data_5T39 # _model_server_result.job_id skIAzPSGtFIrbFGfoQQOow _model_server_result.datetime_utc '2024-10-28 02:33:12' _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 5t39 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5T39 # _exptl.entry_id 5T39 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 98.58 _cell.angle_gamma 90 _cell.entry_id 5T39 _cell.length_a 50.222 _cell.length_b 41.27 _cell.length_c 58.504 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5T39 _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _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 N CA SAH sing 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 5T39 _atom_sites.fract_transf_matrix[1][1] 0.019912 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003003 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024231 _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] 0.017286 _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 B 2 SAH A 1 301 234 SAH SAH . C 3 HOH A 1 401 74 HOH HOH . C 3 HOH A 2 402 124 HOH HOH . C 3 HOH A 3 403 187 HOH HOH . C 3 HOH A 4 404 152 HOH HOH . C 3 HOH A 5 405 177 HOH HOH . C 3 HOH A 6 406 178 HOH HOH . C 3 HOH A 7 407 35 HOH HOH . C 3 HOH A 8 408 84 HOH HOH . C 3 HOH A 9 409 173 HOH HOH . C 3 HOH A 10 410 69 HOH HOH . C 3 HOH A 11 411 93 HOH HOH . C 3 HOH A 12 412 56 HOH HOH . C 3 HOH A 13 413 85 HOH HOH . C 3 HOH A 14 414 19 HOH HOH . C 3 HOH A 15 415 181 HOH HOH . C 3 HOH A 16 416 9 HOH HOH . C 3 HOH A 17 417 109 HOH HOH . C 3 HOH A 18 418 102 HOH HOH . C 3 HOH A 19 419 42 HOH HOH . C 3 HOH A 20 420 14 HOH HOH . C 3 HOH A 21 421 79 HOH HOH . C 3 HOH A 22 422 167 HOH HOH . C 3 HOH A 23 423 26 HOH HOH . C 3 HOH A 24 424 49 HOH HOH . C 3 HOH A 25 425 135 HOH HOH . C 3 HOH A 26 426 53 HOH HOH . C 3 HOH A 27 427 120 HOH HOH . C 3 HOH A 28 428 17 HOH HOH . C 3 HOH A 29 429 121 HOH HOH . C 3 HOH A 30 430 70 HOH HOH . C 3 HOH A 31 431 32 HOH HOH . C 3 HOH A 32 432 29 HOH HOH . C 3 HOH A 33 433 5 HOH HOH . C 3 HOH A 34 434 28 HOH HOH . C 3 HOH A 35 435 16 HOH HOH . C 3 HOH A 36 436 33 HOH HOH . C 3 HOH A 37 437 170 HOH HOH . C 3 HOH A 38 438 18 HOH HOH . C 3 HOH A 39 439 48 HOH HOH . C 3 HOH A 40 440 40 HOH HOH . C 3 HOH A 41 441 99 HOH HOH . C 3 HOH A 42 442 34 HOH HOH . C 3 HOH A 43 443 116 HOH HOH . C 3 HOH A 44 444 164 HOH HOH . C 3 HOH A 45 445 51 HOH HOH . C 3 HOH A 46 446 20 HOH HOH . C 3 HOH A 47 447 180 HOH HOH . C 3 HOH A 48 448 157 HOH HOH . C 3 HOH A 49 449 126 HOH HOH . C 3 HOH A 50 450 166 HOH HOH . C 3 HOH A 51 451 65 HOH HOH . C 3 HOH A 52 452 150 HOH HOH . C 3 HOH A 53 453 139 HOH HOH . C 3 HOH A 54 454 95 HOH HOH . C 3 HOH A 55 455 77 HOH HOH . C 3 HOH A 56 456 98 HOH HOH . C 3 HOH A 57 457 13 HOH HOH . C 3 HOH A 58 458 129 HOH HOH . C 3 HOH A 59 459 148 HOH HOH . C 3 HOH A 60 460 113 HOH HOH . C 3 HOH A 61 461 110 HOH HOH . C 3 HOH A 62 462 44 HOH HOH . C 3 HOH A 63 463 8 HOH HOH . C 3 HOH A 64 464 11 HOH HOH . C 3 HOH A 65 465 1 HOH HOH . C 3 HOH A 66 466 96 HOH HOH . C 3 HOH A 67 467 112 HOH HOH . C 3 HOH A 68 468 2 HOH HOH . C 3 HOH A 69 469 73 HOH HOH . C 3 HOH A 70 470 140 HOH HOH . C 3 HOH A 71 471 146 HOH HOH . C 3 HOH A 72 472 39 HOH HOH . C 3 HOH A 73 473 87 HOH HOH . C 3 HOH A 74 474 91 HOH HOH . C 3 HOH A 75 475 47 HOH HOH . C 3 HOH A 76 476 137 HOH HOH . C 3 HOH A 77 477 72 HOH HOH . C 3 HOH A 78 478 43 HOH HOH . C 3 HOH A 79 479 62 HOH HOH . C 3 HOH A 80 480 71 HOH HOH . C 3 HOH A 81 481 94 HOH HOH . C 3 HOH A 82 482 55 HOH HOH . C 3 HOH A 83 483 4 HOH HOH . C 3 HOH A 84 484 24 HOH HOH . C 3 HOH A 85 485 136 HOH HOH . C 3 HOH A 86 486 52 HOH HOH . C 3 HOH A 87 487 149 HOH HOH . C 3 HOH A 88 488 172 HOH HOH . C 3 HOH A 89 489 31 HOH HOH . C 3 HOH A 90 490 3 HOH HOH . C 3 HOH A 91 491 162 HOH HOH . C 3 HOH A 92 492 75 HOH HOH . C 3 HOH A 93 493 59 HOH HOH . C 3 HOH A 94 494 145 HOH HOH . C 3 HOH A 95 495 169 HOH HOH . C 3 HOH A 96 496 25 HOH HOH . C 3 HOH A 97 497 86 HOH HOH . C 3 HOH A 98 498 104 HOH HOH . C 3 HOH A 99 499 88 HOH HOH . C 3 HOH A 100 500 160 HOH HOH . C 3 HOH A 101 501 147 HOH HOH . C 3 HOH A 102 502 168 HOH HOH . C 3 HOH A 103 503 143 HOH HOH . C 3 HOH A 104 504 21 HOH HOH . C 3 HOH A 105 505 127 HOH HOH . C 3 HOH A 106 506 83 HOH HOH . C 3 HOH A 107 507 27 HOH HOH . C 3 HOH A 108 508 64 HOH HOH . C 3 HOH A 109 509 54 HOH HOH . C 3 HOH A 110 510 103 HOH HOH . C 3 HOH A 111 511 119 HOH HOH . C 3 HOH A 112 512 111 HOH HOH . C 3 HOH A 113 513 118 HOH HOH . C 3 HOH A 114 514 50 HOH HOH . C 3 HOH A 115 515 61 HOH HOH . C 3 HOH A 116 516 155 HOH HOH . C 3 HOH A 117 517 60 HOH HOH . C 3 HOH A 118 518 45 HOH HOH . C 3 HOH A 119 519 128 HOH HOH . C 3 HOH A 120 520 38 HOH HOH . C 3 HOH A 121 521 142 HOH HOH . C 3 HOH A 122 522 10 HOH HOH . C 3 HOH A 123 523 106 HOH HOH . C 3 HOH A 124 524 182 HOH HOH . C 3 HOH A 125 525 105 HOH HOH . C 3 HOH A 126 526 131 HOH HOH . C 3 HOH A 127 527 123 HOH HOH . C 3 HOH A 128 528 67 HOH HOH . C 3 HOH A 129 529 30 HOH HOH . C 3 HOH A 130 530 68 HOH HOH . C 3 HOH A 131 531 12 HOH HOH . C 3 HOH A 132 532 15 HOH HOH . C 3 HOH A 133 533 176 HOH HOH . C 3 HOH A 134 534 41 HOH HOH . C 3 HOH A 135 535 36 HOH HOH . C 3 HOH A 136 536 130 HOH HOH . C 3 HOH A 137 537 81 HOH HOH . C 3 HOH A 138 538 6 HOH HOH . C 3 HOH A 139 539 92 HOH HOH . C 3 HOH A 140 540 37 HOH HOH . C 3 HOH A 141 541 159 HOH HOH . C 3 HOH A 142 542 115 HOH HOH . C 3 HOH A 143 543 138 HOH HOH . C 3 HOH A 144 544 82 HOH HOH . C 3 HOH A 145 545 63 HOH HOH . C 3 HOH A 146 546 76 HOH HOH . C 3 HOH A 147 547 175 HOH HOH . C 3 HOH A 148 548 165 HOH HOH . C 3 HOH A 149 549 188 HOH HOH . C 3 HOH A 150 550 107 HOH HOH . C 3 HOH A 151 551 66 HOH HOH . C 3 HOH A 152 552 7 HOH HOH . C 3 HOH A 153 553 23 HOH HOH . C 3 HOH A 154 554 183 HOH HOH . C 3 HOH A 155 555 97 HOH HOH . C 3 HOH A 156 556 117 HOH HOH . C 3 HOH A 157 557 78 HOH HOH . C 3 HOH A 158 558 179 HOH HOH . C 3 HOH A 159 559 100 HOH HOH . C 3 HOH A 160 560 185 HOH HOH . C 3 HOH A 161 561 184 HOH HOH . C 3 HOH A 162 562 133 HOH HOH . C 3 HOH A 163 563 134 HOH HOH . C 3 HOH A 164 564 158 HOH HOH . C 3 HOH A 165 565 194 HOH HOH . C 3 HOH A 166 566 189 HOH HOH . C 3 HOH A 167 567 192 HOH HOH . C 3 HOH A 168 568 46 HOH HOH . C 3 HOH A 169 569 193 HOH HOH . C 3 HOH A 170 570 161 HOH HOH . C 3 HOH A 171 571 90 HOH HOH . C 3 HOH A 172 572 108 HOH HOH . C 3 HOH A 173 573 80 HOH HOH . C 3 HOH A 174 574 89 HOH HOH . C 3 HOH A 175 575 191 HOH HOH . C 3 HOH A 176 576 22 HOH HOH . C 3 HOH A 177 577 186 HOH HOH . C 3 HOH A 178 578 154 HOH HOH . C 3 HOH A 179 579 144 HOH HOH . C 3 HOH A 180 580 114 HOH HOH . C 3 HOH A 181 581 57 HOH HOH . C 3 HOH A 182 582 125 HOH HOH . C 3 HOH A 183 583 101 HOH HOH . C 3 HOH A 184 584 190 HOH HOH . C 3 HOH A 185 585 156 HOH HOH . C 3 HOH A 186 586 132 HOH HOH . C 3 HOH A 187 587 163 HOH HOH . C 3 HOH A 188 588 122 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 N N SAH . . . B 2 100.124 5.916 70.219 1 10.59 ? N SAH 301 A 1 HETATM 2 C CA SAH . . . B 2 100.795 5.64 68.951 1 11.32 ? CA SAH 301 A 1 HETATM 3 C CB SAH . . . B 2 101.314 4.214 68.872 1 11.06 ? CB SAH 301 A 1 HETATM 4 C CG SAH . . . B 2 100.222 3.153 68.964 1 10.67 ? CG SAH 301 A 1 HETATM 5 S SD SAH . . . B 2 100.882 1.479 68.754 1 10.77 ? SD SAH 301 A 1 HETATM 6 C C SAH . . . B 2 99.837 5.885 67.802 1 13.39 ? C SAH 301 A 1 HETATM 7 O O SAH . . . B 2 100.236 5.834 66.633 1 17.21 ? O SAH 301 A 1 HETATM 8 O OXT SAH . . . B 2 98.656 6.118 68.052 1 12.03 ? OXT SAH 301 A 1 HETATM 9 C C5' SAH . . . B 2 100.829 0.947 70.485 1 9.59 ? C5' SAH 301 A 1 HETATM 10 C C4' SAH . . . B 2 101.982 1.465 71.341 1 8.83 ? C4' SAH 301 A 1 HETATM 11 O O4' SAH . . . B 2 101.653 1.197 72.705 1 8.86 ? O4' SAH 301 A 1 HETATM 12 C C3' SAH . . . B 2 103.305 0.777 71.045 1 8.65 ? C3' SAH 301 A 1 HETATM 13 O O3' SAH . . . B 2 104.402 1.662 71.144 1 9.03 ? O3' SAH 301 A 1 HETATM 14 C C2' SAH . . . B 2 103.341 -0.296 72.122 1 8.43 ? C2' SAH 301 A 1 HETATM 15 O O2' SAH . . . B 2 104.616 -0.822 72.447 1 8.77 ? O2' SAH 301 A 1 HETATM 16 C C1' SAH . . . B 2 102.683 0.427 73.286 1 8.26 ? C1' SAH 301 A 1 HETATM 17 N N9 SAH . . . B 2 102.091 -0.447 74.297 1 8.06 ? N9 SAH 301 A 1 HETATM 18 C C8 SAH . . . B 2 101.339 -1.574 74.086 1 8.96 ? C8 SAH 301 A 1 HETATM 19 N N7 SAH . . . B 2 100.937 -2.088 75.264 1 9.09 ? N7 SAH 301 A 1 HETATM 20 C C5 SAH . . . B 2 101.449 -1.286 76.235 1 7.84 ? C5 SAH 301 A 1 HETATM 21 C C6 SAH . . . B 2 101.385 -1.33 77.626 1 8.02 ? C6 SAH 301 A 1 HETATM 22 N N6 SAH . . . B 2 100.756 -2.287 78.303 1 8.56 ? N6 SAH 301 A 1 HETATM 23 N N1 SAH . . . B 2 102.008 -0.344 78.33 1 8.35 ? N1 SAH 301 A 1 HETATM 24 C C2 SAH . . . B 2 102.69 0.642 77.677 1 8.56 ? C2 SAH 301 A 1 HETATM 25 N N3 SAH . . . B 2 102.803 0.717 76.318 1 8.3 ? N3 SAH 301 A 1 HETATM 26 C C4 SAH . . . B 2 102.162 -0.253 75.637 1 7.87 ? C4 SAH 301 A 1 HETATM 27 H H2 SAH . . . B 2 103.173 1.415 78.276 1 10.28 ? H2 SAH 301 A 1 HETATM 28 H HN1 SAH . . . B 2 100.484 5.529 70.898 1 12.71 ? HN1 SAH 301 A 1 HETATM 29 H HN2 SAH . . . B 2 100.059 6.753 70.406 1 12.71 ? HN2 SAH 301 A 1 HETATM 30 H HA SAH . . . B 2 101.556 6.249 68.848 1 13.59 ? HA SAH 301 A 1 HETATM 31 H HB1 SAH . . . B 2 102.03 4.059 69.679 1 13.28 ? HB1 SAH 301 A 1 HETATM 32 H HB2 SAH . . . B 2 101.85 4.091 67.93 1 13.28 ? HB2 SAH 301 A 1 HETATM 33 H HG1 SAH . . . B 2 99.471 3.342 68.197 1 12.81 ? HG1 SAH 301 A 1 HETATM 34 H HG2 SAH . . . B 2 99.731 3.226 69.934 1 12.81 ? HG2 SAH 301 A 1 HETATM 35 H "H5'1" SAH . . . B 2 100.832 -0.143 70.517 1 11.51 ? "H5'1" SAH 301 A 1 HETATM 36 H "H5'2" SAH . . . B 2 99.889 1.28 70.925 1 11.51 ? "H5'2" SAH 301 A 1 HETATM 37 H H4' SAH . . . B 2 102.092 2.538 71.183 1 10.61 ? H4' SAH 301 A 1 HETATM 38 H H3' SAH . . . B 2 103.266 0.31 70.06 1 10.38 ? H3' SAH 301 A 1 HETATM 39 H HO3' SAH . . . B 2 104.968 1.397 71.899 1 10.84 ? HO3' SAH 301 A 1 HETATM 40 H H2' SAH . . . B 2 102.685 -1.109 71.812 1 10.12 ? H2' SAH 301 A 1 HETATM 41 H HO2' SAH . . . B 2 104.827 -0.612 73.38 1 10.52 ? HO2' SAH 301 A 1 HETATM 42 H H1' SAH . . . B 2 103.418 1.084 73.75 1 9.92 ? H1' SAH 301 A 1 HETATM 43 H H8 SAH . . . B 2 101.101 -1.992 73.108 1 10.75 ? H8 SAH 301 A 1 HETATM 44 H HN61 SAH . . . B 2 100.288 -3.038 77.806 1 10.28 ? HN61 SAH 301 A 1 HETATM 45 H HN62 SAH . . . B 2 100.747 -2.268 79.318 1 10.28 ? HN62 SAH 301 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 45 #