data_5XXG # _model_server_result.job_id GQjh7uQ1NQvO71yYIbKtAg _model_server_result.datetime_utc '2024-11-24 20:09:10' _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 5xxg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 5XXG # _exptl.entry_id 5XXG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 3 _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 5XXG _cell.length_a 61.288 _cell.length_b 66.374 _cell.length_c 107.296 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XXG _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 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 A SG CYS 184 A CYS 186 1_555 B CAJ 8HR . A 8HR 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.754 ? metalc ? metalc1 A SG CYS 47 A CYS 49 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc2 A SG CYS 50 A CYS 52 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc3 A SG CYS 60 A CYS 62 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc4 A SG CYS 63 A CYS 65 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc5 A SG CYS 69 A CYS 71 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc6 A SG CYS 73 A CYS 75 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc7 A NE2 HIS 81 A HIS 83 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc8 A SG CYS 85 A CYS 87 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc9 A SG CYS 206 A CYS 208 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc10 A SG CYS 259 A CYS 261 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc11 A SG CYS 261 A CYS 263 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc12 A SG CYS 264 A CYS 266 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? # _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 335 n n N HN1 SAM sing 336 n n N HN2 SAM sing 337 n n CA C SAM sing 338 n n CA CB SAM sing 339 n n CA HA SAM sing 340 n n C O SAM doub 341 n n C OXT SAM sing 342 n n CB CG SAM sing 343 n n CB HB1 SAM sing 344 n n CB HB2 SAM sing 345 n n CG SD SAM sing 346 n n CG HG1 SAM sing 347 n n CG HG2 SAM sing 348 n n SD CE SAM sing 349 n n SD C5' SAM sing 350 n n CE HE1 SAM sing 351 n n CE HE2 SAM sing 352 n n CE HE3 SAM sing 353 n n C5' C4' SAM sing 354 n n C5' "H5'1" SAM sing 355 n n C5' "H5'2" SAM sing 356 n n C4' O4' SAM sing 357 n n C4' C3' SAM sing 358 n n C4' H4' SAM sing 359 n n O4' C1' SAM sing 360 n n C3' O3' SAM sing 361 n n C3' C2' SAM sing 362 n n C3' H3' SAM sing 363 n n O3' HO3' SAM sing 364 n n C2' O2' SAM sing 365 n n C2' C1' SAM sing 366 n n C2' H2' SAM sing 367 n n O2' HO2' SAM sing 368 n n C1' N9 SAM sing 369 n n C1' H1' SAM sing 370 n n N9 C8 SAM sing 371 n y N9 C4 SAM sing 372 n y C8 N7 SAM doub 373 n y C8 H8 SAM sing 374 n n N7 C5 SAM sing 375 n y C5 C6 SAM sing 376 n y C5 C4 SAM doub 377 n y C6 N6 SAM sing 378 n n C6 N1 SAM doub 379 n y N6 HN61 SAM sing 380 n n N6 HN62 SAM sing 381 n n N1 C2 SAM sing 382 n y C2 N3 SAM doub 383 n y C2 H2 SAM sing 384 n n N3 C4 SAM sing 385 n y # _atom_sites.entry_id 5XXG _atom_sites.fract_transf_matrix[1][1] 0.016316 _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] 0.015066 _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] 0.00932 _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 8HR A 1 501 1 8HR DRG . C 3 SAM A 1 502 510 SAM SAM . D 4 ZN A 1 503 1 ZN ZN . E 4 ZN A 1 504 2 ZN ZN . F 4 ZN A 1 505 3 ZN ZN . G 5 HOH A 1 601 35 HOH HOH . G 5 HOH A 2 602 29 HOH HOH . G 5 HOH A 3 603 120 HOH HOH . G 5 HOH A 4 604 138 HOH HOH . G 5 HOH A 5 605 13 HOH HOH . G 5 HOH A 6 606 92 HOH HOH . G 5 HOH A 7 607 70 HOH HOH . G 5 HOH A 8 608 45 HOH HOH . G 5 HOH A 9 609 10 HOH HOH . G 5 HOH A 10 610 20 HOH HOH . G 5 HOH A 11 611 14 HOH HOH . G 5 HOH A 12 612 101 HOH HOH . G 5 HOH A 13 613 60 HOH HOH . G 5 HOH A 14 614 6 HOH HOH . G 5 HOH A 15 615 71 HOH HOH . G 5 HOH A 16 616 118 HOH HOH . G 5 HOH A 17 617 43 HOH HOH . G 5 HOH A 18 618 19 HOH HOH . G 5 HOH A 19 619 52 HOH HOH . G 5 HOH A 20 620 85 HOH HOH . G 5 HOH A 21 621 39 HOH HOH . G 5 HOH A 22 622 33 HOH HOH . G 5 HOH A 23 623 18 HOH HOH . G 5 HOH A 24 624 146 HOH HOH . G 5 HOH A 25 625 113 HOH HOH . G 5 HOH A 26 626 99 HOH HOH . G 5 HOH A 27 627 155 HOH HOH . G 5 HOH A 28 628 75 HOH HOH . G 5 HOH A 29 629 145 HOH HOH . G 5 HOH A 30 630 83 HOH HOH . G 5 HOH A 31 631 91 HOH HOH . G 5 HOH A 32 632 1 HOH HOH . G 5 HOH A 33 633 135 HOH HOH . G 5 HOH A 34 634 40 HOH HOH . G 5 HOH A 35 635 157 HOH HOH . G 5 HOH A 36 636 69 HOH HOH . G 5 HOH A 37 637 57 HOH HOH . G 5 HOH A 38 638 44 HOH HOH . G 5 HOH A 39 639 21 HOH HOH . G 5 HOH A 40 640 28 HOH HOH . G 5 HOH A 41 641 76 HOH HOH . G 5 HOH A 42 642 144 HOH HOH . G 5 HOH A 43 643 50 HOH HOH . G 5 HOH A 44 644 25 HOH HOH . G 5 HOH A 45 645 8 HOH HOH . G 5 HOH A 46 646 97 HOH HOH . G 5 HOH A 47 647 150 HOH HOH . G 5 HOH A 48 648 37 HOH HOH . G 5 HOH A 49 649 53 HOH HOH . G 5 HOH A 50 650 24 HOH HOH . G 5 HOH A 51 651 62 HOH HOH . G 5 HOH A 52 652 22 HOH HOH . G 5 HOH A 53 653 67 HOH HOH . G 5 HOH A 54 654 82 HOH HOH . G 5 HOH A 55 655 11 HOH HOH . G 5 HOH A 56 656 141 HOH HOH . G 5 HOH A 57 657 134 HOH HOH . G 5 HOH A 58 658 137 HOH HOH . G 5 HOH A 59 659 63 HOH HOH . G 5 HOH A 60 660 9 HOH HOH . G 5 HOH A 61 661 148 HOH HOH . G 5 HOH A 62 662 72 HOH HOH . G 5 HOH A 63 663 61 HOH HOH . G 5 HOH A 64 664 47 HOH HOH . G 5 HOH A 65 665 17 HOH HOH . G 5 HOH A 66 666 112 HOH HOH . G 5 HOH A 67 667 103 HOH HOH . G 5 HOH A 68 668 7 HOH HOH . G 5 HOH A 69 669 46 HOH HOH . G 5 HOH A 70 670 94 HOH HOH . G 5 HOH A 71 671 56 HOH HOH . G 5 HOH A 72 672 58 HOH HOH . G 5 HOH A 73 673 2 HOH HOH . G 5 HOH A 74 674 23 HOH HOH . G 5 HOH A 75 675 42 HOH HOH . G 5 HOH A 76 676 87 HOH HOH . G 5 HOH A 77 677 88 HOH HOH . G 5 HOH A 78 678 84 HOH HOH . G 5 HOH A 79 679 136 HOH HOH . G 5 HOH A 80 680 59 HOH HOH . G 5 HOH A 81 681 38 HOH HOH . G 5 HOH A 82 682 102 HOH HOH . G 5 HOH A 83 683 105 HOH HOH . G 5 HOH A 84 684 114 HOH HOH . G 5 HOH A 85 685 89 HOH HOH . G 5 HOH A 86 686 127 HOH HOH . G 5 HOH A 87 687 106 HOH HOH . G 5 HOH A 88 688 15 HOH HOH . G 5 HOH A 89 689 30 HOH HOH . G 5 HOH A 90 690 130 HOH HOH . G 5 HOH A 91 691 95 HOH HOH . G 5 HOH A 92 692 65 HOH HOH . G 5 HOH A 93 693 100 HOH HOH . G 5 HOH A 94 694 156 HOH HOH . G 5 HOH A 95 695 109 HOH HOH . G 5 HOH A 96 696 149 HOH HOH . G 5 HOH A 97 697 77 HOH HOH . G 5 HOH A 98 698 48 HOH HOH . G 5 HOH A 99 699 16 HOH HOH . G 5 HOH A 100 700 93 HOH HOH . G 5 HOH A 101 701 98 HOH HOH . G 5 HOH A 102 702 36 HOH HOH . G 5 HOH A 103 703 4 HOH HOH . G 5 HOH A 104 704 66 HOH HOH . G 5 HOH A 105 705 143 HOH HOH . G 5 HOH A 106 706 81 HOH HOH . G 5 HOH A 107 707 55 HOH HOH . G 5 HOH A 108 708 116 HOH HOH . G 5 HOH A 109 709 119 HOH HOH . G 5 HOH A 110 710 51 HOH HOH . G 5 HOH A 111 711 73 HOH HOH . G 5 HOH A 112 712 3 HOH HOH . G 5 HOH A 113 713 115 HOH HOH . G 5 HOH A 114 714 80 HOH HOH . G 5 HOH A 115 715 34 HOH HOH . G 5 HOH A 116 716 110 HOH HOH . G 5 HOH A 117 717 5 HOH HOH . G 5 HOH A 118 718 26 HOH HOH . G 5 HOH A 119 719 108 HOH HOH . G 5 HOH A 120 720 31 HOH HOH . G 5 HOH A 121 721 123 HOH HOH . G 5 HOH A 122 722 104 HOH HOH . G 5 HOH A 123 723 140 HOH HOH . G 5 HOH A 124 724 142 HOH HOH . G 5 HOH A 125 725 27 HOH HOH . G 5 HOH A 126 726 79 HOH HOH . G 5 HOH A 127 727 147 HOH HOH . G 5 HOH A 128 728 74 HOH HOH . G 5 HOH A 129 729 86 HOH HOH . G 5 HOH A 130 730 49 HOH HOH . G 5 HOH A 131 731 90 HOH HOH . G 5 HOH A 132 732 152 HOH HOH . G 5 HOH A 133 733 41 HOH HOH . G 5 HOH A 134 734 125 HOH HOH . G 5 HOH A 135 735 64 HOH HOH . G 5 HOH A 136 736 151 HOH HOH . G 5 HOH A 137 737 129 HOH HOH . G 5 HOH A 138 738 96 HOH HOH . G 5 HOH A 139 739 68 HOH HOH . G 5 HOH A 140 740 126 HOH HOH . G 5 HOH A 141 741 78 HOH HOH . G 5 HOH A 142 742 124 HOH HOH . G 5 HOH A 143 743 111 HOH HOH . G 5 HOH A 144 744 107 HOH HOH . G 5 HOH A 145 745 32 HOH HOH . G 5 HOH A 146 746 54 HOH HOH . G 5 HOH A 147 747 131 HOH HOH . G 5 HOH A 148 748 154 HOH HOH . G 5 HOH A 149 749 122 HOH HOH . G 5 HOH A 150 750 132 HOH HOH . G 5 HOH A 151 751 12 HOH HOH . G 5 HOH A 152 752 153 HOH HOH . G 5 HOH A 153 753 128 HOH HOH . G 5 HOH A 154 754 139 HOH HOH . G 5 HOH A 155 755 117 HOH HOH . G 5 HOH A 156 756 133 HOH HOH . G 5 HOH A 157 757 121 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 . . . C 3 11.151 14.75 130.38 1 14.86 ? N SAM 502 A 1 HETATM 2 C CA SAM . . . C 3 11.075 14.649 128.934 1 16.89 ? CA SAM 502 A 1 HETATM 3 C C SAM . . . C 3 10.105 15.667 128.356 1 19.24 ? C SAM 502 A 1 HETATM 4 O O SAM . . . C 3 9.719 16.587 129.068 1 18.23 ? O SAM 502 A 1 HETATM 5 O OXT SAM . . . C 3 9.692 15.599 127.188 1 16.68 -1 OXT SAM 502 A 1 HETATM 6 C CB SAM . . . C 3 10.672 13.241 128.531 1 19.26 ? CB SAM 502 A 1 HETATM 7 C CG SAM . . . C 3 11.866 12.299 128.353 1 17.56 ? CG SAM 502 A 1 HETATM 8 S SD SAM . . . C 3 12.822 12.79 126.891 1 17.14 1 SD SAM 502 A 1 HETATM 9 C CE SAM . . . C 3 12.939 11.218 126.008 1 11.33 ? CE SAM 502 A 1 HETATM 10 C C5' SAM . . . C 3 14.523 12.913 127.527 1 15.09 ? C5' SAM 502 A 1 HETATM 11 C C4' SAM . . . C 3 14.791 14.138 128.397 1 16.92 ? C4' SAM 502 A 1 HETATM 12 O O4' SAM . . . C 3 14.052 14.102 129.613 1 15.61 ? O4' SAM 502 A 1 HETATM 13 C C3' SAM . . . C 3 16.256 14.3 128.808 1 15.22 ? C3' SAM 502 A 1 HETATM 14 O O3' SAM . . . C 3 17.023 14.97 127.821 1 17.91 ? O3' SAM 502 A 1 HETATM 15 C C2' SAM . . . C 3 16.165 15.072 130.11 1 15.71 ? C2' SAM 502 A 1 HETATM 16 O O2' SAM . . . C 3 15.897 16.446 129.873 1 18.41 ? O2' SAM 502 A 1 HETATM 17 C C1' SAM . . . C 3 14.883 14.526 130.69 1 18.24 ? C1' SAM 502 A 1 HETATM 18 N N9 SAM . . . C 3 15.141 13.354 131.551 1 19.95 ? N9 SAM 502 A 1 HETATM 19 C C8 SAM . . . C 3 14.99 12.031 131.213 1 14.98 ? C8 SAM 502 A 1 HETATM 20 N N7 SAM . . . C 3 15.317 11.276 132.296 1 20.8 ? N7 SAM 502 A 1 HETATM 21 C C5 SAM . . . C 3 15.666 12.098 133.317 1 17.62 ? C5 SAM 502 A 1 HETATM 22 C C6 SAM . . . C 3 16.079 11.874 134.62 1 20.41 ? C6 SAM 502 A 1 HETATM 23 N N6 SAM . . . C 3 16.203 10.636 135.127 1 18.6 ? N6 SAM 502 A 1 HETATM 24 N N1 SAM . . . C 3 16.375 12.962 135.408 1 20.07 ? N1 SAM 502 A 1 HETATM 25 C C2 SAM . . . C 3 16.269 14.245 134.94 1 18.4 ? C2 SAM 502 A 1 HETATM 26 N N3 SAM . . . C 3 15.852 14.463 133.647 1 23.03 ? N3 SAM 502 A 1 HETATM 27 C C4 SAM . . . C 3 15.561 13.405 132.853 1 21.21 ? C4 SAM 502 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #