data_5YJI # _model_server_result.job_id '_bBwlQ1F8bX4DIO1HC1omQ' _model_server_result.datetime_utc '2024-11-15 09:55:56' _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 5yji # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 5YJI # _exptl.entry_id 5YJI _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 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 5YJI _cell.length_a 47.356 _cell.length_b 71.622 _cell.length_c 157.408 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YJI _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 C N N ? 2 E N 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 301 n n N HN1 SAH sing 302 n n N HN2 SAH sing 303 n n CA CB SAH sing 304 n n CA C SAH sing 305 n n CA HA SAH sing 306 n n CB CG SAH sing 307 n n CB HB1 SAH sing 308 n n CB HB2 SAH sing 309 n n CG SD SAH sing 310 n n CG HG1 SAH sing 311 n n CG HG2 SAH sing 312 n n SD C5' SAH sing 313 n n C O SAH doub 314 n n C OXT SAH sing 315 n n OXT HXT SAH sing 316 n n C5' C4' SAH sing 317 n n C5' "H5'1" SAH sing 318 n n C5' "H5'2" SAH sing 319 n n C4' O4' SAH sing 320 n n C4' C3' SAH sing 321 n n C4' H4' SAH sing 322 n n O4' C1' SAH sing 323 n n C3' O3' SAH sing 324 n n C3' C2' SAH sing 325 n n C3' H3' SAH sing 326 n n O3' HO3' SAH sing 327 n n C2' O2' SAH sing 328 n n C2' C1' SAH sing 329 n n C2' H2' SAH sing 330 n n O2' HO2' SAH sing 331 n n C1' N9 SAH sing 332 n n C1' H1' SAH sing 333 n n N9 C8 SAH sing 334 n y N9 C4 SAH sing 335 n y C8 N7 SAH doub 336 n y C8 H8 SAH sing 337 n n N7 C5 SAH sing 338 n y C5 C6 SAH sing 339 n y C5 C4 SAH doub 340 n y C6 N6 SAH sing 341 n n C6 N1 SAH doub 342 n y N6 HN61 SAH sing 343 n n N6 HN62 SAH sing 344 n n N1 C2 SAH sing 345 n y C2 N3 SAH doub 346 n y C2 H2 SAH sing 347 n n N3 C4 SAH sing 348 n y # _atom_sites.entry_id 5YJI _atom_sites.fract_transf_matrix[1][1] 0.021117 _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] 0.013962 _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] 0.006353 _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 SAH A 1 301 301 SAH SAH . D 3 8WO A 1 302 302 8WO UNL . E 2 SAH B 1 301 301 SAH SAH . F 3 8WO B 1 302 302 8WO UNL . G 4 HOH A 1 401 6 HOH HOH . G 4 HOH A 2 402 16 HOH HOH . G 4 HOH A 3 403 203 HOH HOH . G 4 HOH A 4 404 58 HOH HOH . G 4 HOH A 5 405 26 HOH HOH . G 4 HOH A 6 406 107 HOH HOH . G 4 HOH A 7 407 184 HOH HOH . G 4 HOH A 8 408 202 HOH HOH . G 4 HOH A 9 409 46 HOH HOH . G 4 HOH A 10 410 133 HOH HOH . G 4 HOH A 11 411 5 HOH HOH . G 4 HOH A 12 412 22 HOH HOH . G 4 HOH A 13 413 1 HOH HOH . G 4 HOH A 14 414 196 HOH HOH . G 4 HOH A 15 415 55 HOH HOH . G 4 HOH A 16 416 44 HOH HOH . G 4 HOH A 17 417 62 HOH HOH . G 4 HOH A 18 418 183 HOH HOH . G 4 HOH A 19 419 39 HOH HOH . G 4 HOH A 20 420 181 HOH HOH . G 4 HOH A 21 421 131 HOH HOH . G 4 HOH A 22 422 189 HOH HOH . G 4 HOH A 23 423 63 HOH HOH . G 4 HOH A 24 424 10 HOH HOH . G 4 HOH A 25 425 53 HOH HOH . G 4 HOH A 26 426 195 HOH HOH . G 4 HOH A 27 427 8 HOH HOH . G 4 HOH A 28 428 38 HOH HOH . G 4 HOH A 29 429 115 HOH HOH . G 4 HOH A 30 430 185 HOH HOH . G 4 HOH A 31 431 49 HOH HOH . G 4 HOH A 32 432 73 HOH HOH . G 4 HOH A 33 433 204 HOH HOH . G 4 HOH A 34 434 48 HOH HOH . G 4 HOH A 35 435 177 HOH HOH . G 4 HOH A 36 436 166 HOH HOH . G 4 HOH A 37 437 122 HOH HOH . G 4 HOH A 38 438 33 HOH HOH . G 4 HOH A 39 439 7 HOH HOH . G 4 HOH A 40 440 64 HOH HOH . G 4 HOH A 41 441 197 HOH HOH . G 4 HOH A 42 442 207 HOH HOH . G 4 HOH A 43 443 34 HOH HOH . G 4 HOH A 44 444 71 HOH HOH . G 4 HOH A 45 445 9 HOH HOH . G 4 HOH A 46 446 18 HOH HOH . G 4 HOH A 47 447 51 HOH HOH . G 4 HOH A 48 448 35 HOH HOH . G 4 HOH A 49 449 128 HOH HOH . G 4 HOH A 50 450 21 HOH HOH . G 4 HOH A 51 451 20 HOH HOH . G 4 HOH A 52 452 132 HOH HOH . G 4 HOH A 53 453 70 HOH HOH . G 4 HOH A 54 454 188 HOH HOH . G 4 HOH A 55 455 57 HOH HOH . G 4 HOH A 56 456 11 HOH HOH . G 4 HOH A 57 457 56 HOH HOH . G 4 HOH A 58 458 192 HOH HOH . G 4 HOH A 59 459 50 HOH HOH . G 4 HOH A 60 460 126 HOH HOH . G 4 HOH A 61 461 60 HOH HOH . G 4 HOH A 62 462 13 HOH HOH . G 4 HOH A 63 463 37 HOH HOH . G 4 HOH A 64 464 113 HOH HOH . G 4 HOH A 65 465 41 HOH HOH . G 4 HOH A 66 466 141 HOH HOH . G 4 HOH A 67 467 200 HOH HOH . G 4 HOH A 68 468 36 HOH HOH . G 4 HOH A 69 469 175 HOH HOH . G 4 HOH A 70 470 25 HOH HOH . G 4 HOH A 71 471 15 HOH HOH . G 4 HOH A 72 472 187 HOH HOH . G 4 HOH A 73 473 127 HOH HOH . G 4 HOH A 74 474 24 HOH HOH . G 4 HOH A 75 475 30 HOH HOH . G 4 HOH A 76 476 170 HOH HOH . G 4 HOH A 77 477 40 HOH HOH . G 4 HOH A 78 478 110 HOH HOH . G 4 HOH A 79 479 14 HOH HOH . G 4 HOH A 80 480 54 HOH HOH . G 4 HOH A 81 481 28 HOH HOH . G 4 HOH A 82 482 106 HOH HOH . G 4 HOH A 83 483 29 HOH HOH . G 4 HOH A 84 484 120 HOH HOH . G 4 HOH A 85 485 4 HOH HOH . G 4 HOH A 86 486 125 HOH HOH . G 4 HOH A 87 487 114 HOH HOH . G 4 HOH A 88 488 186 HOH HOH . G 4 HOH A 89 489 17 HOH HOH . G 4 HOH A 90 490 117 HOH HOH . G 4 HOH A 91 491 3 HOH HOH . G 4 HOH A 92 492 42 HOH HOH . G 4 HOH A 93 493 137 HOH HOH . G 4 HOH A 94 494 47 HOH HOH . G 4 HOH A 95 495 118 HOH HOH . G 4 HOH A 96 496 108 HOH HOH . G 4 HOH A 97 497 65 HOH HOH . G 4 HOH A 98 498 180 HOH HOH . G 4 HOH A 99 499 130 HOH HOH . G 4 HOH A 100 500 123 HOH HOH . G 4 HOH A 101 501 134 HOH HOH . G 4 HOH A 102 502 23 HOH HOH . G 4 HOH A 103 503 124 HOH HOH . G 4 HOH A 104 504 172 HOH HOH . G 4 HOH A 105 505 32 HOH HOH . G 4 HOH A 106 506 109 HOH HOH . G 4 HOH A 107 507 12 HOH HOH . G 4 HOH A 108 508 52 HOH HOH . G 4 HOH A 109 509 179 HOH HOH . G 4 HOH A 110 510 112 HOH HOH . G 4 HOH A 111 511 111 HOH HOH . G 4 HOH A 112 512 138 HOH HOH . G 4 HOH A 113 513 19 HOH HOH . G 4 HOH A 114 514 205 HOH HOH . G 4 HOH A 115 515 61 HOH HOH . G 4 HOH A 116 516 129 HOH HOH . G 4 HOH A 117 517 210 HOH HOH . G 4 HOH A 118 518 206 HOH HOH . G 4 HOH A 119 519 27 HOH HOH . G 4 HOH A 120 520 2 HOH HOH . G 4 HOH A 121 521 142 HOH HOH . G 4 HOH A 122 522 116 HOH HOH . G 4 HOH A 123 523 169 HOH HOH . G 4 HOH A 124 524 119 HOH HOH . G 4 HOH A 125 525 59 HOH HOH . G 4 HOH A 126 526 135 HOH HOH . G 4 HOH A 127 527 45 HOH HOH . G 4 HOH A 128 528 176 HOH HOH . G 4 HOH A 129 529 31 HOH HOH . G 4 HOH A 130 530 43 HOH HOH . G 4 HOH A 131 531 193 HOH HOH . H 4 HOH B 1 401 208 HOH HOH . H 4 HOH B 2 402 96 HOH HOH . H 4 HOH B 3 403 152 HOH HOH . H 4 HOH B 4 404 146 HOH HOH . H 4 HOH B 5 405 147 HOH HOH . H 4 HOH B 6 406 88 HOH HOH . H 4 HOH B 7 407 209 HOH HOH . H 4 HOH B 8 408 158 HOH HOH . H 4 HOH B 9 409 190 HOH HOH . H 4 HOH B 10 410 155 HOH HOH . H 4 HOH B 11 411 182 HOH HOH . H 4 HOH B 12 412 105 HOH HOH . H 4 HOH B 13 413 69 HOH HOH . H 4 HOH B 14 414 87 HOH HOH . H 4 HOH B 15 415 103 HOH HOH . H 4 HOH B 16 416 191 HOH HOH . H 4 HOH B 17 417 167 HOH HOH . H 4 HOH B 18 418 198 HOH HOH . H 4 HOH B 19 419 78 HOH HOH . H 4 HOH B 20 420 160 HOH HOH . H 4 HOH B 21 421 85 HOH HOH . H 4 HOH B 22 422 74 HOH HOH . H 4 HOH B 23 423 140 HOH HOH . H 4 HOH B 24 424 89 HOH HOH . H 4 HOH B 25 425 81 HOH HOH . H 4 HOH B 26 426 121 HOH HOH . H 4 HOH B 27 427 165 HOH HOH . H 4 HOH B 28 428 82 HOH HOH . H 4 HOH B 29 429 72 HOH HOH . H 4 HOH B 30 430 75 HOH HOH . H 4 HOH B 31 431 100 HOH HOH . H 4 HOH B 32 432 66 HOH HOH . H 4 HOH B 33 433 67 HOH HOH . H 4 HOH B 34 434 163 HOH HOH . H 4 HOH B 35 435 154 HOH HOH . H 4 HOH B 36 436 199 HOH HOH . H 4 HOH B 37 437 80 HOH HOH . H 4 HOH B 38 438 151 HOH HOH . H 4 HOH B 39 439 95 HOH HOH . H 4 HOH B 40 440 161 HOH HOH . H 4 HOH B 41 441 76 HOH HOH . H 4 HOH B 42 442 86 HOH HOH . H 4 HOH B 43 443 79 HOH HOH . H 4 HOH B 44 444 93 HOH HOH . H 4 HOH B 45 445 201 HOH HOH . H 4 HOH B 46 446 68 HOH HOH . H 4 HOH B 47 447 98 HOH HOH . H 4 HOH B 48 448 104 HOH HOH . H 4 HOH B 49 449 92 HOH HOH . H 4 HOH B 50 450 211 HOH HOH . H 4 HOH B 51 451 94 HOH HOH . H 4 HOH B 52 452 83 HOH HOH . H 4 HOH B 53 453 157 HOH HOH . H 4 HOH B 54 454 162 HOH HOH . H 4 HOH B 55 455 145 HOH HOH . H 4 HOH B 56 456 77 HOH HOH . H 4 HOH B 57 457 150 HOH HOH . H 4 HOH B 58 458 159 HOH HOH . H 4 HOH B 59 459 149 HOH HOH . H 4 HOH B 60 460 164 HOH HOH . H 4 HOH B 61 461 101 HOH HOH . H 4 HOH B 62 462 90 HOH HOH . H 4 HOH B 63 463 102 HOH HOH . H 4 HOH B 64 464 178 HOH HOH . H 4 HOH B 65 465 156 HOH HOH . H 4 HOH B 66 466 168 HOH HOH . H 4 HOH B 67 467 97 HOH HOH . H 4 HOH B 68 468 153 HOH HOH . H 4 HOH B 69 469 148 HOH HOH . H 4 HOH B 70 470 136 HOH HOH . H 4 HOH B 71 471 144 HOH HOH . H 4 HOH B 72 472 173 HOH HOH . H 4 HOH B 73 473 194 HOH HOH . H 4 HOH B 74 474 143 HOH HOH . H 4 HOH B 75 475 91 HOH HOH . H 4 HOH B 76 476 139 HOH HOH . H 4 HOH B 77 477 99 HOH HOH . H 4 HOH B 78 478 84 HOH HOH . H 4 HOH B 79 479 174 HOH HOH . H 4 HOH B 80 480 171 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 . . . E 2 18.37 7.49 51.36 0.91 15.76 ? N SAH 301 B 1 HETATM 2 C CA SAH . . . E 2 17.084 7.677 52.027 0.91 15.99 ? CA SAH 301 B 1 HETATM 3 C CB SAH . . . E 2 17.081 8.895 52.967 0.91 16.01 ? CB SAH 301 B 1 HETATM 4 C CG SAH . . . E 2 17.396 10.281 52.399 0.91 15.86 ? CG SAH 301 B 1 HETATM 5 S SD SAH . . . E 2 16.826 11.609 53.509 0.91 15.76 ? SD SAH 301 B 1 HETATM 6 C C SAH . . . E 2 15.956 7.694 50.996 0.91 16.23 ? C SAH 301 B 1 HETATM 7 O O SAH . . . E 2 16.2 7.503 49.802 0.91 16.66 ? O SAH 301 B 1 HETATM 8 O OXT SAH . . . E 2 14.785 7.87 51.319 0.91 16.16 ? OXT SAH 301 B 1 HETATM 9 C C5' SAH . . . E 2 18.381 12.533 53.422 0.93 16.71 ? C5' SAH 301 B 1 HETATM 10 C C4' SAH . . . E 2 19.506 11.943 54.276 0.93 17.56 ? C4' SAH 301 B 1 HETATM 11 O O4' SAH . . . E 2 20.715 12.664 54.125 0.93 18.09 ? O4' SAH 301 B 1 HETATM 12 C C3' SAH . . . E 2 19.196 11.939 55.766 0.93 18.52 ? C3' SAH 301 B 1 HETATM 13 O O3' SAH . . . E 2 19.204 10.602 56.217 0.93 18.09 ? O3' SAH 301 B 1 HETATM 14 C C2' SAH . . . E 2 20.317 12.75 56.401 0.93 18.77 ? C2' SAH 301 B 1 HETATM 15 O O2' SAH . . . E 2 20.745 12.219 57.63 0.93 19.85 ? O2' SAH 301 B 1 HETATM 16 C C1' SAH . . . E 2 21.408 12.626 55.363 0.93 20.04 ? C1' SAH 301 B 1 HETATM 17 N N9 SAH . . . E 2 22.446 13.666 55.441 0.91 20.55 ? N9 SAH 301 B 1 HETATM 18 C C8 SAH . . . E 2 22.285 15.004 55.705 0.91 21.17 ? C8 SAH 301 B 1 HETATM 19 N N7 SAH . . . E 2 23.5 15.598 55.666 0.91 21.16 ? N7 SAH 301 B 1 HETATM 20 C C5 SAH . . . E 2 24.436 14.665 55.385 0.91 21.06 ? C5 SAH 301 B 1 HETATM 21 C C6 SAH . . . E 2 25.821 14.727 55.228 0.91 21.18 ? C6 SAH 301 B 1 HETATM 22 N N6 SAH . . . E 2 26.479 15.879 55.359 0.91 20.82 ? N6 SAH 301 B 1 HETATM 23 N N1 SAH . . . E 2 26.522 13.571 54.932 0.91 21.16 ? N1 SAH 301 B 1 HETATM 24 C C2 SAH . . . E 2 25.855 12.365 54.796 0.91 21.05 ? C2 SAH 301 B 1 HETATM 25 N N3 SAH . . . E 2 24.482 12.31 54.953 0.91 20.53 ? N3 SAH 301 B 1 HETATM 26 C C4 SAH . . . E 2 23.782 13.443 55.234 0.91 21.13 ? C4 SAH 301 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #