data_5XXD # _model_server_result.job_id KAHTTciMJQ-vaNDvIPNaqw _model_server_result.datetime_utc '2024-11-04 22:38:42' _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 5xxd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5XXD # _exptl.entry_id 5XXD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 5XXD _cell.length_a 61.458 _cell.length_b 66.472 _cell.length_c 107.062 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XXD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _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,G _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 # 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 A SG CYS 184 A CYS 186 1_555 F CAJ 8NR . A 8NR 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.768 ? metalc ? metalc1 A SG CYS 47 A CYS 49 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc2 A SG CYS 50 A CYS 52 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc3 A SG CYS 60 A CYS 62 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc4 A SG CYS 63 A CYS 65 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc5 A SG CYS 69 A CYS 71 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc6 A SG CYS 73 A CYS 75 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc7 A NE2 HIS 81 A HIS 83 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc8 A SG CYS 85 A CYS 87 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc9 A SG CYS 206 A CYS 208 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc10 A SG CYS 259 A CYS 261 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc11 A SG CYS 261 A CYS 263 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc12 A SG CYS 264 A CYS 266 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _chem_comp.type non-polymer _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 SAM sing 332 n n N HN1 SAM sing 333 n n N HN2 SAM sing 334 n n CA C SAM sing 335 n n CA CB SAM sing 336 n n CA HA SAM sing 337 n n C O SAM doub 338 n n C OXT SAM sing 339 n n CB CG SAM sing 340 n n CB HB1 SAM sing 341 n n CB HB2 SAM sing 342 n n CG SD SAM sing 343 n n CG HG1 SAM sing 344 n n CG HG2 SAM sing 345 n n SD CE SAM sing 346 n n SD C5' SAM sing 347 n n CE HE1 SAM sing 348 n n CE HE2 SAM sing 349 n n CE HE3 SAM sing 350 n n C5' C4' SAM sing 351 n n C5' "H5'1" SAM sing 352 n n C5' "H5'2" SAM sing 353 n n C4' O4' SAM sing 354 n n C4' C3' SAM sing 355 n n C4' H4' SAM sing 356 n n O4' C1' SAM sing 357 n n C3' O3' SAM sing 358 n n C3' C2' SAM sing 359 n n C3' H3' SAM sing 360 n n O3' HO3' SAM sing 361 n n C2' O2' SAM sing 362 n n C2' C1' SAM sing 363 n n C2' H2' SAM sing 364 n n O2' HO2' SAM sing 365 n n C1' N9 SAM sing 366 n n C1' H1' SAM sing 367 n n N9 C8 SAM sing 368 n y N9 C4 SAM sing 369 n y C8 N7 SAM doub 370 n y C8 H8 SAM sing 371 n n N7 C5 SAM sing 372 n y C5 C6 SAM sing 373 n y C5 C4 SAM doub 374 n y C6 N6 SAM sing 375 n n C6 N1 SAM doub 376 n y N6 HN61 SAM sing 377 n n N6 HN62 SAM sing 378 n n N1 C2 SAM sing 379 n y C2 N3 SAM doub 380 n y C2 H2 SAM sing 381 n n N3 C4 SAM sing 382 n y # _atom_sites.entry_id 5XXD _atom_sites.fract_transf_matrix[1][1] 0.016271 _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] 0.015044 _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] 0.00934 _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 SAM A 1 501 510 SAM SAM . C 3 ZN A 1 502 1 ZN ZN . D 3 ZN A 1 503 2 ZN ZN . E 3 ZN A 1 504 3 ZN ZN . F 4 8NR A 1 505 1 8NR DRG . G 5 HOH A 1 601 13 HOH HOH . G 5 HOH A 2 602 64 HOH HOH . G 5 HOH A 3 603 77 HOH HOH . G 5 HOH A 4 604 22 HOH HOH . G 5 HOH A 5 605 80 HOH HOH . G 5 HOH A 6 606 142 HOH HOH . G 5 HOH A 7 607 19 HOH HOH . G 5 HOH A 8 608 26 HOH HOH . G 5 HOH A 9 609 73 HOH HOH . G 5 HOH A 10 610 57 HOH HOH . G 5 HOH A 11 611 51 HOH HOH . G 5 HOH A 12 612 49 HOH HOH . G 5 HOH A 13 613 69 HOH HOH . G 5 HOH A 14 614 6 HOH HOH . G 5 HOH A 15 615 72 HOH HOH . G 5 HOH A 16 616 90 HOH HOH . G 5 HOH A 17 617 75 HOH HOH . G 5 HOH A 18 618 23 HOH HOH . G 5 HOH A 19 619 32 HOH HOH . G 5 HOH A 20 620 52 HOH HOH . G 5 HOH A 21 621 59 HOH HOH . G 5 HOH A 22 622 60 HOH HOH . G 5 HOH A 23 623 97 HOH HOH . G 5 HOH A 24 624 46 HOH HOH . G 5 HOH A 25 625 34 HOH HOH . G 5 HOH A 26 626 4 HOH HOH . G 5 HOH A 27 627 45 HOH HOH . G 5 HOH A 28 628 5 HOH HOH . G 5 HOH A 29 629 40 HOH HOH . G 5 HOH A 30 630 94 HOH HOH . G 5 HOH A 31 631 42 HOH HOH . G 5 HOH A 32 632 136 HOH HOH . G 5 HOH A 33 633 27 HOH HOH . G 5 HOH A 34 634 61 HOH HOH . G 5 HOH A 35 635 66 HOH HOH . G 5 HOH A 36 636 43 HOH HOH . G 5 HOH A 37 637 132 HOH HOH . G 5 HOH A 38 638 8 HOH HOH . G 5 HOH A 39 639 104 HOH HOH . G 5 HOH A 40 640 38 HOH HOH . G 5 HOH A 41 641 128 HOH HOH . G 5 HOH A 42 642 31 HOH HOH . G 5 HOH A 43 643 30 HOH HOH . G 5 HOH A 44 644 28 HOH HOH . G 5 HOH A 45 645 33 HOH HOH . G 5 HOH A 46 646 68 HOH HOH . G 5 HOH A 47 647 36 HOH HOH . G 5 HOH A 48 648 53 HOH HOH . G 5 HOH A 49 649 117 HOH HOH . G 5 HOH A 50 650 116 HOH HOH . G 5 HOH A 51 651 2 HOH HOH . G 5 HOH A 52 652 79 HOH HOH . G 5 HOH A 53 653 9 HOH HOH . G 5 HOH A 54 654 106 HOH HOH . G 5 HOH A 55 655 17 HOH HOH . G 5 HOH A 56 656 16 HOH HOH . G 5 HOH A 57 657 87 HOH HOH . G 5 HOH A 58 658 123 HOH HOH . G 5 HOH A 59 659 21 HOH HOH . G 5 HOH A 60 660 74 HOH HOH . G 5 HOH A 61 661 127 HOH HOH . G 5 HOH A 62 662 76 HOH HOH . G 5 HOH A 63 663 1 HOH HOH . G 5 HOH A 64 664 29 HOH HOH . G 5 HOH A 65 665 25 HOH HOH . G 5 HOH A 66 666 50 HOH HOH . G 5 HOH A 67 667 86 HOH HOH . G 5 HOH A 68 668 41 HOH HOH . G 5 HOH A 69 669 108 HOH HOH . G 5 HOH A 70 670 67 HOH HOH . G 5 HOH A 71 671 115 HOH HOH . G 5 HOH A 72 672 109 HOH HOH . G 5 HOH A 73 673 70 HOH HOH . G 5 HOH A 74 674 124 HOH HOH . G 5 HOH A 75 675 81 HOH HOH . G 5 HOH A 76 676 122 HOH HOH . G 5 HOH A 77 677 63 HOH HOH . G 5 HOH A 78 678 143 HOH HOH . G 5 HOH A 79 679 71 HOH HOH . G 5 HOH A 80 680 65 HOH HOH . G 5 HOH A 81 681 140 HOH HOH . G 5 HOH A 82 682 47 HOH HOH . G 5 HOH A 83 683 84 HOH HOH . G 5 HOH A 84 684 110 HOH HOH . G 5 HOH A 85 685 44 HOH HOH . G 5 HOH A 86 686 12 HOH HOH . G 5 HOH A 87 687 15 HOH HOH . G 5 HOH A 88 688 18 HOH HOH . G 5 HOH A 89 689 55 HOH HOH . G 5 HOH A 90 690 120 HOH HOH . G 5 HOH A 91 691 105 HOH HOH . G 5 HOH A 92 692 35 HOH HOH . G 5 HOH A 93 693 118 HOH HOH . G 5 HOH A 94 694 56 HOH HOH . G 5 HOH A 95 695 58 HOH HOH . G 5 HOH A 96 696 91 HOH HOH . G 5 HOH A 97 697 11 HOH HOH . G 5 HOH A 98 698 48 HOH HOH . G 5 HOH A 99 699 121 HOH HOH . G 5 HOH A 100 700 24 HOH HOH . G 5 HOH A 101 701 89 HOH HOH . G 5 HOH A 102 702 101 HOH HOH . G 5 HOH A 103 703 7 HOH HOH . G 5 HOH A 104 704 92 HOH HOH . G 5 HOH A 105 705 3 HOH HOH . G 5 HOH A 106 706 100 HOH HOH . G 5 HOH A 107 707 99 HOH HOH . G 5 HOH A 108 708 78 HOH HOH . G 5 HOH A 109 709 139 HOH HOH . G 5 HOH A 110 710 83 HOH HOH . G 5 HOH A 111 711 112 HOH HOH . G 5 HOH A 112 712 88 HOH HOH . G 5 HOH A 113 713 62 HOH HOH . G 5 HOH A 114 714 10 HOH HOH . G 5 HOH A 115 715 135 HOH HOH . G 5 HOH A 116 716 82 HOH HOH . G 5 HOH A 117 717 133 HOH HOH . G 5 HOH A 118 718 119 HOH HOH . G 5 HOH A 119 719 54 HOH HOH . G 5 HOH A 120 720 95 HOH HOH . G 5 HOH A 121 721 102 HOH HOH . G 5 HOH A 122 722 37 HOH HOH . G 5 HOH A 123 723 134 HOH HOH . G 5 HOH A 124 724 85 HOH HOH . G 5 HOH A 125 725 144 HOH HOH . G 5 HOH A 126 726 14 HOH HOH . G 5 HOH A 127 727 126 HOH HOH . G 5 HOH A 128 728 137 HOH HOH . G 5 HOH A 129 729 39 HOH HOH . G 5 HOH A 130 730 131 HOH HOH . G 5 HOH A 131 731 98 HOH HOH . G 5 HOH A 132 732 129 HOH HOH . G 5 HOH A 133 733 141 HOH HOH . G 5 HOH A 134 734 20 HOH HOH . G 5 HOH A 135 735 138 HOH HOH . G 5 HOH A 136 736 93 HOH HOH . G 5 HOH A 137 737 111 HOH HOH . G 5 HOH A 138 738 103 HOH HOH . G 5 HOH A 139 739 96 HOH HOH . G 5 HOH A 140 740 114 HOH HOH . G 5 HOH A 141 741 113 HOH HOH . G 5 HOH A 142 742 130 HOH HOH . G 5 HOH A 143 743 107 HOH HOH . G 5 HOH A 144 744 125 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 SAM . . . B 2 11.254 14.727 130.068 1 11.67 ? N SAM 501 A 1 HETATM 2 C CA SAM . . . B 2 11.14 14.583 128.621 1 14.71 ? CA SAM 501 A 1 HETATM 3 C C SAM . . . B 2 10.111 15.549 128.042 1 12.67 ? C SAM 501 A 1 HETATM 4 O O SAM . . . B 2 9.527 16.358 128.763 1 10.25 ? O SAM 501 A 1 HETATM 5 O OXT SAM . . . B 2 9.844 15.549 126.839 1 11.76 -1 OXT SAM 501 A 1 HETATM 6 C CB SAM . . . B 2 10.78 13.147 128.258 1 8.86 ? CB SAM 501 A 1 HETATM 7 C CG SAM . . . B 2 11.984 12.236 128.043 1 11.62 ? CG SAM 501 A 1 HETATM 8 S SD SAM . . . B 2 12.99 12.763 126.632 1 10.5 1 SD SAM 501 A 1 HETATM 9 C CE SAM . . . B 2 13.157 11.213 125.715 1 9.4 ? CE SAM 501 A 1 HETATM 10 C C5' SAM . . . B 2 14.636 12.851 127.376 1 11.94 ? C5' SAM 501 A 1 HETATM 11 C C4' SAM . . . B 2 14.886 14.142 128.14 1 10.41 ? C4' SAM 501 A 1 HETATM 12 O O4' SAM . . . B 2 14.211 14.108 129.386 1 16.21 ? O4' SAM 501 A 1 HETATM 13 C C3' SAM . . . B 2 16.366 14.33 128.436 1 13.82 ? C3' SAM 501 A 1 HETATM 14 O O3' SAM . . . B 2 16.962 15.199 127.502 1 15.56 ? O3' SAM 501 A 1 HETATM 15 C C2' SAM . . . B 2 16.388 14.932 129.82 1 12.8 ? C2' SAM 501 A 1 HETATM 16 O O2' SAM . . . B 2 16.376 16.334 129.709 1 14.87 ? O2' SAM 501 A 1 HETATM 17 C C1' SAM . . . B 2 15.076 14.497 130.436 1 14.63 ? C1' SAM 501 A 1 HETATM 18 N N9 SAM . . . B 2 15.296 13.33 131.307 1 14.59 ? N9 SAM 501 A 1 HETATM 19 C C8 SAM . . . B 2 15.062 12.026 130.956 1 10.75 ? C8 SAM 501 A 1 HETATM 20 N N7 SAM . . . B 2 15.381 11.236 132.003 1 12.26 ? N7 SAM 501 A 1 HETATM 21 C C5 SAM . . . B 2 15.825 12.012 133.015 1 14.55 ? C5 SAM 501 A 1 HETATM 22 C C6 SAM . . . B 2 16.275 11.708 134.293 1 13.87 ? C6 SAM 501 A 1 HETATM 23 N N6 SAM . . . B 2 16.322 10.444 134.704 1 10.42 ? N6 SAM 501 A 1 HETATM 24 N N1 SAM . . . B 2 16.675 12.728 135.13 1 16.71 ? N1 SAM 501 A 1 HETATM 25 C C2 SAM . . . B 2 16.628 14.038 134.693 1 13.41 ? C2 SAM 501 A 1 HETATM 26 N N3 SAM . . . B 2 16.174 14.329 133.422 1 15.71 ? N3 SAM 501 A 1 HETATM 27 C C4 SAM . . . B 2 15.776 13.334 132.593 1 15.16 ? C4 SAM 501 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #