data_5EX3 # _model_server_result.job_id MI0bklfB9GwopXpIqaeROg _model_server_result.datetime_utc '2024-11-28 20:46:19' _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 5ex3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":504}' # _entry.id 5EX3 # _exptl.entry_id 5EX3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 4 _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 5EX3 _cell.length_a 53.378 _cell.length_b 104.659 _cell.length_c 117.599 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EX3 _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 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,L _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 4 _struct_asym.id F _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 57 A CYS 49 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc2 A SG CYS 60 A CYS 52 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc3 A SG CYS 70 A CYS 62 1_555 D ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc4 A SG CYS 73 A CYS 65 1_555 D ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc5 A SG CYS 79 A CYS 71 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc6 A SG CYS 83 A CYS 75 1_555 C ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc7 A NE2 HIS 91 A HIS 83 1_555 D ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc8 A SG CYS 95 A CYS 87 1_555 D ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? metalc ? metalc9 A SG CYS 216 A CYS 208 1_555 E ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc10 A SG CYS 269 A CYS 261 1_555 E ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc11 A SG CYS 271 A CYS 263 1_555 E ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc12 A SG CYS 274 A CYS 266 1_555 E ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? covale ? covale1 B C GLY 4 D GLY 830 1_555 B N MLY 5 D MLY 831 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 B C MLY 5 D MLY 831 1_555 B N SER 6 D SER 832 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _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 5EX3 _atom_sites.fract_transf_matrix[1][1] 0.018734 _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] 0.009555 _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] 0.008503 _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 ZN A 1 501 1 ZN ZN . D 3 ZN A 1 502 2 ZN ZN . E 3 ZN A 1 503 3 ZN ZN . F 4 SAH A 1 504 1 SAH SAH . G 5 ACY A 1 505 1 ACY ACT . H 5 ACY A 1 506 2 ACY ACT . I 5 ACY A 1 507 3 ACY ACT . J 5 ACY A 1 508 4 ACY ACT . K 6 HOH A 1 601 61 HOH HOH . K 6 HOH A 2 602 7 HOH HOH . K 6 HOH A 3 603 3 HOH HOH . K 6 HOH A 4 604 98 HOH HOH . K 6 HOH A 5 605 83 HOH HOH . K 6 HOH A 6 606 2 HOH HOH . K 6 HOH A 7 607 84 HOH HOH . K 6 HOH A 8 608 14 HOH HOH . K 6 HOH A 9 609 44 HOH HOH . K 6 HOH A 10 610 22 HOH HOH . K 6 HOH A 11 611 87 HOH HOH . K 6 HOH A 12 612 101 HOH HOH . K 6 HOH A 13 613 92 HOH HOH . K 6 HOH A 14 614 111 HOH HOH . K 6 HOH A 15 615 16 HOH HOH . K 6 HOH A 16 616 30 HOH HOH . K 6 HOH A 17 617 63 HOH HOH . K 6 HOH A 18 618 103 HOH HOH . K 6 HOH A 19 619 18 HOH HOH . K 6 HOH A 20 620 110 HOH HOH . K 6 HOH A 21 621 62 HOH HOH . K 6 HOH A 22 622 105 HOH HOH . K 6 HOH A 23 623 67 HOH HOH . K 6 HOH A 24 624 6 HOH HOH . K 6 HOH A 25 625 28 HOH HOH . K 6 HOH A 26 626 55 HOH HOH . K 6 HOH A 27 627 46 HOH HOH . K 6 HOH A 28 628 12 HOH HOH . K 6 HOH A 29 629 5 HOH HOH . K 6 HOH A 30 630 47 HOH HOH . K 6 HOH A 31 631 76 HOH HOH . K 6 HOH A 32 632 74 HOH HOH . K 6 HOH A 33 633 26 HOH HOH . K 6 HOH A 34 634 109 HOH HOH . K 6 HOH A 35 635 25 HOH HOH . K 6 HOH A 36 636 40 HOH HOH . K 6 HOH A 37 637 93 HOH HOH . K 6 HOH A 38 638 69 HOH HOH . K 6 HOH A 39 639 71 HOH HOH . K 6 HOH A 40 640 90 HOH HOH . K 6 HOH A 41 641 39 HOH HOH . K 6 HOH A 42 642 15 HOH HOH . K 6 HOH A 43 643 77 HOH HOH . K 6 HOH A 44 644 104 HOH HOH . K 6 HOH A 45 645 9 HOH HOH . K 6 HOH A 46 646 1 HOH HOH . K 6 HOH A 47 647 80 HOH HOH . K 6 HOH A 48 648 23 HOH HOH . K 6 HOH A 49 649 45 HOH HOH . K 6 HOH A 50 650 68 HOH HOH . K 6 HOH A 51 651 13 HOH HOH . K 6 HOH A 52 652 89 HOH HOH . K 6 HOH A 53 653 10 HOH HOH . K 6 HOH A 54 654 64 HOH HOH . K 6 HOH A 55 655 66 HOH HOH . K 6 HOH A 56 656 21 HOH HOH . K 6 HOH A 57 657 32 HOH HOH . K 6 HOH A 58 658 33 HOH HOH . K 6 HOH A 59 659 43 HOH HOH . K 6 HOH A 60 660 24 HOH HOH . K 6 HOH A 61 661 49 HOH HOH . K 6 HOH A 62 662 36 HOH HOH . K 6 HOH A 63 663 58 HOH HOH . K 6 HOH A 64 664 31 HOH HOH . K 6 HOH A 65 665 102 HOH HOH . K 6 HOH A 66 666 19 HOH HOH . K 6 HOH A 67 667 94 HOH HOH . K 6 HOH A 68 668 70 HOH HOH . K 6 HOH A 69 669 91 HOH HOH . K 6 HOH A 70 670 54 HOH HOH . K 6 HOH A 71 671 82 HOH HOH . K 6 HOH A 72 672 38 HOH HOH . K 6 HOH A 73 673 27 HOH HOH . K 6 HOH A 74 674 97 HOH HOH . K 6 HOH A 75 675 8 HOH HOH . K 6 HOH A 76 676 106 HOH HOH . K 6 HOH A 77 677 53 HOH HOH . K 6 HOH A 78 678 37 HOH HOH . K 6 HOH A 79 679 4 HOH HOH . K 6 HOH A 80 680 52 HOH HOH . K 6 HOH A 81 681 29 HOH HOH . K 6 HOH A 82 682 48 HOH HOH . K 6 HOH A 83 683 35 HOH HOH . K 6 HOH A 84 684 78 HOH HOH . K 6 HOH A 85 685 57 HOH HOH . K 6 HOH A 86 686 81 HOH HOH . K 6 HOH A 87 687 88 HOH HOH . K 6 HOH A 88 688 72 HOH HOH . K 6 HOH A 89 689 73 HOH HOH . K 6 HOH A 90 690 79 HOH HOH . L 6 HOH D 1 901 96 HOH HOH . L 6 HOH D 2 902 41 HOH HOH . L 6 HOH D 3 903 107 HOH HOH . L 6 HOH D 4 904 17 HOH HOH . L 6 HOH D 5 905 75 HOH HOH . L 6 HOH D 6 906 100 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 . . . F 4 29.325 2.536 6.356 1 60.51 ? N SAH 504 A 1 HETATM 2 C CA SAH . . . F 4 28.236 2.095 7.213 1 57.1 ? CA SAH 504 A 1 HETATM 3 C CB SAH . . . F 4 27.785 0.712 6.751 1 57.88 ? CB SAH 504 A 1 HETATM 4 C CG SAH . . . F 4 26.722 0.782 5.655 1 57.1 ? CG SAH 504 A 1 HETATM 5 S SD SAH . . . F 4 25.165 1.5 6.27 1 55.77 ? SD SAH 504 A 1 HETATM 6 C C SAH . . . F 4 28.624 2.137 8.692 1 61.02 ? C SAH 504 A 1 HETATM 7 O O SAH . . . F 4 29.749 2.504 9.049 1 61.67 ? O SAH 504 A 1 HETATM 8 O OXT SAH . . . F 4 27.823 1.813 9.57 1 61.82 ? OXT SAH 504 A 1 HETATM 9 C C5' SAH . . . F 4 24.957 2.589 4.845 1 58.32 ? C5' SAH 504 A 1 HETATM 10 C C4' SAH . . . F 4 25.751 3.88 4.988 1 60.98 ? C4' SAH 504 A 1 HETATM 11 O O4' SAH . . . F 4 27.124 3.654 4.687 1 64.67 ? O4' SAH 504 A 1 HETATM 12 C C3' SAH . . . F 4 25.256 4.965 4.044 1 60.01 ? C3' SAH 504 A 1 HETATM 13 O O3' SAH . . . F 4 24.338 5.829 4.664 1 60.23 ? O3' SAH 504 A 1 HETATM 14 C C2' SAH . . . F 4 26.518 5.713 3.697 1 65.03 ? C2' SAH 504 A 1 HETATM 15 O O2' SAH . . . F 4 26.745 6.684 4.698 1 69.51 ? O2' SAH 504 A 1 HETATM 16 C C1' SAH . . . F 4 27.6 4.656 3.809 1 60.93 ? C1' SAH 504 A 1 HETATM 17 N N9 SAH . . . F 4 27.909 4.044 2.491 1 64.01 ? N9 SAH 504 A 1 HETATM 18 C C8 SAH . . . F 4 27.429 2.847 2.013 1 59.55 ? C8 SAH 504 A 1 HETATM 19 N N7 SAH . . . F 4 27.955 2.628 0.787 1 58.98 ? N7 SAH 504 A 1 HETATM 20 C C5 SAH . . . F 4 28.755 3.677 0.464 1 63.59 ? C5 SAH 504 A 1 HETATM 21 C C6 SAH . . . F 4 29.523 3.975 -0.668 1 65.07 ? C6 SAH 504 A 1 HETATM 22 N N6 SAH . . . F 4 29.556 3.141 -1.705 1 63.06 ? N6 SAH 504 A 1 HETATM 23 N N1 SAH . . . F 4 30.251 5.145 -0.719 1 62.13 ? N1 SAH 504 A 1 HETATM 24 C C2 SAH . . . F 4 30.212 6.019 0.347 1 64.1 ? C2 SAH 504 A 1 HETATM 25 N N3 SAH . . . F 4 29.45 5.719 1.465 1 61.16 ? N3 SAH 504 A 1 HETATM 26 C C4 SAH . . . F 4 28.735 4.571 1.525 1 59.76 ? C4 SAH 504 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 26 #