8 C C1 SCG . . . D 2 70.92 27.046 20.704 1 79.1 ? C1 SCG 1001 B 1 HETATM 9 O O5 SCG . . . D 2 72.295 26.854 20.415 1 79.94 ? O5 SCG 1001 B 1 HETATM 10 C C5 SCG . . . D 2 72.919 26.088 21.352 1 81.96 ? C5 SCG 1001 B 1 HETATM 11 C C4 SCG . . . D 2 72.295 25.026 22.009 1 82.55 ? C4 SCG 1001 B 1 HETATM 12 C C12 SCG . . . D 2 73.116 24.224 23.04 1 83.42 ? C12 SCG 1001 B 1 HETATM 13 O O14 SCG . . . D 2 74.411 24.591 23.308 1 84 ? O14 SCG 1001 B 1 HETATM 14 C C15 SCG . . . D 2 75.339 24.102 22.229 1 84.83 ? C15 SCG 1001 B 1 HETATM 15 O O13 SCG . . . D 2 72.615 23.276 23.652 1 83.54 ? O13 SCG 1001 B 1 HETATM 16 O O1 SCG . . . D 2 70.535 27.825 19.551 1 76.87 ? O1 SCG 1001 B 1 HETATM 17 C C17 SCG . . . D 2 70.63 29.273 19.714 1 74.36 ? C17 SCG 1001 B 1 HETATM 18 O O22 SCG . . . D 2 69.648 29.528 20.739 1 72.61 ? O22 SCG 1001 B 1 HETATM 19 C C21 SCG . . . D 2 69.499 30.923 20.962 1 71.61 ? C21 SCG 1001 B 1 HETATM 20 C C23 SCG . . . D 2 68.63 31.091 22.227 1 70.27 ? C23 SCG 1001 B 1 HETATM 21 O O24 SCG . . . D 2 67.319 30.55 22.005 1 68.57 ? O24 SCG 1001 B 1 HETATM 22 C C20 SCG . . . D 2 68.831 31.56 19.727 1 71.07 ? C20 SCG 1001 B 1 HETATM 23 O O25 SCG . . . D 2 68.579 32.959 19.981 1 69.04 ? O25 SCG 1001 B 1 HETATM 24 C C19 SCG . . . D 2 69.648 31.346 18.417 1 71.04 ? C19 SCG 1001 B 1 HETATM 25 O O26 SCG . . . D 2 68.772 31.473 17.273 1 67.18 ? O26 SCG 1001 B 1 HETATM 26 C C18 SCG . . . D 2 70.376 29.978 18.337 1 73 ? C18 SCG 1001 B 1 HETATM 27 O O27 SCG . . . D 2 71.599 30.098 17.551 1 73.41 ? O27 SCG 1001 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #