data_5JD2 # _model_server_result.job_id 5YdrmlpfeBIcnN1BATakkg _model_server_result.datetime_utc '2024-12-22 17:30:44' _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 5jd2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":5200}' # _entry.id 5JD2 # _exptl.entry_id 5JD2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 291.206 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '5-[(3aS,4S,6aR)-2-oxohexahydro-1H-selenopheno[3,4-d]imidazol-4-yl]pentanoic acid' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 112.38 _cell.angle_gamma 90 _cell.entry_id 5JD2 _cell.length_a 50.84 _cell.length_b 98.52 _cell.length_c 53.43 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JD2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,I,J,K,L _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # _chem_comp.formula 'C10 H16 N2 O3 Se' _chem_comp.formula_weight 291.206 _chem_comp.id BYY _chem_comp.mon_nstd_flag . _chem_comp.name '5-[(3aS,4S,6aR)-2-oxohexahydro-1H-selenopheno[3,4-d]imidazol-4-yl]pentanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms selenobiotin # 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 O12 C11 BYY doub 70 n n C10 C11 BYY sing 71 n n C10 C9 BYY sing 72 n n C11 O11 BYY sing 73 n n C9 C8 BYY sing 74 n n C8 C7 BYY sing 75 n n C7 C2 BYY sing 76 n n SE1 C2 BYY sing 77 n n SE1 C6 BYY sing 78 n n C2 C4 BYY sing 79 n n N2 C4 BYY sing 80 n n N2 C3 BYY sing 81 n n C4 C5 BYY sing 82 n n C6 C5 BYY sing 83 n n C3 O3 BYY doub 84 n n C3 N1 BYY sing 85 n n C5 N1 BYY sing 86 n n N1 H1 BYY sing 87 n n N2 H2 BYY sing 88 n n C4 H3 BYY sing 89 n n C5 H4 BYY sing 90 n n C6 H5 BYY sing 91 n n C6 H6 BYY sing 92 n n C2 H7 BYY sing 93 n n C7 H8 BYY sing 94 n n C7 H9 BYY sing 95 n n C8 H10 BYY sing 96 n n C8 H11 BYY sing 97 n n C9 H12 BYY sing 98 n n C9 H13 BYY sing 99 n n C10 H14 BYY sing 100 n n C10 H15 BYY sing 101 n n O11 H16 BYY sing 102 n n # _atom_sites.entry_id 5JD2 _atom_sites.fract_transf_matrix[1][1] 0.01967 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008099 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01015 _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] 0.020241 _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 E 2 BYY A 1 5100 5100 BYY BYY . F 2 BYY B 1 5200 5200 BYY BYY . G 2 BYY C 1 5300 5300 BYY BYY . H 2 BYY D 1 5400 5400 BYY BYY . I 3 HOH A 1 5201 91 HOH HOH . I 3 HOH A 2 5202 296 HOH HOH . I 3 HOH A 3 5203 8 HOH HOH . I 3 HOH A 4 5204 156 HOH HOH . I 3 HOH A 5 5205 161 HOH HOH . I 3 HOH A 6 5206 145 HOH HOH . I 3 HOH A 7 5207 187 HOH HOH . I 3 HOH A 8 5208 173 HOH HOH . I 3 HOH A 9 5209 17 HOH HOH . I 3 HOH A 10 5210 148 HOH HOH . I 3 HOH A 11 5211 139 HOH HOH . I 3 HOH A 12 5212 35 HOH HOH . I 3 HOH A 13 5213 3 HOH HOH . I 3 HOH A 14 5214 2 HOH HOH . I 3 HOH A 15 5215 38 HOH HOH . I 3 HOH A 16 5216 141 HOH HOH . I 3 HOH A 17 5217 154 HOH HOH . I 3 HOH A 18 5218 218 HOH HOH . I 3 HOH A 19 5219 120 HOH HOH . I 3 HOH A 20 5220 166 HOH HOH . I 3 HOH A 21 5221 36 HOH HOH . I 3 HOH A 22 5222 68 HOH HOH . I 3 HOH A 23 5223 29 HOH HOH . I 3 HOH A 24 5224 351 HOH HOH . I 3 HOH A 25 5225 26 HOH HOH . I 3 HOH A 26 5226 13 HOH HOH . I 3 HOH A 27 5227 126 HOH HOH . I 3 HOH A 28 5228 113 HOH HOH . I 3 HOH A 29 5229 5 HOH HOH . I 3 HOH A 30 5230 257 HOH HOH . I 3 HOH A 31 5231 179 HOH HOH . I 3 HOH A 32 5232 365 HOH HOH . I 3 HOH A 33 5233 22 HOH HOH . I 3 HOH A 34 5234 100 HOH HOH . I 3 HOH A 35 5235 174 HOH HOH . I 3 HOH A 36 5236 116 HOH HOH . I 3 HOH A 37 5237 41 HOH HOH . I 3 HOH A 38 5238 65 HOH HOH . I 3 HOH A 39 5239 81 HOH HOH . I 3 HOH A 40 5240 18 HOH HOH . I 3 HOH A 41 5241 62 HOH HOH . I 3 HOH A 42 5242 110 HOH HOH . I 3 HOH A 43 5243 27 HOH HOH . I 3 HOH A 44 5244 74 HOH HOH . I 3 HOH A 45 5245 88 HOH HOH . I 3 HOH A 46 5246 136 HOH HOH . I 3 HOH A 47 5247 119 HOH HOH . I 3 HOH A 48 5248 76 HOH HOH . I 3 HOH A 49 5249 84 HOH HOH . I 3 HOH A 50 5250 95 HOH HOH . I 3 HOH A 51 5251 345 HOH HOH . I 3 HOH A 52 5252 185 HOH HOH . I 3 HOH A 53 5253 106 HOH HOH . I 3 HOH A 54 5254 162 HOH HOH . I 3 HOH A 55 5255 144 HOH HOH . I 3 HOH A 56 5256 221 HOH HOH . I 3 HOH A 57 5257 348 HOH HOH . I 3 HOH A 58 5258 118 HOH HOH . I 3 HOH A 59 5259 89 HOH HOH . I 3 HOH A 60 5260 237 HOH HOH . I 3 HOH A 61 5261 21 HOH HOH . I 3 HOH A 62 5262 150 HOH HOH . I 3 HOH A 63 5263 72 HOH HOH . I 3 HOH A 64 5264 276 HOH HOH . I 3 HOH A 65 5265 77 HOH HOH . I 3 HOH A 66 5266 273 HOH HOH . I 3 HOH A 67 5267 358 HOH HOH . I 3 HOH A 68 5268 82 HOH HOH . I 3 HOH A 69 5269 303 HOH HOH . J 3 HOH B 1 5301 48 HOH HOH . J 3 HOH B 2 5302 37 HOH HOH . J 3 HOH B 3 5303 104 HOH HOH . J 3 HOH B 4 5304 305 HOH HOH . J 3 HOH B 5 5305 70 HOH HOH . J 3 HOH B 6 5306 234 HOH HOH . J 3 HOH B 7 5307 171 HOH HOH . J 3 HOH B 8 5308 140 HOH HOH . J 3 HOH B 9 5309 53 HOH HOH . J 3 HOH B 10 5310 9 HOH HOH . J 3 HOH B 11 5311 31 HOH HOH . J 3 HOH B 12 5312 133 HOH HOH . J 3 HOH B 13 5313 261 HOH HOH . J 3 HOH B 14 5314 107 HOH HOH . J 3 HOH B 15 5315 7 HOH HOH . J 3 HOH B 16 5316 243 HOH HOH . J 3 HOH B 17 5317 51 HOH HOH . J 3 HOH B 18 5318 192 HOH HOH . J 3 HOH B 19 5319 96 HOH HOH . J 3 HOH B 20 5320 24 HOH HOH . J 3 HOH B 21 5321 61 HOH HOH . J 3 HOH B 22 5322 229 HOH HOH . J 3 HOH B 23 5323 90 HOH HOH . J 3 HOH B 24 5324 79 HOH HOH . J 3 HOH B 25 5325 278 HOH HOH . J 3 HOH B 26 5326 147 HOH HOH . J 3 HOH B 27 5327 123 HOH HOH . J 3 HOH B 28 5328 40 HOH HOH . J 3 HOH B 29 5329 143 HOH HOH . J 3 HOH B 30 5330 214 HOH HOH . J 3 HOH B 31 5331 42 HOH HOH . J 3 HOH B 32 5332 87 HOH HOH . J 3 HOH B 33 5333 125 HOH HOH . J 3 HOH B 34 5334 165 HOH HOH . J 3 HOH B 35 5335 127 HOH HOH . J 3 HOH B 36 5336 274 HOH HOH . J 3 HOH B 37 5337 242 HOH HOH . J 3 HOH B 38 5338 167 HOH HOH . J 3 HOH B 39 5339 285 HOH HOH . J 3 HOH B 40 5340 249 HOH HOH . J 3 HOH B 41 5341 160 HOH HOH . J 3 HOH B 42 5342 39 HOH HOH . J 3 HOH B 43 5343 138 HOH HOH . J 3 HOH B 44 5344 252 HOH HOH . J 3 HOH B 45 5345 101 HOH HOH . J 3 HOH B 46 5346 291 HOH HOH . J 3 HOH B 47 5347 97 HOH HOH . J 3 HOH B 48 5348 334 HOH HOH . J 3 HOH B 49 5349 307 HOH HOH . J 3 HOH B 50 5350 317 HOH HOH . J 3 HOH B 51 5351 60 HOH HOH . J 3 HOH B 52 5352 195 HOH HOH . J 3 HOH B 53 5353 308 HOH HOH . J 3 HOH B 54 5354 157 HOH HOH . J 3 HOH B 55 5355 279 HOH HOH . J 3 HOH B 56 5356 330 HOH HOH . J 3 HOH B 57 5357 324 HOH HOH . J 3 HOH B 58 5358 283 HOH HOH . J 3 HOH B 59 5359 299 HOH HOH . J 3 HOH B 60 5360 352 HOH HOH . K 3 HOH C 1 5401 122 HOH HOH . K 3 HOH C 2 5402 129 HOH HOH . K 3 HOH C 3 5403 135 HOH HOH . K 3 HOH C 4 5404 69 HOH HOH . K 3 HOH C 5 5405 149 HOH HOH . K 3 HOH C 6 5406 132 HOH HOH . K 3 HOH C 7 5407 300 HOH HOH . K 3 HOH C 8 5408 253 HOH HOH . K 3 HOH C 9 5409 98 HOH HOH . K 3 HOH C 10 5410 233 HOH HOH . K 3 HOH C 11 5411 6 HOH HOH . K 3 HOH C 12 5412 108 HOH HOH . K 3 HOH C 13 5413 111 HOH HOH . K 3 HOH C 14 5414 94 HOH HOH . K 3 HOH C 15 5415 1 HOH HOH . K 3 HOH C 16 5416 19 HOH HOH . K 3 HOH C 17 5417 4 HOH HOH . K 3 HOH C 18 5418 56 HOH HOH . K 3 HOH C 19 5419 58 HOH HOH . K 3 HOH C 20 5420 20 HOH HOH . K 3 HOH C 21 5421 67 HOH HOH . K 3 HOH C 22 5422 240 HOH HOH . K 3 HOH C 23 5423 57 HOH HOH . K 3 HOH C 24 5424 232 HOH HOH . K 3 HOH C 25 5425 250 HOH HOH . K 3 HOH C 26 5426 14 HOH HOH . K 3 HOH C 27 5427 109 HOH HOH . K 3 HOH C 28 5428 83 HOH HOH . K 3 HOH C 29 5429 99 HOH HOH . K 3 HOH C 30 5430 268 HOH HOH . K 3 HOH C 31 5431 12 HOH HOH . K 3 HOH C 32 5432 50 HOH HOH . K 3 HOH C 33 5433 202 HOH HOH . K 3 HOH C 34 5434 102 HOH HOH . K 3 HOH C 35 5435 205 HOH HOH . K 3 HOH C 36 5436 193 HOH HOH . K 3 HOH C 37 5437 189 HOH HOH . K 3 HOH C 38 5438 199 HOH HOH . K 3 HOH C 39 5439 23 HOH HOH . K 3 HOH C 40 5440 16 HOH HOH . K 3 HOH C 41 5441 78 HOH HOH . K 3 HOH C 42 5442 190 HOH HOH . K 3 HOH C 43 5443 25 HOH HOH . K 3 HOH C 44 5444 178 HOH HOH . K 3 HOH C 45 5445 277 HOH HOH . K 3 HOH C 46 5446 159 HOH HOH . K 3 HOH C 47 5447 93 HOH HOH . K 3 HOH C 48 5448 52 HOH HOH . K 3 HOH C 49 5449 33 HOH HOH . K 3 HOH C 50 5450 46 HOH HOH . K 3 HOH C 51 5451 15 HOH HOH . K 3 HOH C 52 5452 235 HOH HOH . K 3 HOH C 53 5453 155 HOH HOH . K 3 HOH C 54 5454 223 HOH HOH . K 3 HOH C 55 5455 146 HOH HOH . K 3 HOH C 56 5456 63 HOH HOH . K 3 HOH C 57 5457 172 HOH HOH . K 3 HOH C 58 5458 134 HOH HOH . K 3 HOH C 59 5459 103 HOH HOH . K 3 HOH C 60 5460 105 HOH HOH . K 3 HOH C 61 5461 137 HOH HOH . K 3 HOH C 62 5462 54 HOH HOH . K 3 HOH C 63 5463 142 HOH HOH . K 3 HOH C 64 5464 256 HOH HOH . K 3 HOH C 65 5465 34 HOH HOH . K 3 HOH C 66 5466 92 HOH HOH . K 3 HOH C 67 5467 75 HOH HOH . K 3 HOH C 68 5468 208 HOH HOH . K 3 HOH C 69 5469 188 HOH HOH . K 3 HOH C 70 5470 184 HOH HOH . K 3 HOH C 71 5471 217 HOH HOH . K 3 HOH C 72 5472 239 HOH HOH . K 3 HOH C 73 5473 209 HOH HOH . K 3 HOH C 74 5474 328 HOH HOH . K 3 HOH C 75 5475 306 HOH HOH . K 3 HOH C 76 5476 222 HOH HOH . K 3 HOH C 77 5477 131 HOH HOH . K 3 HOH C 78 5478 230 HOH HOH . K 3 HOH C 79 5479 293 HOH HOH . L 3 HOH D 1 5501 170 HOH HOH . L 3 HOH D 2 5502 30 HOH HOH . L 3 HOH D 3 5503 114 HOH HOH . L 3 HOH D 4 5504 64 HOH HOH . L 3 HOH D 5 5505 44 HOH HOH . L 3 HOH D 6 5506 10 HOH HOH . L 3 HOH D 7 5507 11 HOH HOH . L 3 HOH D 8 5508 71 HOH HOH . L 3 HOH D 9 5509 28 HOH HOH . L 3 HOH D 10 5510 49 HOH HOH . L 3 HOH D 11 5511 32 HOH HOH . L 3 HOH D 12 5512 245 HOH HOH . L 3 HOH D 13 5513 85 HOH HOH . L 3 HOH D 14 5514 227 HOH HOH . L 3 HOH D 15 5515 59 HOH HOH . L 3 HOH D 16 5516 163 HOH HOH . L 3 HOH D 17 5517 115 HOH HOH . L 3 HOH D 18 5518 47 HOH HOH . L 3 HOH D 19 5519 284 HOH HOH . L 3 HOH D 20 5520 275 HOH HOH . L 3 HOH D 21 5521 43 HOH HOH . L 3 HOH D 22 5522 117 HOH HOH . L 3 HOH D 23 5523 121 HOH HOH . L 3 HOH D 24 5524 164 HOH HOH . L 3 HOH D 25 5525 186 HOH HOH . L 3 HOH D 26 5526 168 HOH HOH . L 3 HOH D 27 5527 238 HOH HOH . L 3 HOH D 28 5528 266 HOH HOH . L 3 HOH D 29 5529 55 HOH HOH . L 3 HOH D 30 5530 45 HOH HOH . L 3 HOH D 31 5531 244 HOH HOH . L 3 HOH D 32 5532 86 HOH HOH . L 3 HOH D 33 5533 236 HOH HOH . L 3 HOH D 34 5534 66 HOH HOH . L 3 HOH D 35 5535 301 HOH HOH . L 3 HOH D 36 5536 219 HOH HOH . L 3 HOH D 37 5537 151 HOH HOH . L 3 HOH D 38 5538 124 HOH HOH . L 3 HOH D 39 5539 289 HOH HOH . L 3 HOH D 40 5540 346 HOH HOH . L 3 HOH D 41 5541 211 HOH HOH . L 3 HOH D 42 5542 272 HOH HOH . L 3 HOH D 43 5543 153 HOH HOH . L 3 HOH D 44 5544 228 HOH HOH . L 3 HOH D 45 5545 80 HOH HOH . L 3 HOH D 46 5546 181 HOH HOH . L 3 HOH D 47 5547 130 HOH HOH . L 3 HOH D 48 5548 247 HOH HOH . L 3 HOH D 49 5549 225 HOH HOH . L 3 HOH D 50 5550 353 HOH HOH . L 3 HOH D 51 5551 182 HOH HOH . L 3 HOH D 52 5552 282 HOH HOH . L 3 HOH D 53 5553 320 HOH HOH . L 3 HOH D 54 5554 366 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 O3 BYY . . . F 2 -2.408 -12.269 0.039 1 35.1 ? O3 BYY 5200 B 1 HETATM 2 C C3 BYY . . . F 2 -1.965 -12.22 1.19 1 34.91 ? C3 BYY 5200 B 1 HETATM 3 N N1 BYY . . . F 2 -0.691 -12.476 1.511 1 33.31 ? N1 BYY 5200 B 1 HETATM 4 N N2 BYY . . . F 2 -2.727 -11.906 2.245 1 34.93 ? N2 BYY 5200 B 1 HETATM 5 C C4 BYY . . . F 2 -1.917 -11.961 3.496 1 33.18 ? C4 BYY 5200 B 1 HETATM 6 C C5 BYY . . . F 2 -0.487 -12.301 2.977 1 32.15 ? C5 BYY 5200 B 1 HETATM 7 C C6 BYY . . . F 2 0.456 -11.111 3.226 1 29.95 ? C6 BYY 5200 B 1 HETATM 8 SE SE1 BYY . . . F 2 -0.728 -9.567 3.158 0.52 27.05 ? SE1 BYY 5200 B 1 HETATM 9 C C2 BYY . . . F 2 -1.918 -10.61 4.269 1 31.4 ? C2 BYY 5200 B 1 HETATM 10 C C7 BYY . . . F 2 -3.338 -10.033 4.347 1 32.67 ? C7 BYY 5200 B 1 HETATM 11 C C8 BYY . . . F 2 -3.38 -8.92 5.397 1 34.56 ? C8 BYY 5200 B 1 HETATM 12 C C9 BYY . . . F 2 -4.805 -8.347 5.515 1 36.15 ? C9 BYY 5200 B 1 HETATM 13 C C10 BYY . . . F 2 -4.782 -7.105 6.418 1 37.02 ? C10 BYY 5200 B 1 HETATM 14 C C11 BYY . . . F 2 -4.648 -7.542 7.882 1 38.51 ? C11 BYY 5200 B 1 HETATM 15 O O11 BYY . . . F 2 -3.99 -6.801 8.656 1 38.84 ? O11 BYY 5200 B 1 HETATM 16 O O12 BYY . . . F 2 -5.212 -8.612 8.191 1 38.94 ? O12 BYY 5200 B 1 # _model_server_stats.io_time_ms 77 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 16 #