data_5KJL # _model_server_result.job_id jpGPlb1W3QDd5yjZsV2qhA _model_server_result.datetime_utc '2024-12-23 14:24:40' _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 5kjl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5KJL # _exptl.entry_id 5KJL _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 5KJL _cell.length_a 155.098 _cell.length_b 155.098 _cell.length_c 52.553 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KJL _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 ? _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 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 metalc ? metalc1 A SG CYS 48 A CYS 52 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc2 A SG CYS 51 A CYS 55 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc3 A SG CYS 61 A CYS 65 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc4 A SG CYS 64 A CYS 68 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc5 A SG CYS 70 A CYS 74 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc6 A SG CYS 74 A CYS 78 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc7 A NE2 HIS 82 A HIS 86 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc8 A SG CYS 86 A CYS 90 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc9 A SG CYS 205 A CYS 209 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc10 A SG CYS 258 A CYS 262 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc11 A SG CYS 260 A CYS 264 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc12 A SG CYS 263 A CYS 267 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? # _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 277 n n N HN1 SAM sing 278 n n N HN2 SAM sing 279 n n CA C SAM sing 280 n n CA CB SAM sing 281 n n CA HA SAM sing 282 n n C O SAM doub 283 n n C OXT SAM sing 284 n n CB CG SAM sing 285 n n CB HB1 SAM sing 286 n n CB HB2 SAM sing 287 n n CG SD SAM sing 288 n n CG HG1 SAM sing 289 n n CG HG2 SAM sing 290 n n SD CE SAM sing 291 n n SD C5' SAM sing 292 n n CE HE1 SAM sing 293 n n CE HE2 SAM sing 294 n n CE HE3 SAM sing 295 n n C5' C4' SAM sing 296 n n C5' "H5'1" SAM sing 297 n n C5' "H5'2" SAM sing 298 n n C4' O4' SAM sing 299 n n C4' C3' SAM sing 300 n n C4' H4' SAM sing 301 n n O4' C1' SAM sing 302 n n C3' O3' SAM sing 303 n n C3' C2' SAM sing 304 n n C3' H3' SAM sing 305 n n O3' HO3' SAM sing 306 n n C2' O2' SAM sing 307 n n C2' C1' SAM sing 308 n n C2' H2' SAM sing 309 n n O2' HO2' SAM sing 310 n n C1' N9 SAM sing 311 n n C1' H1' SAM sing 312 n n N9 C8 SAM sing 313 n y N9 C4 SAM sing 314 n y C8 N7 SAM doub 315 n y C8 H8 SAM sing 316 n n N7 C5 SAM sing 317 n y C5 C6 SAM sing 318 n y C5 C4 SAM doub 319 n y C6 N6 SAM sing 320 n n C6 N1 SAM doub 321 n y N6 HN61 SAM sing 322 n n N6 HN62 SAM sing 323 n n N1 C2 SAM sing 324 n y C2 N3 SAM doub 325 n y C2 H2 SAM sing 326 n n N3 C4 SAM sing 327 n y # _atom_sites.entry_id 5KJL _atom_sites.fract_transf_matrix[1][1] 0.006448 _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] 0.006448 _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] 0.019028 _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 1000 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 HOH A 1 601 113 HOH HOH . F 4 HOH A 2 602 16 HOH HOH . F 4 HOH A 3 603 68 HOH HOH . F 4 HOH A 4 604 106 HOH HOH . F 4 HOH A 5 605 78 HOH HOH . F 4 HOH A 6 606 108 HOH HOH . F 4 HOH A 7 607 64 HOH HOH . F 4 HOH A 8 608 79 HOH HOH . F 4 HOH A 9 609 118 HOH HOH . F 4 HOH A 10 610 13 HOH HOH . F 4 HOH A 11 611 121 HOH HOH . F 4 HOH A 12 612 71 HOH HOH . F 4 HOH A 13 613 100 HOH HOH . F 4 HOH A 14 614 109 HOH HOH . F 4 HOH A 15 615 131 HOH HOH . F 4 HOH A 16 616 97 HOH HOH . F 4 HOH A 17 617 125 HOH HOH . F 4 HOH A 18 618 4 HOH HOH . F 4 HOH A 19 619 62 HOH HOH . F 4 HOH A 20 620 38 HOH HOH . F 4 HOH A 21 621 3 HOH HOH . F 4 HOH A 22 622 80 HOH HOH . F 4 HOH A 23 623 112 HOH HOH . F 4 HOH A 24 624 105 HOH HOH . F 4 HOH A 25 625 103 HOH HOH . F 4 HOH A 26 626 46 HOH HOH . F 4 HOH A 27 627 75 HOH HOH . F 4 HOH A 28 628 124 HOH HOH . F 4 HOH A 29 629 47 HOH HOH . F 4 HOH A 30 630 115 HOH HOH . F 4 HOH A 31 631 6 HOH HOH . F 4 HOH A 32 632 22 HOH HOH . F 4 HOH A 33 633 122 HOH HOH . F 4 HOH A 34 634 63 HOH HOH . F 4 HOH A 35 635 33 HOH HOH . F 4 HOH A 36 636 10 HOH HOH . F 4 HOH A 37 637 129 HOH HOH . F 4 HOH A 38 638 8 HOH HOH . F 4 HOH A 39 639 130 HOH HOH . F 4 HOH A 40 640 53 HOH HOH . F 4 HOH A 41 641 77 HOH HOH . F 4 HOH A 42 642 85 HOH HOH . F 4 HOH A 43 643 34 HOH HOH . F 4 HOH A 44 644 65 HOH HOH . F 4 HOH A 45 645 66 HOH HOH . F 4 HOH A 46 646 83 HOH HOH . F 4 HOH A 47 647 107 HOH HOH . F 4 HOH A 48 648 94 HOH HOH . F 4 HOH A 49 649 104 HOH HOH . F 4 HOH A 50 650 7 HOH HOH . F 4 HOH A 51 651 92 HOH HOH . F 4 HOH A 52 652 9 HOH HOH . F 4 HOH A 53 653 21 HOH HOH . F 4 HOH A 54 654 45 HOH HOH . F 4 HOH A 55 655 96 HOH HOH . F 4 HOH A 56 656 49 HOH HOH . F 4 HOH A 57 657 123 HOH HOH . F 4 HOH A 58 658 81 HOH HOH . F 4 HOH A 59 659 24 HOH HOH . F 4 HOH A 60 660 14 HOH HOH . F 4 HOH A 61 661 88 HOH HOH . F 4 HOH A 62 662 30 HOH HOH . F 4 HOH A 63 663 74 HOH HOH . F 4 HOH A 64 664 35 HOH HOH . F 4 HOH A 65 665 17 HOH HOH . F 4 HOH A 66 666 25 HOH HOH . F 4 HOH A 67 667 20 HOH HOH . F 4 HOH A 68 668 18 HOH HOH . F 4 HOH A 69 669 11 HOH HOH . F 4 HOH A 70 670 72 HOH HOH . F 4 HOH A 71 671 31 HOH HOH . F 4 HOH A 72 672 70 HOH HOH . F 4 HOH A 73 673 93 HOH HOH . F 4 HOH A 74 674 56 HOH HOH . F 4 HOH A 75 675 27 HOH HOH . F 4 HOH A 76 676 133 HOH HOH . F 4 HOH A 77 677 67 HOH HOH . F 4 HOH A 78 678 110 HOH HOH . F 4 HOH A 79 679 50 HOH HOH . F 4 HOH A 80 680 60 HOH HOH . F 4 HOH A 81 681 19 HOH HOH . F 4 HOH A 82 682 52 HOH HOH . F 4 HOH A 83 683 101 HOH HOH . F 4 HOH A 84 684 111 HOH HOH . F 4 HOH A 85 685 69 HOH HOH . F 4 HOH A 86 686 29 HOH HOH . F 4 HOH A 87 687 12 HOH HOH . F 4 HOH A 88 688 114 HOH HOH . F 4 HOH A 89 689 26 HOH HOH . F 4 HOH A 90 690 91 HOH HOH . F 4 HOH A 91 691 89 HOH HOH . F 4 HOH A 92 692 102 HOH HOH . F 4 HOH A 93 693 36 HOH HOH . F 4 HOH A 94 694 58 HOH HOH . F 4 HOH A 95 695 76 HOH HOH . F 4 HOH A 96 696 40 HOH HOH . F 4 HOH A 97 697 23 HOH HOH . F 4 HOH A 98 698 2 HOH HOH . F 4 HOH A 99 699 73 HOH HOH . F 4 HOH A 100 700 95 HOH HOH . F 4 HOH A 101 701 117 HOH HOH . F 4 HOH A 102 702 5 HOH HOH . F 4 HOH A 103 703 98 HOH HOH . F 4 HOH A 104 704 99 HOH HOH . F 4 HOH A 105 705 132 HOH HOH . F 4 HOH A 106 706 44 HOH HOH . F 4 HOH A 107 707 1 HOH HOH . F 4 HOH A 108 708 57 HOH HOH . F 4 HOH A 109 709 120 HOH HOH . F 4 HOH A 110 710 55 HOH HOH . F 4 HOH A 111 711 82 HOH HOH . F 4 HOH A 112 712 126 HOH HOH . F 4 HOH A 113 713 127 HOH HOH . F 4 HOH A 114 714 42 HOH HOH . F 4 HOH A 115 715 116 HOH HOH . F 4 HOH A 116 716 48 HOH HOH . F 4 HOH A 117 717 119 HOH HOH . F 4 HOH A 118 718 54 HOH HOH . F 4 HOH A 119 719 37 HOH HOH . F 4 HOH A 120 720 86 HOH HOH . F 4 HOH A 121 721 15 HOH HOH . F 4 HOH A 122 722 90 HOH HOH . F 4 HOH A 123 723 61 HOH HOH . F 4 HOH A 124 724 87 HOH HOH . F 4 HOH A 125 725 84 HOH HOH . F 4 HOH A 126 726 39 HOH HOH . F 4 HOH A 127 727 41 HOH HOH . F 4 HOH A 128 728 32 HOH HOH . F 4 HOH A 129 729 128 HOH HOH . F 4 HOH A 130 730 51 HOH HOH . F 4 HOH A 131 731 43 HOH HOH . F 4 HOH A 132 732 59 HOH HOH . F 4 HOH A 133 733 28 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 -58.248 -15.568 -42.031 1 37.68 ? N SAM 501 A 1 HETATM 2 C CA SAM . . . B 2 -58.116 -14.393 -41.138 1 39.24 ? CA SAM 501 A 1 HETATM 3 C C SAM . . . B 2 -58.595 -13.058 -41.822 1 40.2 ? C SAM 501 A 1 HETATM 4 O O SAM . . . B 2 -59.015 -13.138 -43.001 1 43.1 ? O SAM 501 A 1 HETATM 5 O OXT SAM . . . B 2 -58.562 -12.014 -41.137 1 38.59 ? OXT SAM 501 A 1 HETATM 6 C CB SAM . . . B 2 -56.671 -14.264 -40.591 1 38.35 ? CB SAM 501 A 1 HETATM 7 C CG SAM . . . B 2 -56.429 -15.181 -39.4 1 37.87 ? CG SAM 501 A 1 HETATM 8 S SD SAM . . . B 2 -57.23 -14.503 -37.925 1 38.92 ? SD SAM 501 A 1 HETATM 9 C CE SAM . . . B 2 -55.979 -14.481 -36.693 1 37.13 ? CE SAM 501 A 1 HETATM 10 C C5' SAM . . . B 2 -58.114 -16.029 -37.298 1 37.18 ? C5' SAM 501 A 1 HETATM 11 C C4' SAM . . . B 2 -59.405 -16.38 -37.994 1 35.61 ? C4' SAM 501 A 1 HETATM 12 O O4' SAM . . . B 2 -59.126 -16.884 -39.32 1 35.63 ? O4' SAM 501 A 1 HETATM 13 C C3' SAM . . . B 2 -60.192 -17.49 -37.316 1 38.04 ? C3' SAM 501 A 1 HETATM 14 O O3' SAM . . . B 2 -60.968 -17.041 -36.214 1 41.7 ? O3' SAM 501 A 1 HETATM 15 C C2' SAM . . . B 2 -60.978 -18.095 -38.481 1 35.08 ? C2' SAM 501 A 1 HETATM 16 O O2' SAM . . . B 2 -62.123 -17.349 -38.852 1 35.31 ? O2' SAM 501 A 1 HETATM 17 C C1' SAM . . . B 2 -59.958 -17.993 -39.615 1 34.52 ? C1' SAM 501 A 1 HETATM 18 N N9 SAM . . . B 2 -59.125 -19.185 -39.771 1 31.22 ? N9 SAM 501 A 1 HETATM 19 C C8 SAM . . . B 2 -57.808 -19.337 -39.43 1 30.57 ? C8 SAM 501 A 1 HETATM 20 N N7 SAM . . . B 2 -57.317 -20.523 -39.698 1 32.5 ? N7 SAM 501 A 1 HETATM 21 C C5 SAM . . . B 2 -58.393 -21.205 -40.247 1 32.42 ? C5 SAM 501 A 1 HETATM 22 C C6 SAM . . . B 2 -58.535 -22.519 -40.736 1 32.01 ? C6 SAM 501 A 1 HETATM 23 N N6 SAM . . . B 2 -57.525 -23.383 -40.837 1 30.92 ? N6 SAM 501 A 1 HETATM 24 N N1 SAM . . . B 2 -59.758 -22.898 -41.179 1 33.78 ? N1 SAM 501 A 1 HETATM 25 C C2 SAM . . . B 2 -60.759 -22.009 -41.146 1 32.85 ? C2 SAM 501 A 1 HETATM 26 N N3 SAM . . . B 2 -60.741 -20.741 -40.721 1 30.69 ? N3 SAM 501 A 1 HETATM 27 C C4 SAM . . . B 2 -59.518 -20.395 -40.287 1 30.47 ? C4 SAM 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #