data_8PEM # _model_server_result.job_id 6pHlUnjLjhR5ZzFxHwDCSA _model_server_result.datetime_utc '2025-07-10 04:48:27' _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 8pem # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 8PEM # _exptl.entry_id 8PEM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _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 96.25 _cell.angle_gamma 90 _cell.entry_id 8PEM _cell.length_a 39.556 _cell.length_b 41.016 _cell.length_c 69.035 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8PEM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OG SER 150 A SER 156 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc2 B O1A AT9 . A AT9 301 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc3 B O1B AT9 . A AT9 301 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? metalc ? metalc4 B O3B AT9 . A AT9 301 1_555 E MG MG . A MG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? # _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 329 n n N HN1 SAH sing 330 n n N HN2 SAH sing 331 n n CA CB SAH sing 332 n n CA C SAH sing 333 n n CA HA SAH sing 334 n n CB CG SAH sing 335 n n CB HB1 SAH sing 336 n n CB HB2 SAH sing 337 n n CG SD SAH sing 338 n n CG HG1 SAH sing 339 n n CG HG2 SAH sing 340 n n SD C5' SAH sing 341 n n C O SAH doub 342 n n C OXT SAH sing 343 n n OXT HXT SAH sing 344 n n C5' C4' SAH sing 345 n n C5' "H5'1" SAH sing 346 n n C5' "H5'2" SAH sing 347 n n C4' O4' SAH sing 348 n n C4' C3' SAH sing 349 n n C4' H4' SAH sing 350 n n O4' C1' SAH sing 351 n n C3' O3' SAH sing 352 n n C3' C2' SAH sing 353 n n C3' H3' SAH sing 354 n n O3' HO3' SAH sing 355 n n C2' O2' SAH sing 356 n n C2' C1' SAH sing 357 n n C2' H2' SAH sing 358 n n O2' HO2' SAH sing 359 n n C1' N9 SAH sing 360 n n C1' H1' SAH sing 361 n n N9 C8 SAH sing 362 n y N9 C4 SAH sing 363 n y C8 N7 SAH doub 364 n y C8 H8 SAH sing 365 n n N7 C5 SAH sing 366 n y C5 C6 SAH sing 367 n y C5 C4 SAH doub 368 n y C6 N6 SAH sing 369 n n C6 N1 SAH doub 370 n y N6 HN61 SAH sing 371 n n N6 HN62 SAH sing 372 n n N1 C2 SAH sing 373 n y C2 N3 SAH doub 374 n y C2 H2 SAH sing 375 n n N3 C4 SAH sing 376 n y # _atom_sites.entry_id 8PEM _atom_sites.fract_transf_matrix[1][1] 0.025281 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002769 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024381 _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] 0.014572 _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 AT9 A 1 301 271 AT9 AT9 . C 3 SAH A 1 302 272 SAH SAH . D 4 SO4 A 1 303 273 SO4 SO4 . E 5 MG A 1 304 274 MG MG . F 6 HOH A 1 401 71 HOH HOH . F 6 HOH A 2 402 44 HOH HOH . F 6 HOH A 3 403 39 HOH HOH . F 6 HOH A 4 404 77 HOH HOH . F 6 HOH A 5 405 93 HOH HOH . F 6 HOH A 6 406 36 HOH HOH . F 6 HOH A 7 407 41 HOH HOH . F 6 HOH A 8 408 28 HOH HOH . F 6 HOH A 9 409 47 HOH HOH . F 6 HOH A 10 410 46 HOH HOH . F 6 HOH A 11 411 1 HOH HOH . F 6 HOH A 12 412 55 HOH HOH . F 6 HOH A 13 413 57 HOH HOH . F 6 HOH A 14 414 75 HOH HOH . F 6 HOH A 15 415 91 HOH HOH . F 6 HOH A 16 416 29 HOH HOH . F 6 HOH A 17 417 16 HOH HOH . F 6 HOH A 18 418 27 HOH HOH . F 6 HOH A 19 419 19 HOH HOH . F 6 HOH A 20 420 13 HOH HOH . F 6 HOH A 21 421 49 HOH HOH . F 6 HOH A 22 422 6 HOH HOH . F 6 HOH A 23 423 18 HOH HOH . F 6 HOH A 24 424 14 HOH HOH . F 6 HOH A 25 425 7 HOH HOH . F 6 HOH A 26 426 89 HOH HOH . F 6 HOH A 27 427 26 HOH HOH . F 6 HOH A 28 428 24 HOH HOH . F 6 HOH A 29 429 25 HOH HOH . F 6 HOH A 30 430 9 HOH HOH . F 6 HOH A 31 431 65 HOH HOH . F 6 HOH A 32 432 2 HOH HOH . F 6 HOH A 33 433 72 HOH HOH . F 6 HOH A 34 434 38 HOH HOH . F 6 HOH A 35 435 74 HOH HOH . F 6 HOH A 36 436 63 HOH HOH . F 6 HOH A 37 437 20 HOH HOH . F 6 HOH A 38 438 22 HOH HOH . F 6 HOH A 39 439 54 HOH HOH . F 6 HOH A 40 440 15 HOH HOH . F 6 HOH A 41 441 83 HOH HOH . F 6 HOH A 42 442 52 HOH HOH . F 6 HOH A 43 443 31 HOH HOH . F 6 HOH A 44 444 79 HOH HOH . F 6 HOH A 45 445 81 HOH HOH . F 6 HOH A 46 446 87 HOH HOH . F 6 HOH A 47 447 78 HOH HOH . F 6 HOH A 48 448 21 HOH HOH . F 6 HOH A 49 449 10 HOH HOH . F 6 HOH A 50 450 69 HOH HOH . F 6 HOH A 51 451 58 HOH HOH . F 6 HOH A 52 452 32 HOH HOH . F 6 HOH A 53 453 5 HOH HOH . F 6 HOH A 54 454 45 HOH HOH . F 6 HOH A 55 455 68 HOH HOH . F 6 HOH A 56 456 59 HOH HOH . F 6 HOH A 57 457 67 HOH HOH . F 6 HOH A 58 458 4 HOH HOH . F 6 HOH A 59 459 8 HOH HOH . F 6 HOH A 60 460 85 HOH HOH . F 6 HOH A 61 461 90 HOH HOH . F 6 HOH A 62 462 42 HOH HOH . F 6 HOH A 63 463 43 HOH HOH . F 6 HOH A 64 464 50 HOH HOH . F 6 HOH A 65 465 3 HOH HOH . F 6 HOH A 66 466 17 HOH HOH . F 6 HOH A 67 467 70 HOH HOH . F 6 HOH A 68 468 80 HOH HOH . F 6 HOH A 69 469 51 HOH HOH . F 6 HOH A 70 470 30 HOH HOH . F 6 HOH A 71 471 73 HOH HOH . F 6 HOH A 72 472 76 HOH HOH . F 6 HOH A 73 473 82 HOH HOH . F 6 HOH A 74 474 23 HOH HOH . F 6 HOH A 75 475 33 HOH HOH . F 6 HOH A 76 476 64 HOH HOH . F 6 HOH A 77 477 12 HOH HOH . F 6 HOH A 78 478 86 HOH HOH . F 6 HOH A 79 479 11 HOH HOH . F 6 HOH A 80 480 61 HOH HOH . F 6 HOH A 81 481 92 HOH HOH . F 6 HOH A 82 482 53 HOH HOH . F 6 HOH A 83 483 40 HOH HOH . F 6 HOH A 84 484 62 HOH HOH . F 6 HOH A 85 485 48 HOH HOH . F 6 HOH A 86 486 37 HOH HOH . F 6 HOH A 87 487 60 HOH HOH . F 6 HOH A 88 488 84 HOH HOH . F 6 HOH A 89 489 94 HOH HOH . F 6 HOH A 90 490 35 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 . . . C 3 10.02 3.13 18.062 1 10.59 ? N SAH 302 A 1 HETATM 2 C CA SAH . . . C 3 10.199 1.691 17.723 1 8.29 ? CA SAH 302 A 1 HETATM 3 C CB SAH . . . C 3 8.897 1.098 17.174 1 13.59 ? CB SAH 302 A 1 HETATM 4 C CG SAH . . . C 3 7.652 1.921 17.487 1 13.04 ? CG SAH 302 A 1 HETATM 5 S SD SAH . . . C 3 6.08 1.145 17.002 1 22.4 ? SD SAH 302 A 1 HETATM 6 C C SAH . . . C 3 11.341 1.542 16.708 1 15.86 ? C SAH 302 A 1 HETATM 7 O O SAH . . . C 3 11.416 0.473 16.071 1 16.16 ? O SAH 302 A 1 HETATM 8 O OXT SAH . . . C 3 12.108 2.529 16.565 1 14.46 ? OXT SAH 302 A 1 HETATM 9 C C5' SAH . . . C 3 5.103 1.203 18.534 1 8.41 ? C5' SAH 302 A 1 HETATM 10 C C4' SAH . . . C 3 5.171 -0.129 19.257 1 13.52 ? C4' SAH 302 A 1 HETATM 11 O O4' SAH . . . C 3 4.464 -0.019 20.507 1 16.38 ? O4' SAH 302 A 1 HETATM 12 C C3' SAH . . . C 3 4.477 -1.231 18.448 1 14.35 ? C3' SAH 302 A 1 HETATM 13 O O3' SAH . . . C 3 5.385 -2.229 17.995 1 27.53 ? O3' SAH 302 A 1 HETATM 14 C C2' SAH . . . C 3 3.427 -1.802 19.409 1 24.77 ? C2' SAH 302 A 1 HETATM 15 O O2' SAH . . . C 3 3.456 -3.222 19.409 1 22.01 ? O2' SAH 302 A 1 HETATM 16 C C1' SAH . . . C 3 3.877 -1.272 20.762 1 14.92 ? C1' SAH 302 A 1 HETATM 17 N N9 SAH . . . C 3 2.782 -1.095 21.702 1 17.1 ? N9 SAH 302 A 1 HETATM 18 C C8 SAH . . . C 3 1.501 -0.698 21.412 1 17.68 ? C8 SAH 302 A 1 HETATM 19 N N7 SAH . . . C 3 0.702 -0.683 22.447 1 25.27 ? N7 SAH 302 A 1 HETATM 20 C C5 SAH . . . C 3 1.504 -1.098 23.493 1 22.94 ? C5 SAH 302 A 1 HETATM 21 C C6 SAH . . . C 3 1.247 -1.309 24.861 1 26.81 ? C6 SAH 302 A 1 HETATM 22 N N6 SAH . . . C 3 0.045 -1.131 25.412 1 14.01 ? N6 SAH 302 A 1 HETATM 23 N N1 SAH . . . C 3 2.265 -1.739 25.637 1 22.24 ? N1 SAH 302 A 1 HETATM 24 C C2 SAH . . . C 3 3.459 -1.943 25.066 1 20.66 ? C2 SAH 302 A 1 HETATM 25 N N3 SAH . . . C 3 3.816 -1.779 23.787 1 18.87 ? N3 SAH 302 A 1 HETATM 26 C C4 SAH . . . C 3 2.791 -1.355 23.051 1 22.82 ? C4 SAH 302 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #