data_5IS7 # _model_server_result.job_id nk2zvZ3ST-WPTJa8G3lfNQ _model_server_result.datetime_utc '2024-11-16 11:01:01' _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 5is7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":504}' # _entry.id 5IS7 # _exptl.entry_id 5IS7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 340.401 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-S-(3-aminopropyl)-5'-thioadenosine" _entity.pdbx_number_of_molecules 4 _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 5IS7 _cell.length_a 74.528 _cell.length_b 98.935 _cell.length_c 206.914 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5IS7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details 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,M,N,O,P,Q,R,S _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 H N N ? 4 K N N ? 4 M N N ? 4 O N N # _chem_comp.formula 'C13 H20 N6 O3 S' _chem_comp.formula_weight 340.401 _chem_comp.id DSH _chem_comp.mon_nstd_flag . _chem_comp.name "5'-S-(3-aminopropyl)-5'-thioadenosine" _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 DSH sing 83 n n N1 C2 DSH doub 84 n y N1 C6 DSH sing 85 n y C2 N3 DSH sing 86 n y N3 C4 DSH doub 87 n y C4 C5 DSH sing 88 n y C4 N9 DSH sing 89 n y C5 C6 DSH doub 90 n y C5 N7 DSH sing 91 n y C6 N6 DSH sing 92 n n N7 C8 DSH doub 93 n y C8 N9 DSH sing 94 n y N9 C1' DSH sing 95 n n CA CB DSH sing 96 n n CB CG DSH sing 97 n n SD CG DSH sing 98 n n SD C5' DSH sing 99 n n C1' C2' DSH sing 100 n n C1' O4' DSH sing 101 n n C2' O2' DSH sing 102 n n C2' C3' DSH sing 103 n n C3' O3' DSH sing 104 n n C3' C4' DSH sing 105 n n C4' O4' DSH sing 106 n n C4' C5' DSH sing 107 n n N HN DSH sing 108 n n N HNA DSH sing 109 n n C2 H2 DSH sing 110 n n N6 HN6 DSH sing 111 n n N6 HN6A DSH sing 112 n n C8 H8 DSH sing 113 n n CA HA DSH sing 114 n n CB HB DSH sing 115 n n CG HG DSH sing 116 n n CG HGA DSH sing 117 n n C1' H1' DSH sing 118 n n C2' H2' DSH sing 119 n n O2' HO2' DSH sing 120 n n C3' H3' DSH sing 121 n n O3' HO3' DSH sing 122 n n C4' H4' DSH sing 123 n n C5' H5' DSH sing 124 n n C5' "H5'A" DSH sing 125 n n CA HAA DSH sing 126 n n CB HBA DSH sing 127 n n # _atom_sites.entry_id 5IS7 _atom_sites.fract_transf_matrix[1][1] 0.013418 _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] 0.010108 _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] 0.004833 _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 E 2 EDO A 1 501 4 EDO EDO . F 3 PEG A 1 502 6 PEG PEG . G 3 PEG A 1 503 7 PEG PEG . H 4 DSH A 1 504 1 DSH DSH . I 2 EDO B 1 501 2 EDO EDO . J 2 EDO B 1 502 3 EDO EDO . K 4 DSH B 1 503 2 DSH DSH . L 2 EDO C 1 501 1 EDO EDO . M 4 DSH C 1 502 3 DSH DSH . N 2 EDO D 1 501 5 EDO EDO . O 4 DSH D 1 502 4 DSH DSH . P 5 HOH A 1 601 30 HOH HOH . P 5 HOH A 2 602 12 HOH HOH . P 5 HOH A 3 603 104 HOH HOH . P 5 HOH A 4 604 94 HOH HOH . P 5 HOH A 5 605 37 HOH HOH . P 5 HOH A 6 606 79 HOH HOH . P 5 HOH A 7 607 35 HOH HOH . P 5 HOH A 8 608 65 HOH HOH . P 5 HOH A 9 609 31 HOH HOH . P 5 HOH A 10 610 119 HOH HOH . P 5 HOH A 11 611 28 HOH HOH . P 5 HOH A 12 612 74 HOH HOH . P 5 HOH A 13 613 106 HOH HOH . P 5 HOH A 14 614 8 HOH HOH . P 5 HOH A 15 615 6 HOH HOH . P 5 HOH A 16 616 105 HOH HOH . P 5 HOH A 17 617 26 HOH HOH . P 5 HOH A 18 618 111 HOH HOH . P 5 HOH A 19 619 96 HOH HOH . P 5 HOH A 20 620 5 HOH HOH . P 5 HOH A 21 621 39 HOH HOH . P 5 HOH A 22 622 13 HOH HOH . P 5 HOH A 23 623 101 HOH HOH . P 5 HOH A 24 624 80 HOH HOH . P 5 HOH A 25 625 23 HOH HOH . P 5 HOH A 26 626 46 HOH HOH . P 5 HOH A 27 627 48 HOH HOH . P 5 HOH A 28 628 10 HOH HOH . P 5 HOH A 29 629 83 HOH HOH . P 5 HOH A 30 630 18 HOH HOH . P 5 HOH A 31 631 9 HOH HOH . P 5 HOH A 32 632 42 HOH HOH . P 5 HOH A 33 633 52 HOH HOH . P 5 HOH A 34 634 4 HOH HOH . P 5 HOH A 35 635 103 HOH HOH . P 5 HOH A 36 636 45 HOH HOH . P 5 HOH A 37 637 38 HOH HOH . P 5 HOH A 38 638 21 HOH HOH . P 5 HOH A 39 639 60 HOH HOH . P 5 HOH A 40 640 86 HOH HOH . P 5 HOH A 41 641 36 HOH HOH . P 5 HOH A 42 642 25 HOH HOH . P 5 HOH A 43 643 116 HOH HOH . P 5 HOH A 44 644 57 HOH HOH . P 5 HOH A 45 645 81 HOH HOH . P 5 HOH A 46 646 99 HOH HOH . P 5 HOH A 47 647 67 HOH HOH . P 5 HOH A 48 648 118 HOH HOH . P 5 HOH A 49 649 63 HOH HOH . P 5 HOH A 50 650 114 HOH HOH . P 5 HOH A 51 651 120 HOH HOH . P 5 HOH A 52 652 91 HOH HOH . P 5 HOH A 53 653 115 HOH HOH . P 5 HOH A 54 654 59 HOH HOH . P 5 HOH A 55 655 40 HOH HOH . P 5 HOH A 56 656 82 HOH HOH . P 5 HOH A 57 657 117 HOH HOH . P 5 HOH A 58 658 84 HOH HOH . P 5 HOH A 59 659 100 HOH HOH . P 5 HOH A 60 660 53 HOH HOH . P 5 HOH A 61 661 110 HOH HOH . Q 5 HOH B 1 601 2 HOH HOH . Q 5 HOH B 2 602 3 HOH HOH . Q 5 HOH B 3 603 108 HOH HOH . Q 5 HOH B 4 604 107 HOH HOH . Q 5 HOH B 5 605 44 HOH HOH . Q 5 HOH B 6 606 77 HOH HOH . Q 5 HOH B 7 607 24 HOH HOH . Q 5 HOH B 8 608 49 HOH HOH . Q 5 HOH B 9 609 43 HOH HOH . Q 5 HOH B 10 610 71 HOH HOH . Q 5 HOH B 11 611 1 HOH HOH . Q 5 HOH B 12 612 33 HOH HOH . Q 5 HOH B 13 613 14 HOH HOH . Q 5 HOH B 14 614 15 HOH HOH . Q 5 HOH B 15 615 7 HOH HOH . Q 5 HOH B 16 616 95 HOH HOH . Q 5 HOH B 17 617 51 HOH HOH . Q 5 HOH B 18 618 58 HOH HOH . Q 5 HOH B 19 619 27 HOH HOH . Q 5 HOH B 20 620 47 HOH HOH . Q 5 HOH B 21 621 70 HOH HOH . Q 5 HOH B 22 622 56 HOH HOH . Q 5 HOH B 23 623 32 HOH HOH . Q 5 HOH B 24 624 98 HOH HOH . Q 5 HOH B 25 625 19 HOH HOH . Q 5 HOH B 26 626 92 HOH HOH . Q 5 HOH B 27 627 90 HOH HOH . Q 5 HOH B 28 628 34 HOH HOH . Q 5 HOH B 29 629 62 HOH HOH . Q 5 HOH B 30 630 54 HOH HOH . Q 5 HOH B 31 631 22 HOH HOH . Q 5 HOH B 32 632 88 HOH HOH . Q 5 HOH B 33 633 66 HOH HOH . Q 5 HOH B 34 634 85 HOH HOH . Q 5 HOH B 35 635 29 HOH HOH . Q 5 HOH B 36 636 73 HOH HOH . Q 5 HOH B 37 637 61 HOH HOH . Q 5 HOH B 38 638 55 HOH HOH . Q 5 HOH B 39 639 41 HOH HOH . Q 5 HOH B 40 640 113 HOH HOH . Q 5 HOH B 41 641 102 HOH HOH . Q 5 HOH B 42 642 75 HOH HOH . Q 5 HOH B 43 643 69 HOH HOH . Q 5 HOH B 44 644 76 HOH HOH . R 5 HOH C 1 601 50 HOH HOH . R 5 HOH C 2 602 11 HOH HOH . R 5 HOH C 3 603 64 HOH HOH . R 5 HOH C 4 604 17 HOH HOH . R 5 HOH C 5 605 16 HOH HOH . R 5 HOH C 6 606 72 HOH HOH . R 5 HOH C 7 607 78 HOH HOH . R 5 HOH C 8 608 97 HOH HOH . R 5 HOH C 9 609 68 HOH HOH . R 5 HOH C 10 610 93 HOH HOH . R 5 HOH C 11 611 87 HOH HOH . S 5 HOH D 1 601 109 HOH HOH . S 5 HOH D 2 602 89 HOH HOH . S 5 HOH D 3 603 112 HOH HOH . S 5 HOH D 4 604 20 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 DSH . . . H 4 52.668 30.226 132.12 1 76.2 ? N DSH 504 A 1 HETATM 2 N N1 DSH . . . H 4 50.107 42.743 126.762 1 69 ? N1 DSH 504 A 1 HETATM 3 C C2 DSH . . . H 4 49.969 42.61 128.085 1 68.62 ? C2 DSH 504 A 1 HETATM 4 N N3 DSH . . . H 4 49.745 41.504 128.799 1 65.84 ? N3 DSH 504 A 1 HETATM 5 C C4 DSH . . . H 4 49.665 40.431 128.006 1 66.41 ? C4 DSH 504 A 1 HETATM 6 C C5 DSH . . . H 4 49.789 40.407 126.625 1 68.37 ? C5 DSH 504 A 1 HETATM 7 C C6 DSH . . . H 4 50.02 41.641 125.987 1 69.73 ? C6 DSH 504 A 1 HETATM 8 N N6 DSH . . . H 4 50.149 41.782 124.664 1 69.34 ? N6 DSH 504 A 1 HETATM 9 N N7 DSH . . . H 4 49.657 39.116 126.141 1 63.54 ? N7 DSH 504 A 1 HETATM 10 C C8 DSH . . . H 4 49.456 38.399 127.221 1 64.9 ? C8 DSH 504 A 1 HETATM 11 N N9 DSH . . . H 4 49.448 39.126 128.381 1 66.19 ? N9 DSH 504 A 1 HETATM 12 C CA DSH . . . H 4 52.157 30.687 130.803 1 76.83 ? CA DSH 504 A 1 HETATM 13 C CB DSH . . . H 4 51.166 31.819 130.95 1 76.18 ? CB DSH 504 A 1 HETATM 14 S SD DSH . . . H 4 50.817 34.428 131.908 1 73.08 ? SD DSH 504 A 1 HETATM 15 C CG DSH . . . H 4 51.864 33.15 131.152 1 78.32 ? CG DSH 504 A 1 HETATM 16 C C1' DSH . . . H 4 49.246 38.623 129.736 1 64.74 ? C1' DSH 504 A 1 HETATM 17 C C2' DSH . . . H 4 48.039 37.706 129.893 1 59.85 ? C2' DSH 504 A 1 HETATM 18 O O2' DSH . . . H 4 46.857 38.471 130.097 1 59.25 ? O2' DSH 504 A 1 HETATM 19 C C3' DSH . . . H 4 48.432 36.917 131.144 1 60.9 ? C3' DSH 504 A 1 HETATM 20 O O3' DSH . . . H 4 48.055 37.599 132.335 1 57.71 ? O3' DSH 504 A 1 HETATM 21 C C4' DSH . . . H 4 49.956 36.815 131.03 1 68.88 ? C4' DSH 504 A 1 HETATM 22 O O4' DSH . . . H 4 50.366 37.845 130.101 1 63.44 ? O4' DSH 504 A 1 HETATM 23 C C5' DSH . . . H 4 50.357 35.456 130.491 1 67.19 ? C5' DSH 504 A 1 HETATM 24 H HN DSH . . . H 4 51.976 30.348 132.853 1 91.44 ? HN DSH 504 A 1 HETATM 25 H HNA DSH . . . H 4 52.91 29.241 132.09 1 91.44 ? HNA DSH 504 A 1 HETATM 26 H H2 DSH . . . H 4 50.054 43.539 128.647 1 82.35 ? H2 DSH 504 A 1 HETATM 27 H HN6 DSH . . . H 4 50.088 40.99 124.032 1 83.21 ? HN6 DSH 504 A 1 HETATM 28 H HN6A DSH . . . H 4 50.315 42.7 124.265 1 83.21 ? HN6A DSH 504 A 1 HETATM 29 H H8 DSH . . . H 4 49.309 37.32 127.196 1 77.88 ? H8 DSH 504 A 1 HETATM 30 H HA DSH . . . H 4 52.996 30.993 130.18 1 92.2 ? HA DSH 504 A 1 HETATM 31 H HB DSH . . . H 4 50.503 31.655 131.799 1 91.41 ? HB DSH 504 A 1 HETATM 32 H HG DSH . . . H 4 52.224 33.55 130.205 1 93.99 ? HG DSH 504 A 1 HETATM 33 H HGA DSH . . . H 4 52.759 33.021 131.758 1 93.99 ? HGA DSH 504 A 1 HETATM 34 H H1' DSH . . . H 4 49.203 39.466 130.424 1 77.69 ? H1' DSH 504 A 1 HETATM 35 H H2' DSH . . . H 4 47.912 37.04 129.04 1 71.82 ? H2' DSH 504 A 1 HETATM 36 H HO2' DSH . . . H 4 46.928 38.888 130.995 1 71.1 ? HO2' DSH 504 A 1 HETATM 37 H H3' DSH . . . H 4 47.969 35.931 131.149 1 73.08 ? H3' DSH 504 A 1 HETATM 38 H HO3' DSH . . . H 4 48.407 38.524 132.257 1 69.25 ? HO3' DSH 504 A 1 HETATM 39 H H4' DSH . . . H 4 50.483 37.056 131.952 1 82.65 ? H4' DSH 504 A 1 HETATM 40 H H5' DSH . . . H 4 51.22 35.523 129.83 1 80.63 ? H5' DSH 504 A 1 HETATM 41 H "H5'A" DSH . . . H 4 49.585 34.976 129.89 1 80.63 ? "H5'A" DSH 504 A 1 HETATM 42 H HAA DSH . . . H 4 51.706 29.852 130.269 1 92.2 ? HAA DSH 504 A 1 HETATM 43 H HBA DSH . . . H 4 50.521 31.899 130.076 1 91.41 ? HBA DSH 504 A 1 HETATM 44 H H21 DSH . . . H 4 53.497 30.745 132.394 1 91.44 ? H21 DSH 504 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 100 _model_server_stats.query_time_ms 395 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 44 #