data_3S7D # _model_server_result.job_id YrH8leB4cJ1vKeQeMWAWbQ _model_server_result.datetime_utc '2025-02-18 04:22:18' _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 3s7d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1000}' # _entry.id 3S7D # _exptl.entry_id 3S7D _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 90 _cell.angle_gamma 90 _cell.entry_id 3S7D _cell.length_a 153.835 _cell.length_b 153.835 _cell.length_c 52.727 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3S7D _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _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,I,J,K _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 covale ? covale1 B C LEU 4 I LEU 369 1_555 B N MLZ 5 I MLZ 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.353 ? covale ? covale2 B C MLZ 5 I MLZ 370 1_555 B N SER 6 I SER 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? metalc ? metalc1 A NE2 HIS 86 A HIS 86 1_555 H ZN ZN . A ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc2 A SG CYS 267 A CYS 267 1_555 I ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc3 A SG CYS 68 A CYS 68 1_555 H ZN ZN . A ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc4 A SG CYS 78 A CYS 78 1_555 G ZN ZN . A ZN 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc5 A SG CYS 90 A CYS 90 1_555 H ZN ZN . A ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc6 A SG CYS 262 A CYS 262 1_555 I ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc7 A SG CYS 52 A CYS 52 1_555 G ZN ZN . A ZN 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc8 A SG CYS 65 A CYS 65 1_555 H ZN ZN . A ZN 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc9 A SG CYS 55 A CYS 55 1_555 G ZN ZN . A ZN 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc10 A SG CYS 74 A CYS 74 1_555 G ZN ZN . A ZN 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc11 A SG CYS 264 A CYS 264 1_555 I ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc12 A SG CYS 209 A CYS 209 1_555 I ZN ZN . A ZN 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? # _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 ? # _atom_sites.entry_id 3S7D _atom_sites.fract_transf_matrix[1][1] 0.0065 _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] 0.0065 _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] 0.018966 _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 3 SAH A 1 1000 1000 SAH SAH . D 4 BU3 A 1 434 1 BU3 BU3 . E 4 BU3 A 1 435 2 BU3 BU3 . F 4 BU3 A 1 436 4 BU3 BU3 . G 5 ZN A 1 437 1 ZN ZN . H 5 ZN A 1 438 2 ZN ZN . I 5 ZN A 1 439 3 ZN ZN . J 6 HOH A 1 440 1 HOH HOH . J 6 HOH A 2 441 2 HOH HOH . J 6 HOH A 3 442 3 HOH HOH . J 6 HOH A 4 443 4 HOH HOH . J 6 HOH A 5 444 5 HOH HOH . J 6 HOH A 6 445 6 HOH HOH . J 6 HOH A 7 446 7 HOH HOH . J 6 HOH A 8 447 8 HOH HOH . J 6 HOH A 9 448 9 HOH HOH . J 6 HOH A 10 449 10 HOH HOH . J 6 HOH A 11 450 11 HOH HOH . J 6 HOH A 12 451 12 HOH HOH . J 6 HOH A 13 452 13 HOH HOH . J 6 HOH A 14 453 14 HOH HOH . J 6 HOH A 15 454 15 HOH HOH . J 6 HOH A 16 455 16 HOH HOH . J 6 HOH A 17 456 17 HOH HOH . J 6 HOH A 18 457 18 HOH HOH . J 6 HOH A 19 458 19 HOH HOH . J 6 HOH A 20 459 20 HOH HOH . J 6 HOH A 21 460 21 HOH HOH . J 6 HOH A 22 461 22 HOH HOH . J 6 HOH A 23 462 23 HOH HOH . J 6 HOH A 24 463 24 HOH HOH . J 6 HOH A 25 464 25 HOH HOH . J 6 HOH A 26 465 26 HOH HOH . J 6 HOH A 27 466 27 HOH HOH . J 6 HOH A 28 467 28 HOH HOH . J 6 HOH A 29 468 29 HOH HOH . J 6 HOH A 30 469 30 HOH HOH . J 6 HOH A 31 470 31 HOH HOH . J 6 HOH A 32 471 32 HOH HOH . J 6 HOH A 33 472 33 HOH HOH . J 6 HOH A 34 473 34 HOH HOH . J 6 HOH A 35 474 35 HOH HOH . J 6 HOH A 36 475 36 HOH HOH . J 6 HOH A 37 476 37 HOH HOH . J 6 HOH A 38 477 38 HOH HOH . J 6 HOH A 39 478 39 HOH HOH . J 6 HOH A 40 479 40 HOH HOH . J 6 HOH A 41 480 41 HOH HOH . J 6 HOH A 42 481 42 HOH HOH . J 6 HOH A 43 482 43 HOH HOH . J 6 HOH A 44 483 44 HOH HOH . J 6 HOH A 45 484 45 HOH HOH . J 6 HOH A 46 485 46 HOH HOH . J 6 HOH A 47 486 47 HOH HOH . J 6 HOH A 48 487 48 HOH HOH . J 6 HOH A 49 488 49 HOH HOH . J 6 HOH A 50 489 50 HOH HOH . J 6 HOH A 51 490 51 HOH HOH . J 6 HOH A 52 491 52 HOH HOH . J 6 HOH A 53 492 53 HOH HOH . J 6 HOH A 54 493 54 HOH HOH . J 6 HOH A 55 494 55 HOH HOH . J 6 HOH A 56 495 56 HOH HOH . J 6 HOH A 57 496 57 HOH HOH . J 6 HOH A 58 497 58 HOH HOH . J 6 HOH A 59 498 59 HOH HOH . J 6 HOH A 60 499 60 HOH HOH . J 6 HOH A 61 500 61 HOH HOH . J 6 HOH A 62 501 62 HOH HOH . J 6 HOH A 63 502 63 HOH HOH . J 6 HOH A 64 503 64 HOH HOH . J 6 HOH A 65 504 65 HOH HOH . J 6 HOH A 66 505 66 HOH HOH . J 6 HOH A 67 506 67 HOH HOH . J 6 HOH A 68 507 68 HOH HOH . J 6 HOH A 69 508 69 HOH HOH . J 6 HOH A 70 509 70 HOH HOH . J 6 HOH A 71 510 71 HOH HOH . J 6 HOH A 72 511 72 HOH HOH . J 6 HOH A 73 512 73 HOH HOH . J 6 HOH A 74 513 74 HOH HOH . J 6 HOH A 75 514 75 HOH HOH . J 6 HOH A 76 515 76 HOH HOH . J 6 HOH A 77 516 77 HOH HOH . J 6 HOH A 78 517 78 HOH HOH . J 6 HOH A 79 518 80 HOH HOH . J 6 HOH A 80 519 81 HOH HOH . J 6 HOH A 81 520 82 HOH HOH . J 6 HOH A 82 521 83 HOH HOH . J 6 HOH A 83 522 84 HOH HOH . J 6 HOH A 84 523 85 HOH HOH . J 6 HOH A 85 524 86 HOH HOH . J 6 HOH A 86 525 87 HOH HOH . J 6 HOH A 87 526 88 HOH HOH . J 6 HOH A 88 527 89 HOH HOH . J 6 HOH A 89 528 90 HOH HOH . J 6 HOH A 90 529 91 HOH HOH . J 6 HOH A 91 530 92 HOH HOH . J 6 HOH A 92 531 93 HOH HOH . J 6 HOH A 93 532 94 HOH HOH . J 6 HOH A 94 533 95 HOH HOH . J 6 HOH A 95 534 96 HOH HOH . J 6 HOH A 96 535 97 HOH HOH . J 6 HOH A 97 536 98 HOH HOH . J 6 HOH A 98 537 99 HOH HOH . J 6 HOH A 99 538 100 HOH HOH . J 6 HOH A 100 539 101 HOH HOH . J 6 HOH A 101 540 102 HOH HOH . J 6 HOH A 102 541 103 HOH HOH . J 6 HOH A 103 542 104 HOH HOH . J 6 HOH A 104 543 105 HOH HOH . J 6 HOH A 105 544 106 HOH HOH . J 6 HOH A 106 545 108 HOH HOH . J 6 HOH A 107 546 109 HOH HOH . J 6 HOH A 108 547 111 HOH HOH . J 6 HOH A 109 548 112 HOH HOH . J 6 HOH A 110 549 113 HOH HOH . J 6 HOH A 111 550 114 HOH HOH . J 6 HOH A 112 551 115 HOH HOH . J 6 HOH A 113 552 116 HOH HOH . J 6 HOH A 114 553 117 HOH HOH . J 6 HOH A 115 554 118 HOH HOH . J 6 HOH A 116 555 119 HOH HOH . J 6 HOH A 117 556 120 HOH HOH . K 6 HOH I 1 79 79 HOH HOH . K 6 HOH I 2 107 107 HOH HOH . K 6 HOH I 3 110 110 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 -15.446 -57.599 -10.627 1 40.92 ? N SAH 1000 A 1 HETATM 2 C CA SAH . . . C 3 -14.289 -57.466 -11.561 1 40.65 ? CA SAH 1000 A 1 HETATM 3 C CB SAH . . . C 3 -14.154 -55.988 -12.082 1 38.93 ? CB SAH 1000 A 1 HETATM 4 C CG SAH . . . C 3 -15.032 -55.727 -13.317 1 37.69 ? CG SAH 1000 A 1 HETATM 5 S SD SAH . . . C 3 -14.336 -56.62 -14.723 1 36.12 ? SD SAH 1000 A 1 HETATM 6 C C SAH . . . C 3 -12.983 -57.986 -10.975 1 42.32 ? C SAH 1000 A 1 HETATM 7 O O SAH . . . C 3 -11.97 -57.898 -11.582 1 41.33 ? O SAH 1000 A 1 HETATM 8 O OXT SAH . . . C 3 -12.973 -58.516 -9.793 1 44.29 ? OXT SAH 1000 A 1 HETATM 9 C C5' SAH . . . C 3 -15.75 -57.532 -15.481 1 35.62 ? C5' SAH 1000 A 1 HETATM 10 C C4' SAH . . . C 3 -16.059 -58.794 -14.684 1 37.16 ? C4' SAH 1000 A 1 HETATM 11 O O4' SAH . . . C 3 -16.649 -58.482 -13.411 1 37.05 ? O4' SAH 1000 A 1 HETATM 12 C C3' SAH . . . C 3 -17.147 -59.595 -15.377 1 37.57 ? C3' SAH 1000 A 1 HETATM 13 O O3' SAH . . . C 3 -16.723 -60.337 -16.537 1 37.74 ? O3' SAH 1000 A 1 HETATM 14 C C2' SAH . . . C 3 -17.827 -60.357 -14.226 1 37.94 ? C2' SAH 1000 A 1 HETATM 15 O O2' SAH . . . C 3 -17.109 -61.516 -13.757 1 39.83 ? O2' SAH 1000 A 1 HETATM 16 C C1' SAH . . . C 3 -17.789 -59.295 -13.125 1 38.17 ? C1' SAH 1000 A 1 HETATM 17 N N9 SAH . . . C 3 -18.994 -58.419 -13.044 1 37.71 ? N9 SAH 1000 A 1 HETATM 18 C C8 SAH . . . C 3 -19.162 -57.133 -13.446 1 36.76 ? C8 SAH 1000 A 1 HETATM 19 N N7 SAH . . . C 3 -20.368 -56.717 -13.173 1 37.52 ? N7 SAH 1000 A 1 HETATM 20 C C5 SAH . . . C 3 -21.037 -57.709 -12.607 1 37.84 ? C5 SAH 1000 A 1 HETATM 21 C C6 SAH . . . C 3 -22.392 -57.862 -12.087 1 38.77 ? C6 SAH 1000 A 1 HETATM 22 N N6 SAH . . . C 3 -23.241 -56.863 -12.15 1 38.66 ? N6 SAH 1000 A 1 HETATM 23 N N1 SAH . . . C 3 -22.726 -59.082 -11.571 1 39.61 ? N1 SAH 1000 A 1 HETATM 24 C C2 SAH . . . C 3 -21.833 -60.106 -11.511 1 40.38 ? C2 SAH 1000 A 1 HETATM 25 N N3 SAH . . . C 3 -20.576 -59.987 -11.957 1 39.03 ? N3 SAH 1000 A 1 HETATM 26 C C4 SAH . . . C 3 -20.16 -58.834 -12.499 1 38.35 ? C4 SAH 1000 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 343 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #