data_5VYU # _model_server_result.job_id '_lPfVDZ3-u2PvquVGmuSkQ' _model_server_result.datetime_utc '2024-11-25 08:37:28' _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 5vyu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 5VYU # _exptl.entry_id 5VYU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 588.357 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description GDP-perosamine _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 90 _cell.entry_id 5VYU _cell.length_a 66.835 _cell.length_b 66.835 _cell.length_c 235.947 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5VYU _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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,G,H _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 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C16 H26 N6 O14 P2' _chem_comp.formula_weight 588.357 _chem_comp.id JB2 _chem_comp.mon_nstd_flag . _chem_comp.name GDP-perosamine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O3' C3' JB2 sing 277 n n O2' C2' JB2 sing 278 n n C3' C2' JB2 sing 279 n n C3' C4' JB2 sing 280 n n O1P P JB2 doub 281 n n C2' C1' JB2 sing 282 n n C4' O4' JB2 sing 283 n n C4' C5' JB2 sing 284 n n O5' P JB2 sing 285 n n O5' C5' JB2 sing 286 n n C1' O4' JB2 sing 287 n n C1' N9 JB2 sing 288 n n N2 C2 JB2 sing 289 n n P O2P JB2 sing 290 n n P OPP JB2 sing 291 n n O4P P2 JB2 doub 292 n n N3 C2 JB2 doub 293 n n N3 C4 JB2 sing 294 n n C2 N1 JB2 sing 295 n n N9 C4 JB2 sing 296 n y N9 C8 JB2 sing 297 n y C4 C5 JB2 doub 298 n y OPP P2 JB2 sing 299 n n P2 O1G JB2 sing 300 n n P2 O3P JB2 sing 301 n n N1 C6 JB2 sing 302 n n O1G C1G JB2 sing 303 n n C8 N7 JB2 doub 304 n y O3G C3G JB2 sing 305 n n C3G C2G JB2 sing 306 n n C3G C4G JB2 sing 307 n n N4A C4G JB2 sing 308 n n C5 C6 JB2 sing 309 n n C5 N7 JB2 sing 310 n y C6 O6 JB2 doub 311 n n C2G C1G JB2 sing 312 n n C2G O2G JB2 sing 313 n n C4G C5G JB2 sing 314 n n C1G O5G JB2 sing 315 n n C5G O5G JB2 sing 316 n n C5G C6G JB2 sing 317 n n C8 H1 JB2 sing 318 n n N1 H2 JB2 sing 319 n n N2 H3 JB2 sing 320 n n N2 H4 JB2 sing 321 n n C1' H5 JB2 sing 322 n n C2' H6 JB2 sing 323 n n O2' H7 JB2 sing 324 n n C3' H8 JB2 sing 325 n n O3' H9 JB2 sing 326 n n C4' H10 JB2 sing 327 n n C5' H11 JB2 sing 328 n n C5' H12 JB2 sing 329 n n O2P H13 JB2 sing 330 n n O3P H14 JB2 sing 331 n n C1G H15 JB2 sing 332 n n C5G H16 JB2 sing 333 n n C6G H17 JB2 sing 334 n n C6G H18 JB2 sing 335 n n C6G H19 JB2 sing 336 n n C2G H20 JB2 sing 337 n n O2G H21 JB2 sing 338 n n C3G H22 JB2 sing 339 n n O3G H23 JB2 sing 340 n n C4G H24 JB2 sing 341 n n N4A H25 JB2 sing 342 n n N4A H26 JB2 sing 343 n n # _atom_sites.entry_id 5VYU _atom_sites.fract_transf_matrix[1][1] 0.014962 _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] 0.014962 _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] 0.004238 _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 1YA A 1 301 300 1YA 1YA . D 3 JB2 A 1 302 2002 JB2 JB2 . E 2 1YA B 1 301 300 1YA 1YA . F 4 GDP B 1 302 1 GDP GDP . G 5 HOH A 1 401 187 HOH HOH . G 5 HOH A 2 402 44 HOH HOH . G 5 HOH A 3 403 28 HOH HOH . G 5 HOH A 4 404 198 HOH HOH . G 5 HOH A 5 405 213 HOH HOH . G 5 HOH A 6 406 237 HOH HOH . G 5 HOH A 7 407 221 HOH HOH . G 5 HOH A 8 408 177 HOH HOH . G 5 HOH A 9 409 96 HOH HOH . G 5 HOH A 10 410 191 HOH HOH . G 5 HOH A 11 411 74 HOH HOH . G 5 HOH A 12 412 210 HOH HOH . G 5 HOH A 13 413 216 HOH HOH . G 5 HOH A 14 414 37 HOH HOH . G 5 HOH A 15 415 203 HOH HOH . G 5 HOH A 16 416 222 HOH HOH . G 5 HOH A 17 417 78 HOH HOH . G 5 HOH A 18 418 50 HOH HOH . G 5 HOH A 19 419 29 HOH HOH . G 5 HOH A 20 420 223 HOH HOH . G 5 HOH A 21 421 10 HOH HOH . G 5 HOH A 22 422 188 HOH HOH . G 5 HOH A 23 423 184 HOH HOH . G 5 HOH A 24 424 55 HOH HOH . G 5 HOH A 25 425 104 HOH HOH . G 5 HOH A 26 426 174 HOH HOH . G 5 HOH A 27 427 105 HOH HOH . G 5 HOH A 28 428 3 HOH HOH . G 5 HOH A 29 429 41 HOH HOH . G 5 HOH A 30 430 86 HOH HOH . G 5 HOH A 31 431 114 HOH HOH . G 5 HOH A 32 432 90 HOH HOH . G 5 HOH A 33 433 139 HOH HOH . G 5 HOH A 34 434 93 HOH HOH . G 5 HOH A 35 435 196 HOH HOH . G 5 HOH A 36 436 110 HOH HOH . G 5 HOH A 37 437 18 HOH HOH . G 5 HOH A 38 438 66 HOH HOH . G 5 HOH A 39 439 45 HOH HOH . G 5 HOH A 40 440 21 HOH HOH . G 5 HOH A 41 441 98 HOH HOH . G 5 HOH A 42 442 186 HOH HOH . G 5 HOH A 43 443 8 HOH HOH . G 5 HOH A 44 444 131 HOH HOH . G 5 HOH A 45 445 181 HOH HOH . G 5 HOH A 46 446 211 HOH HOH . G 5 HOH A 47 447 64 HOH HOH . G 5 HOH A 48 448 4 HOH HOH . G 5 HOH A 49 449 42 HOH HOH . G 5 HOH A 50 450 103 HOH HOH . G 5 HOH A 51 451 53 HOH HOH . G 5 HOH A 52 452 75 HOH HOH . G 5 HOH A 53 453 199 HOH HOH . G 5 HOH A 54 454 65 HOH HOH . G 5 HOH A 55 455 243 HOH HOH . G 5 HOH A 56 456 14 HOH HOH . G 5 HOH A 57 457 244 HOH HOH . G 5 HOH A 58 458 80 HOH HOH . G 5 HOH A 59 459 207 HOH HOH . G 5 HOH A 60 460 52 HOH HOH . G 5 HOH A 61 461 5 HOH HOH . G 5 HOH A 62 462 239 HOH HOH . G 5 HOH A 63 463 220 HOH HOH . G 5 HOH A 64 464 51 HOH HOH . G 5 HOH A 65 465 94 HOH HOH . G 5 HOH A 66 466 142 HOH HOH . G 5 HOH A 67 467 152 HOH HOH . G 5 HOH A 68 468 85 HOH HOH . G 5 HOH A 69 469 122 HOH HOH . G 5 HOH A 70 470 70 HOH HOH . G 5 HOH A 71 471 208 HOH HOH . G 5 HOH A 72 472 11 HOH HOH . G 5 HOH A 73 473 48 HOH HOH . G 5 HOH A 74 474 151 HOH HOH . G 5 HOH A 75 475 1 HOH HOH . G 5 HOH A 76 476 26 HOH HOH . G 5 HOH A 77 477 62 HOH HOH . G 5 HOH A 78 478 240 HOH HOH . G 5 HOH A 79 479 39 HOH HOH . G 5 HOH A 80 480 100 HOH HOH . G 5 HOH A 81 481 46 HOH HOH . G 5 HOH A 82 482 192 HOH HOH . G 5 HOH A 83 483 54 HOH HOH . G 5 HOH A 84 484 47 HOH HOH . G 5 HOH A 85 485 215 HOH HOH . G 5 HOH A 86 486 16 HOH HOH . G 5 HOH A 87 487 189 HOH HOH . G 5 HOH A 88 488 212 HOH HOH . G 5 HOH A 89 489 200 HOH HOH . G 5 HOH A 90 490 190 HOH HOH . G 5 HOH A 91 491 115 HOH HOH . G 5 HOH A 92 492 204 HOH HOH . G 5 HOH A 93 493 102 HOH HOH . G 5 HOH A 94 494 238 HOH HOH . G 5 HOH A 95 495 32 HOH HOH . G 5 HOH A 96 496 81 HOH HOH . G 5 HOH A 97 497 218 HOH HOH . G 5 HOH A 98 498 209 HOH HOH . H 5 HOH B 1 401 72 HOH HOH . H 5 HOH B 2 402 241 HOH HOH . H 5 HOH B 3 403 6 HOH HOH . H 5 HOH B 4 404 227 HOH HOH . H 5 HOH B 5 405 206 HOH HOH . H 5 HOH B 6 406 91 HOH HOH . H 5 HOH B 7 407 173 HOH HOH . H 5 HOH B 8 408 20 HOH HOH . H 5 HOH B 9 409 224 HOH HOH . H 5 HOH B 10 410 193 HOH HOH . H 5 HOH B 11 411 225 HOH HOH . H 5 HOH B 12 412 234 HOH HOH . H 5 HOH B 13 413 95 HOH HOH . H 5 HOH B 14 414 87 HOH HOH . H 5 HOH B 15 415 180 HOH HOH . H 5 HOH B 16 416 106 HOH HOH . H 5 HOH B 17 417 7 HOH HOH . H 5 HOH B 18 418 73 HOH HOH . H 5 HOH B 19 419 145 HOH HOH . H 5 HOH B 20 420 230 HOH HOH . H 5 HOH B 21 421 201 HOH HOH . H 5 HOH B 22 422 116 HOH HOH . H 5 HOH B 23 423 141 HOH HOH . H 5 HOH B 24 424 22 HOH HOH . H 5 HOH B 25 425 31 HOH HOH . H 5 HOH B 26 426 58 HOH HOH . H 5 HOH B 27 427 182 HOH HOH . H 5 HOH B 28 428 33 HOH HOH . H 5 HOH B 29 429 219 HOH HOH . H 5 HOH B 30 430 92 HOH HOH . H 5 HOH B 31 431 228 HOH HOH . H 5 HOH B 32 432 236 HOH HOH . H 5 HOH B 33 433 63 HOH HOH . H 5 HOH B 34 434 76 HOH HOH . H 5 HOH B 35 435 43 HOH HOH . H 5 HOH B 36 436 59 HOH HOH . H 5 HOH B 37 437 146 HOH HOH . H 5 HOH B 38 438 242 HOH HOH . H 5 HOH B 39 439 194 HOH HOH . H 5 HOH B 40 440 71 HOH HOH . H 5 HOH B 41 441 13 HOH HOH . H 5 HOH B 42 442 178 HOH HOH . H 5 HOH B 43 443 24 HOH HOH . H 5 HOH B 44 444 17 HOH HOH . H 5 HOH B 45 445 23 HOH HOH . H 5 HOH B 46 446 107 HOH HOH . H 5 HOH B 47 447 148 HOH HOH . H 5 HOH B 48 448 57 HOH HOH . H 5 HOH B 49 449 144 HOH HOH . H 5 HOH B 50 450 119 HOH HOH . H 5 HOH B 51 451 157 HOH HOH . H 5 HOH B 52 452 9 HOH HOH . H 5 HOH B 53 453 67 HOH HOH . H 5 HOH B 54 454 233 HOH HOH . H 5 HOH B 55 455 185 HOH HOH . H 5 HOH B 56 456 205 HOH HOH . H 5 HOH B 57 457 12 HOH HOH . H 5 HOH B 58 458 126 HOH HOH . H 5 HOH B 59 459 77 HOH HOH . H 5 HOH B 60 460 113 HOH HOH . H 5 HOH B 61 461 202 HOH HOH . H 5 HOH B 62 462 34 HOH HOH . H 5 HOH B 63 463 169 HOH HOH . H 5 HOH B 64 464 25 HOH HOH . H 5 HOH B 65 465 56 HOH HOH . H 5 HOH B 66 466 19 HOH HOH . H 5 HOH B 67 467 89 HOH HOH . H 5 HOH B 68 468 183 HOH HOH . H 5 HOH B 69 469 179 HOH HOH . H 5 HOH B 70 470 226 HOH HOH . H 5 HOH B 71 471 30 HOH HOH . H 5 HOH B 72 472 83 HOH HOH . H 5 HOH B 73 473 68 HOH HOH . H 5 HOH B 74 474 101 HOH HOH . H 5 HOH B 75 475 36 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 O6 JB2 . . . D 3 -7.858 10.286 29.949 1 29.89 ? O6 JB2 302 A 1 HETATM 2 C C6 JB2 . . . D 3 -6.886 10.791 30.516 1 31.09 ? C6 JB2 302 A 1 HETATM 3 C C5 JB2 . . . D 3 -6.08 11.672 29.771 1 32.19 ? C5 JB2 302 A 1 HETATM 4 N N7 JB2 . . . D 3 -6.139 12.117 28.49 1 31.23 ? N7 JB2 302 A 1 HETATM 5 C C8 JB2 . . . D 3 -5.093 12.95 28.317 1 30.2 ? C8 JB2 302 A 1 HETATM 6 N N1 JB2 . . . D 3 -6.583 10.505 31.808 1 29.46 ? N1 JB2 302 A 1 HETATM 7 C C2 JB2 . . . D 3 -5.482 11.061 32.396 1 29.16 ? C2 JB2 302 A 1 HETATM 8 N N2 JB2 . . . D 3 -5.191 10.76 33.668 1 27.02 ? N2 JB2 302 A 1 HETATM 9 N N3 JB2 . . . D 3 -4.671 11.942 31.713 1 29.99 ? N3 JB2 302 A 1 HETATM 10 C C4 JB2 . . . D 3 -4.958 12.251 30.396 1 30.2 ? C4 JB2 302 A 1 HETATM 11 N N9 JB2 . . . D 3 -4.386 13.031 29.474 1 30.21 ? N9 JB2 302 A 1 HETATM 12 C C1' JB2 . . . D 3 -3.136 13.842 29.681 1 30.65 ? C1' JB2 302 A 1 HETATM 13 O O4' JB2 . . . D 3 -3.178 15.131 29.044 1 30.07 ? O4' JB2 302 A 1 HETATM 14 C C2' JB2 . . . D 3 -1.919 13.122 29.098 1 29.2 ? C2' JB2 302 A 1 HETATM 15 O O2' JB2 . . . D 3 -0.957 13.068 30.148 1 28.31 ? O2' JB2 302 A 1 HETATM 16 C C3' JB2 . . . D 3 -1.487 13.937 27.881 1 29.36 ? C3' JB2 302 A 1 HETATM 17 O O3' JB2 . . . D 3 -0.069 13.992 27.583 1 29.89 ? O3' JB2 302 A 1 HETATM 18 C C4' JB2 . . . D 3 -2.016 15.321 28.235 1 29.75 ? C4' JB2 302 A 1 HETATM 19 C C5' JB2 . . . D 3 -2.384 16.173 27.037 1 31.48 ? C5' JB2 302 A 1 HETATM 20 O O5' JB2 . . . D 3 -3.419 15.528 26.3 1 33.76 ? O5' JB2 302 A 1 HETATM 21 P P JB2 . . . D 3 -3.596 15.843 24.746 1 35.72 ? P JB2 302 A 1 HETATM 22 O O1P JB2 . . . D 3 -4.655 14.921 24.187 1 32.23 ? O1P JB2 302 A 1 HETATM 23 O O2P JB2 . . . D 3 -3.932 17.318 24.651 1 32.8 ? O2P JB2 302 A 1 HETATM 24 O OPP JB2 . . . D 3 -2.175 15.577 24.009 1 37.58 ? OPP JB2 302 A 1 HETATM 25 P P2 JB2 . . . D 3 -1.795 14.257 23.138 1 40.33 ? P2 JB2 302 A 1 HETATM 26 O O3P JB2 . . . D 3 -0.414 14.49 22.54 1 39.82 ? O3P JB2 302 A 1 HETATM 27 O O4P JB2 . . . D 3 -1.629 13.009 23.992 1 39.1 ? O4P JB2 302 A 1 HETATM 28 O O1G JB2 . . . D 3 -2.952 13.951 22.01 1 44.66 ? O1G JB2 302 A 1 HETATM 29 C C1G JB2 . . . D 3 -3.38 14.742 20.877 1 46.54 ? C1G JB2 302 A 1 HETATM 30 O O5G JB2 . . . D 3 -2.242 15.088 20.086 1 52.09 ? O5G JB2 302 A 1 HETATM 31 C C5G JB2 . . . D 3 -1.48 13.925 19.702 1 52.41 ? C5G JB2 302 A 1 HETATM 32 C C6G JB2 . . . D 3 -0.024 14.313 19.386 1 52.78 ? C6G JB2 302 A 1 HETATM 33 C C2G JB2 . . . D 3 -4.388 13.983 19.981 1 47.18 ? C2G JB2 302 A 1 HETATM 34 O O2G JB2 . . . D 3 -5.018 14.893 19.068 1 43.02 ? O2G JB2 302 A 1 HETATM 35 C C3G JB2 . . . D 3 -3.726 12.823 19.204 1 49.24 ? C3G JB2 302 A 1 HETATM 36 O O3G JB2 . . . D 3 -4.587 12.332 18.17 1 47.2 ? O3G JB2 302 A 1 HETATM 37 C C4G JB2 . . . D 3 -2.326 13.204 18.629 1 51.98 ? C4G JB2 302 A 1 HETATM 38 N N4A JB2 . . . D 3 -1.581 12.05 18.062 1 51.05 ? N4A JB2 302 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 487 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 38 #