data_8D5B # _model_server_result.job_id TgVzTx9o6TCsDYGlx-N54A _model_server_result.datetime_utc '2024-11-21 17:34:46' _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 8d5b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 8D5B # _exptl.entry_id 8D5B _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 90 _cell.angle_gamma 120 _cell.entry_id 8D5B _cell.length_a 86.034 _cell.length_b 86.034 _cell.length_c 65.483 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8D5B _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall 'P 61' _symmetry.space_group_name_H-M 'P 61' # _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,D,E,F,G,H,I _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 300 n n N HN1 SAH sing 301 n n N HN2 SAH sing 302 n n CA CB SAH sing 303 n n CA C SAH sing 304 n n CA HA SAH sing 305 n n CB CG SAH sing 306 n n CB HB1 SAH sing 307 n n CB HB2 SAH sing 308 n n CG SD SAH sing 309 n n CG HG1 SAH sing 310 n n CG HG2 SAH sing 311 n n SD C5' SAH sing 312 n n C O SAH doub 313 n n C OXT SAH sing 314 n n OXT HXT SAH sing 315 n n C5' C4' SAH sing 316 n n C5' "H5'1" SAH sing 317 n n C5' "H5'2" SAH sing 318 n n C4' O4' SAH sing 319 n n C4' C3' SAH sing 320 n n C4' H4' SAH sing 321 n n O4' C1' SAH sing 322 n n C3' O3' SAH sing 323 n n C3' C2' SAH sing 324 n n C3' H3' SAH sing 325 n n O3' HO3' SAH sing 326 n n C2' O2' SAH sing 327 n n C2' C1' SAH sing 328 n n C2' H2' SAH sing 329 n n O2' HO2' SAH sing 330 n n C1' N9 SAH sing 331 n n C1' H1' SAH sing 332 n n N9 C8 SAH sing 333 n y N9 C4 SAH sing 334 n y C8 N7 SAH doub 335 n y C8 H8 SAH sing 336 n n N7 C5 SAH sing 337 n y C5 C6 SAH sing 338 n y C5 C4 SAH doub 339 n y C6 N6 SAH sing 340 n n C6 N1 SAH doub 341 n y N6 HN61 SAH sing 342 n n N6 HN62 SAH sing 343 n n N1 C2 SAH sing 344 n y C2 N3 SAH doub 345 n y C2 H2 SAH sing 346 n n N3 C4 SAH sing 347 n y # _atom_sites.entry_id 8D5B _atom_sites.fract_transf_matrix[1][1] 0.011623 _atom_sites.fract_transf_matrix[1][2] 0.006711 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013421 _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] 0.015271 _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 1 SAH SAH . C 3 SO4 A 1 302 2 SO4 SO4 . D 4 GOL A 1 303 3 GOL GOL . E 5 CL A 1 304 4 CL CL . F 6 CAC A 1 305 5 CAC CAC . G 3 SO4 A 1 306 6 SO4 SO4 . H 4 GOL A 1 307 302 GOL GOL . I 7 HOH A 1 401 188 HOH HOH . I 7 HOH A 2 402 28 HOH HOH . I 7 HOH A 3 403 186 HOH HOH . I 7 HOH A 4 404 111 HOH HOH . I 7 HOH A 5 405 71 HOH HOH . I 7 HOH A 6 406 50 HOH HOH . I 7 HOH A 7 407 76 HOH HOH . I 7 HOH A 8 408 47 HOH HOH . I 7 HOH A 9 409 94 HOH HOH . I 7 HOH A 10 410 9 HOH HOH . I 7 HOH A 11 411 98 HOH HOH . I 7 HOH A 12 412 73 HOH HOH . I 7 HOH A 13 413 8 HOH HOH . I 7 HOH A 14 414 133 HOH HOH . I 7 HOH A 15 415 115 HOH HOH . I 7 HOH A 16 416 30 HOH HOH . I 7 HOH A 17 417 53 HOH HOH . I 7 HOH A 18 418 110 HOH HOH . I 7 HOH A 19 419 44 HOH HOH . I 7 HOH A 20 420 41 HOH HOH . I 7 HOH A 21 421 77 HOH HOH . I 7 HOH A 22 422 74 HOH HOH . I 7 HOH A 23 423 2 HOH HOH . I 7 HOH A 24 424 38 HOH HOH . I 7 HOH A 25 425 90 HOH HOH . I 7 HOH A 26 426 7 HOH HOH . I 7 HOH A 27 427 118 HOH HOH . I 7 HOH A 28 428 137 HOH HOH . I 7 HOH A 29 429 27 HOH HOH . I 7 HOH A 30 430 37 HOH HOH . I 7 HOH A 31 431 59 HOH HOH . I 7 HOH A 32 432 3 HOH HOH . I 7 HOH A 33 433 17 HOH HOH . I 7 HOH A 34 434 15 HOH HOH . I 7 HOH A 35 435 10 HOH HOH . I 7 HOH A 36 436 178 HOH HOH . I 7 HOH A 37 437 60 HOH HOH . I 7 HOH A 38 438 5 HOH HOH . I 7 HOH A 39 439 39 HOH HOH . I 7 HOH A 40 440 26 HOH HOH . I 7 HOH A 41 441 33 HOH HOH . I 7 HOH A 42 442 80 HOH HOH . I 7 HOH A 43 443 72 HOH HOH . I 7 HOH A 44 444 79 HOH HOH . I 7 HOH A 45 445 19 HOH HOH . I 7 HOH A 46 446 89 HOH HOH . I 7 HOH A 47 447 177 HOH HOH . I 7 HOH A 48 448 12 HOH HOH . I 7 HOH A 49 449 55 HOH HOH . I 7 HOH A 50 450 32 HOH HOH . I 7 HOH A 51 451 4 HOH HOH . I 7 HOH A 52 452 120 HOH HOH . I 7 HOH A 53 453 11 HOH HOH . I 7 HOH A 54 454 36 HOH HOH . I 7 HOH A 55 455 189 HOH HOH . I 7 HOH A 56 456 83 HOH HOH . I 7 HOH A 57 457 40 HOH HOH . I 7 HOH A 58 458 108 HOH HOH . I 7 HOH A 59 459 31 HOH HOH . I 7 HOH A 60 460 23 HOH HOH . I 7 HOH A 61 461 35 HOH HOH . I 7 HOH A 62 462 113 HOH HOH . I 7 HOH A 63 463 104 HOH HOH . I 7 HOH A 64 464 24 HOH HOH . I 7 HOH A 65 465 48 HOH HOH . I 7 HOH A 66 466 25 HOH HOH . I 7 HOH A 67 467 54 HOH HOH . I 7 HOH A 68 468 187 HOH HOH . I 7 HOH A 69 469 29 HOH HOH . I 7 HOH A 70 470 21 HOH HOH . I 7 HOH A 71 471 57 HOH HOH . I 7 HOH A 72 472 95 HOH HOH . I 7 HOH A 73 473 190 HOH HOH . I 7 HOH A 74 474 68 HOH HOH . I 7 HOH A 75 475 136 HOH HOH . I 7 HOH A 76 476 22 HOH HOH . I 7 HOH A 77 477 87 HOH HOH . I 7 HOH A 78 478 66 HOH HOH . I 7 HOH A 79 479 6 HOH HOH . I 7 HOH A 80 480 162 HOH HOH . I 7 HOH A 81 481 141 HOH HOH . I 7 HOH A 82 482 63 HOH HOH . I 7 HOH A 83 483 52 HOH HOH . I 7 HOH A 84 484 107 HOH HOH . I 7 HOH A 85 485 146 HOH HOH . I 7 HOH A 86 486 93 HOH HOH . I 7 HOH A 87 487 45 HOH HOH . I 7 HOH A 88 488 82 HOH HOH . I 7 HOH A 89 489 179 HOH HOH . I 7 HOH A 90 490 193 HOH HOH . I 7 HOH A 91 491 18 HOH HOH . I 7 HOH A 92 492 62 HOH HOH . I 7 HOH A 93 493 97 HOH HOH . I 7 HOH A 94 494 92 HOH HOH . I 7 HOH A 95 495 16 HOH HOH . I 7 HOH A 96 496 122 HOH HOH . I 7 HOH A 97 497 14 HOH HOH . I 7 HOH A 98 498 142 HOH HOH . I 7 HOH A 99 499 119 HOH HOH . I 7 HOH A 100 500 58 HOH HOH . I 7 HOH A 101 501 81 HOH HOH . I 7 HOH A 102 502 174 HOH HOH . I 7 HOH A 103 503 65 HOH HOH . I 7 HOH A 104 504 100 HOH HOH . I 7 HOH A 105 505 176 HOH HOH . I 7 HOH A 106 506 127 HOH HOH . I 7 HOH A 107 507 103 HOH HOH . I 7 HOH A 108 508 164 HOH HOH . I 7 HOH A 109 509 99 HOH HOH . I 7 HOH A 110 510 195 HOH HOH . I 7 HOH A 111 511 85 HOH HOH . I 7 HOH A 112 512 185 HOH HOH . I 7 HOH A 113 513 191 HOH HOH . I 7 HOH A 114 514 132 HOH HOH . I 7 HOH A 115 515 88 HOH HOH . I 7 HOH A 116 516 165 HOH HOH . I 7 HOH A 117 517 126 HOH HOH . I 7 HOH A 118 518 157 HOH HOH . I 7 HOH A 119 519 84 HOH HOH . I 7 HOH A 120 520 192 HOH HOH . I 7 HOH A 121 521 91 HOH HOH . I 7 HOH A 122 522 147 HOH HOH . I 7 HOH A 123 523 144 HOH HOH . I 7 HOH A 124 524 143 HOH HOH . I 7 HOH A 125 525 194 HOH HOH . I 7 HOH A 126 526 75 HOH HOH . I 7 HOH A 127 527 78 HOH HOH . I 7 HOH A 128 528 160 HOH HOH . I 7 HOH A 129 529 170 HOH HOH . I 7 HOH A 130 530 140 HOH HOH . I 7 HOH A 131 531 155 HOH HOH . I 7 HOH A 132 532 149 HOH HOH . I 7 HOH A 133 533 148 HOH HOH . I 7 HOH A 134 534 51 HOH HOH . I 7 HOH A 135 535 117 HOH HOH . I 7 HOH A 136 536 153 HOH HOH . I 7 HOH A 137 537 69 HOH HOH . I 7 HOH A 138 538 20 HOH HOH . I 7 HOH A 139 539 46 HOH HOH . I 7 HOH A 140 540 161 HOH HOH . I 7 HOH A 141 541 134 HOH HOH . I 7 HOH A 142 542 49 HOH HOH . I 7 HOH A 143 543 106 HOH HOH . I 7 HOH A 144 544 152 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 -38.431 13.264 5.928 1 23.06 ? N SAH 301 A 1 HETATM 2 C CA SAH . . . B 2 -39.632 13.979 5.507 1 27.47 ? CA SAH 301 A 1 HETATM 3 C CB SAH . . . B 2 -40.901 13.22 5.866 1 25.96 ? CB SAH 301 A 1 HETATM 4 C CG SAH . . . B 2 -40.951 12.764 7.329 1 27.26 ? CG SAH 301 A 1 HETATM 5 S SD SAH . . . B 2 -42.584 12.069 7.792 1 32.14 ? SD SAH 301 A 1 HETATM 6 C C SAH . . . B 2 -39.666 15.348 6.16 1 35.33 ? C SAH 301 A 1 HETATM 7 O O SAH . . . B 2 -38.797 15.652 6.979 1 25.29 ? O SAH 301 A 1 HETATM 8 O OXT SAH . . . B 2 -40.564 16.15 5.898 1 27.01 ? OXT SAH 301 A 1 HETATM 9 C C5' SAH . . . B 2 -42.04 10.351 7.617 1 27.37 ? C5' SAH 301 A 1 HETATM 10 C C4' SAH . . . B 2 -42.093 9.819 6.181 1 29.31 ? C4' SAH 301 A 1 HETATM 11 O O4' SAH . . . B 2 -41.656 8.464 6.15 1 33.52 ? O4' SAH 301 A 1 HETATM 12 C C3' SAH . . . B 2 -43.493 9.819 5.597 1 27.29 ? C3' SAH 301 A 1 HETATM 13 O O3' SAH . . . B 2 -43.486 10.406 4.307 1 29.16 ? O3' SAH 301 A 1 HETATM 14 C C2' SAH . . . B 2 -43.847 8.346 5.459 1 34.24 ? C2' SAH 301 A 1 HETATM 15 O O2' SAH . . . B 2 -44.754 8.107 4.395 1 30.24 ? O2' SAH 301 A 1 HETATM 16 C C1' SAH . . . B 2 -42.464 7.73 5.256 1 30.18 ? C1' SAH 301 A 1 HETATM 17 N N9 SAH . . . B 2 -42.38 6.288 5.578 1 28.17 ? N9 SAH 301 A 1 HETATM 18 C C8 SAH . . . B 2 -42.964 5.599 6.612 1 30.88 ? C8 SAH 301 A 1 HETATM 19 N N7 SAH . . . B 2 -42.625 4.285 6.518 1 30.54 ? N7 SAH 301 A 1 HETATM 20 C C5 SAH . . . B 2 -41.827 4.13 5.442 1 30.72 ? C5 SAH 301 A 1 HETATM 21 C C6 SAH . . . B 2 -41.197 3.025 4.886 1 35.82 ? C6 SAH 301 A 1 HETATM 22 N N6 SAH . . . B 2 -41.323 1.813 5.431 1 31.51 ? N6 SAH 301 A 1 HETATM 23 N N1 SAH . . . B 2 -40.421 3.196 3.756 1 31.65 ? N1 SAH 301 A 1 HETATM 24 C C2 SAH . . . B 2 -40.281 4.446 3.176 1 33.73 ? C2 SAH 301 A 1 HETATM 25 N N3 SAH . . . B 2 -40.915 5.541 3.733 1 25.39 ? N3 SAH 301 A 1 HETATM 26 C C4 SAH . . . B 2 -41.668 5.384 4.846 1 28.7 ? C4 SAH 301 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 26 #