data_5CCM # _model_server_result.job_id WAMURxYkd8f-NV_dUa8myg _model_server_result.datetime_utc '2024-10-19 17:41:07' _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 5ccm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":504}' # _entry.id 5CCM # _exptl.entry_id 5CCM _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 5CCM _cell.length_a 60.484 _cell.length_b 65.852 _cell.length_c 107.358 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CCM _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 E _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 49 A CYS 49 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc2 A SG CYS 52 A CYS 52 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc3 A SG CYS 62 A CYS 62 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc4 A SG CYS 65 A CYS 65 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc5 A SG CYS 71 A CYS 71 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc6 A SG CYS 75 A CYS 75 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc7 A NE2 HIS 83 A HIS 83 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc8 A SG CYS 87 A CYS 87 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc9 A SG CYS 208 A CYS 208 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc10 A SG CYS 261 A CYS 261 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc11 A SG CYS 263 A CYS 263 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc12 A SG CYS 266 A CYS 266 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? # _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 355 n n N HN1 SAM sing 356 n n N HN2 SAM sing 357 n n CA C SAM sing 358 n n CA CB SAM sing 359 n n CA HA SAM sing 360 n n C O SAM doub 361 n n C OXT SAM sing 362 n n CB CG SAM sing 363 n n CB HB1 SAM sing 364 n n CB HB2 SAM sing 365 n n CG SD SAM sing 366 n n CG HG1 SAM sing 367 n n CG HG2 SAM sing 368 n n SD CE SAM sing 369 n n SD C5' SAM sing 370 n n CE HE1 SAM sing 371 n n CE HE2 SAM sing 372 n n CE HE3 SAM sing 373 n n C5' C4' SAM sing 374 n n C5' "H5'1" SAM sing 375 n n C5' "H5'2" SAM sing 376 n n C4' O4' SAM sing 377 n n C4' C3' SAM sing 378 n n C4' H4' SAM sing 379 n n O4' C1' SAM sing 380 n n C3' O3' SAM sing 381 n n C3' C2' SAM sing 382 n n C3' H3' SAM sing 383 n n O3' HO3' SAM sing 384 n n C2' O2' SAM sing 385 n n C2' C1' SAM sing 386 n n C2' H2' SAM sing 387 n n O2' HO2' SAM sing 388 n n C1' N9 SAM sing 389 n n C1' H1' SAM sing 390 n n N9 C8 SAM sing 391 n y N9 C4 SAM sing 392 n y C8 N7 SAM doub 393 n y C8 H8 SAM sing 394 n n N7 C5 SAM sing 395 n y C5 C6 SAM sing 396 n y C5 C4 SAM doub 397 n y C6 N6 SAM sing 398 n n C6 N1 SAM doub 399 n y N6 HN61 SAM sing 400 n n N6 HN62 SAM sing 401 n n N1 C2 SAM sing 402 n y C2 N3 SAM doub 403 n y C2 H2 SAM sing 404 n n N3 C4 SAM sing 405 n y # _atom_sites.entry_id 5CCM _atom_sites.fract_transf_matrix[1][1] 0.016533 _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] 0.015186 _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] 0.009315 _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 ZN A 1 501 1 ZN ZN . C 2 ZN A 1 502 2 ZN ZN . D 2 ZN A 1 503 3 ZN ZN . E 3 SAM A 1 504 1 SAM SAM . F 4 4ZX A 1 505 1 4ZX EPZ . G 5 HOH A 1 601 55 HOH HOH . G 5 HOH A 2 602 40 HOH HOH . G 5 HOH A 3 603 74 HOH HOH . G 5 HOH A 4 604 16 HOH HOH . G 5 HOH A 5 605 63 HOH HOH . G 5 HOH A 6 606 31 HOH HOH . G 5 HOH A 7 607 83 HOH HOH . G 5 HOH A 8 608 97 HOH HOH . G 5 HOH A 9 609 100 HOH HOH . G 5 HOH A 10 610 58 HOH HOH . G 5 HOH A 11 611 7 HOH HOH . G 5 HOH A 12 612 106 HOH HOH . G 5 HOH A 13 613 104 HOH HOH . G 5 HOH A 14 614 92 HOH HOH . G 5 HOH A 15 615 80 HOH HOH . G 5 HOH A 16 616 99 HOH HOH . G 5 HOH A 17 617 120 HOH HOH . G 5 HOH A 18 618 45 HOH HOH . G 5 HOH A 19 619 57 HOH HOH . G 5 HOH A 20 620 75 HOH HOH . G 5 HOH A 21 621 91 HOH HOH . G 5 HOH A 22 622 36 HOH HOH . G 5 HOH A 23 623 111 HOH HOH . G 5 HOH A 24 624 43 HOH HOH . G 5 HOH A 25 625 22 HOH HOH . G 5 HOH A 26 626 118 HOH HOH . G 5 HOH A 27 627 121 HOH HOH . G 5 HOH A 28 628 78 HOH HOH . G 5 HOH A 29 629 2 HOH HOH . G 5 HOH A 30 630 34 HOH HOH . G 5 HOH A 31 631 82 HOH HOH . G 5 HOH A 32 632 122 HOH HOH . G 5 HOH A 33 633 123 HOH HOH . G 5 HOH A 34 634 81 HOH HOH . G 5 HOH A 35 635 113 HOH HOH . G 5 HOH A 36 636 18 HOH HOH . G 5 HOH A 37 637 51 HOH HOH . G 5 HOH A 38 638 19 HOH HOH . G 5 HOH A 39 639 53 HOH HOH . G 5 HOH A 40 640 46 HOH HOH . G 5 HOH A 41 641 26 HOH HOH . G 5 HOH A 42 642 44 HOH HOH . G 5 HOH A 43 643 110 HOH HOH . G 5 HOH A 44 644 109 HOH HOH . G 5 HOH A 45 645 35 HOH HOH . G 5 HOH A 46 646 33 HOH HOH . G 5 HOH A 47 647 86 HOH HOH . G 5 HOH A 48 648 72 HOH HOH . G 5 HOH A 49 649 47 HOH HOH . G 5 HOH A 50 650 37 HOH HOH . G 5 HOH A 51 651 25 HOH HOH . G 5 HOH A 52 652 102 HOH HOH . G 5 HOH A 53 653 67 HOH HOH . G 5 HOH A 54 654 21 HOH HOH . G 5 HOH A 55 655 32 HOH HOH . G 5 HOH A 56 656 88 HOH HOH . G 5 HOH A 57 657 13 HOH HOH . G 5 HOH A 58 658 50 HOH HOH . G 5 HOH A 59 659 38 HOH HOH . G 5 HOH A 60 660 1 HOH HOH . G 5 HOH A 61 661 9 HOH HOH . G 5 HOH A 62 662 103 HOH HOH . G 5 HOH A 63 663 61 HOH HOH . G 5 HOH A 64 664 12 HOH HOH . G 5 HOH A 65 665 17 HOH HOH . G 5 HOH A 66 666 3 HOH HOH . G 5 HOH A 67 667 28 HOH HOH . G 5 HOH A 68 668 117 HOH HOH . G 5 HOH A 69 669 6 HOH HOH . G 5 HOH A 70 670 108 HOH HOH . G 5 HOH A 71 671 42 HOH HOH . G 5 HOH A 72 672 84 HOH HOH . G 5 HOH A 73 673 14 HOH HOH . G 5 HOH A 74 674 94 HOH HOH . G 5 HOH A 75 675 23 HOH HOH . G 5 HOH A 76 676 5 HOH HOH . G 5 HOH A 77 677 115 HOH HOH . G 5 HOH A 78 678 4 HOH HOH . G 5 HOH A 79 679 30 HOH HOH . G 5 HOH A 80 680 68 HOH HOH . G 5 HOH A 81 681 10 HOH HOH . G 5 HOH A 82 682 105 HOH HOH . G 5 HOH A 83 683 64 HOH HOH . G 5 HOH A 84 684 48 HOH HOH . G 5 HOH A 85 685 73 HOH HOH . G 5 HOH A 86 686 77 HOH HOH . G 5 HOH A 87 687 107 HOH HOH . G 5 HOH A 88 688 27 HOH HOH . G 5 HOH A 89 689 98 HOH HOH . G 5 HOH A 90 690 85 HOH HOH . G 5 HOH A 91 691 114 HOH HOH . G 5 HOH A 92 692 54 HOH HOH . G 5 HOH A 93 693 29 HOH HOH . G 5 HOH A 94 694 8 HOH HOH . G 5 HOH A 95 695 11 HOH HOH . G 5 HOH A 96 696 65 HOH HOH . G 5 HOH A 97 697 41 HOH HOH . G 5 HOH A 98 698 119 HOH HOH . G 5 HOH A 99 699 95 HOH HOH . G 5 HOH A 100 700 15 HOH HOH . G 5 HOH A 101 701 24 HOH HOH . G 5 HOH A 102 702 93 HOH HOH . G 5 HOH A 103 703 79 HOH HOH . G 5 HOH A 104 704 39 HOH HOH . G 5 HOH A 105 705 59 HOH HOH . G 5 HOH A 106 706 116 HOH HOH . G 5 HOH A 107 707 90 HOH HOH . G 5 HOH A 108 708 60 HOH HOH . G 5 HOH A 109 709 49 HOH HOH . G 5 HOH A 110 710 70 HOH HOH . G 5 HOH A 111 711 71 HOH HOH . G 5 HOH A 112 712 87 HOH HOH . G 5 HOH A 113 713 66 HOH HOH . G 5 HOH A 114 714 20 HOH HOH . G 5 HOH A 115 715 112 HOH HOH . G 5 HOH A 116 716 89 HOH HOH . G 5 HOH A 117 717 62 HOH HOH . G 5 HOH A 118 718 96 HOH HOH . G 5 HOH A 119 719 76 HOH HOH . G 5 HOH A 120 720 101 HOH HOH . G 5 HOH A 121 721 52 HOH HOH . G 5 HOH A 122 722 69 HOH HOH . G 5 HOH A 123 723 56 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 . . . E 3 10.815 14.686 22.957 1 23.16 ? N SAM 504 A 1 HETATM 2 C CA SAM . . . E 3 10.61 14.639 21.518 1 23.41 ? CA SAM 504 A 1 HETATM 3 C C SAM . . . E 3 9.536 15.604 21.093 1 23.5 ? C SAM 504 A 1 HETATM 4 O O SAM . . . E 3 9.104 15.548 19.921 1 23.23 ? O SAM 504 A 1 HETATM 5 O OXT SAM . . . E 3 9.12 16.447 21.916 1 23.56 ? OXT SAM 504 A 1 HETATM 6 C CB SAM . . . E 3 10.248 13.209 21.114 1 23.97 ? CB SAM 504 A 1 HETATM 7 C CG SAM . . . E 3 11.475 12.297 21.016 1 24.82 ? CG SAM 504 A 1 HETATM 8 S SD SAM . . . E 3 12.485 12.733 19.751 1 26.4 ? SD SAM 504 A 1 HETATM 9 C CE SAM . . . E 3 12.607 11.471 18.681 1 24.86 ? CE SAM 504 A 1 HETATM 10 C C5' SAM . . . E 3 14.038 13.047 20.314 1 26.29 ? C5' SAM 504 A 1 HETATM 11 C C4' SAM . . . E 3 14.201 14.263 21.238 1 25.76 ? C4' SAM 504 A 1 HETATM 12 O O4' SAM . . . E 3 13.467 14.181 22.474 1 25.18 ? O4' SAM 504 A 1 HETATM 13 C C3' SAM . . . E 3 15.663 14.45 21.658 1 25.06 ? C3' SAM 504 A 1 HETATM 14 O O3' SAM . . . E 3 16.415 15.171 20.675 1 24.77 ? O3' SAM 504 A 1 HETATM 15 C C2' SAM . . . E 3 15.529 15.201 22.962 1 24.86 ? C2' SAM 504 A 1 HETATM 16 O O2' SAM . . . E 3 15.282 16.583 22.696 1 23.52 ? O2' SAM 504 A 1 HETATM 17 C C1' SAM . . . E 3 14.288 14.579 23.579 1 25.02 ? C1' SAM 504 A 1 HETATM 18 N N9 SAM . . . E 3 14.585 13.395 24.411 1 24.47 ? N9 SAM 504 A 1 HETATM 19 C C8 SAM . . . E 3 14.423 12.107 24.05 1 25.27 ? C8 SAM 504 A 1 HETATM 20 N N7 SAM . . . E 3 14.762 11.262 25.048 1 24.81 ? N7 SAM 504 A 1 HETATM 21 C C5 SAM . . . E 3 15.163 12.026 26.082 1 24.9 ? C5 SAM 504 A 1 HETATM 22 C C6 SAM . . . E 3 15.651 11.796 27.464 1 24.4 ? C6 SAM 504 A 1 HETATM 23 N N6 SAM . . . E 3 15.804 10.542 27.965 1 23.61 ? N6 SAM 504 A 1 HETATM 24 N N1 SAM . . . E 3 15.948 12.885 28.21 1 23.68 ? N1 SAM 504 A 1 HETATM 25 C C2 SAM . . . E 3 15.804 14.135 27.753 1 23.42 ? C2 SAM 504 A 1 HETATM 26 N N3 SAM . . . E 3 15.365 14.416 26.521 1 24.3 ? N3 SAM 504 A 1 HETATM 27 C C4 SAM . . . E 3 15.04 13.428 25.653 1 24.92 ? C4 SAM 504 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #