data_5ISD # _model_server_result.job_id K5YI8BgAjQqewmC-lvHVSg _model_server_result.datetime_utc '2024-11-13 19:15:35' _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 5isd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":504}' # _entry.id 5ISD # _exptl.entry_id 5ISD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 385.419 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine" _entity.pdbx_number_of_molecules 3 _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 5ISD _cell.length_a 74.555 _cell.length_b 98.446 _cell.length_c 205.792 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ISD _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,T,U,V,W,X,Y _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 ? 5 K N N ? 5 S N N ? 5 U N N # _chem_comp.formula 'C14 H21 N6 O5 S 1' _chem_comp.formula_weight 385.419 _chem_comp.id SAO _chem_comp.mon_nstd_flag . _chem_comp.name "5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine" _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms S-ADENOSYL-L-HOMOCYSTEINE # 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 N6 C6 SAO sing 387 n n C6 C5 SAO doub 388 n y C6 N1 SAO sing 389 n y N7 C5 SAO sing 390 n y N7 C8 SAO doub 391 n y C5 C4 SAO sing 392 n y N1 C2 SAO doub 393 n y C8 N9 SAO sing 394 n y C4 N9 SAO sing 395 n y C4 N3 SAO doub 396 n y C2 N3 SAO sing 397 n y N9 C1' SAO sing 398 n n C1' C2' SAO sing 399 n n C1' O4' SAO sing 400 n n C2' O2' SAO sing 401 n n C2' C3' SAO sing 402 n n O4' C4' SAO sing 403 n n C5' C4' SAO sing 404 n n C5' SD SAO sing 405 n n C3' C4' SAO sing 406 n n C3' O3' SAO sing 407 n n SD CG SAO sing 408 n n CG CB SAO sing 409 n n CB CA SAO sing 410 n n N CA SAO sing 411 n n CA C SAO sing 412 n n O C SAO doub 413 n n C OXT SAO sing 414 n n N HN2 SAO sing 415 n n N H3 SAO sing 416 n n N HN1 SAO sing 417 n n CA HA SAO sing 418 n n CB HB1 SAO sing 419 n n CB HB2 SAO sing 420 n n CG HG2 SAO sing 421 n n CG HG1 SAO sing 422 n n OXT H1 SAO sing 423 n n C5' "H5'2" SAO sing 424 n n C5' "H5'1" SAO sing 425 n n C4' H4' SAO sing 426 n n C3' H3' SAO sing 427 n n O3' HO3' SAO sing 428 n n C2' H2' SAO sing 429 n n O2' HO2' SAO sing 430 n n C1' H1' SAO sing 431 n n C8 H8 SAO sing 432 n n N6 HN61 SAO sing 433 n n N6 HN62 SAO sing 434 n n C2 H2 SAO sing 435 n n # _atom_sites.entry_id 5ISD _atom_sites.fract_transf_matrix[1][1] 0.013413 _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] 0.010158 _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] 0.004859 _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 2 EDO EDO . F 2 EDO A 1 502 7 EDO EDO . G 2 EDO A 1 503 8 EDO EDO . H 3 PEG A 1 504 10 PEG PEG . I 3 PEG A 1 505 11 PEG PEG . J 4 M2M A 1 506 13 M2M M2M . K 5 SAO A 1 507 1 SAO SAH . L 2 EDO B 1 501 1 EDO EDO . M 2 EDO B 1 502 6 EDO EDO . N 3 PEG B 1 503 12 PEG PEG . O 6 6CZ B 1 504 2 6CZ 592 . P 2 EDO C 1 501 3 EDO EDO . Q 2 EDO C 1 502 4 EDO EDO . R 2 EDO C 1 503 9 EDO EDO . S 5 SAO C 1 504 3 SAO SAH . T 2 EDO D 1 501 5 EDO EDO . U 5 SAO D 1 502 4 SAO SAH . V 7 HOH A 1 601 49 HOH HOH . V 7 HOH A 2 602 114 HOH HOH . V 7 HOH A 3 603 137 HOH HOH . V 7 HOH A 4 604 134 HOH HOH . V 7 HOH A 5 605 95 HOH HOH . V 7 HOH A 6 606 35 HOH HOH . V 7 HOH A 7 607 85 HOH HOH . V 7 HOH A 8 608 43 HOH HOH . V 7 HOH A 9 609 32 HOH HOH . V 7 HOH A 10 610 107 HOH HOH . V 7 HOH A 11 611 19 HOH HOH . V 7 HOH A 12 612 122 HOH HOH . V 7 HOH A 13 613 84 HOH HOH . V 7 HOH A 14 614 68 HOH HOH . V 7 HOH A 15 615 108 HOH HOH . V 7 HOH A 16 616 36 HOH HOH . V 7 HOH A 17 617 152 HOH HOH . V 7 HOH A 18 618 155 HOH HOH . V 7 HOH A 19 619 39 HOH HOH . V 7 HOH A 20 620 90 HOH HOH . V 7 HOH A 21 621 88 HOH HOH . V 7 HOH A 22 622 29 HOH HOH . V 7 HOH A 23 623 3 HOH HOH . V 7 HOH A 24 624 100 HOH HOH . V 7 HOH A 25 625 156 HOH HOH . V 7 HOH A 26 626 7 HOH HOH . V 7 HOH A 27 627 106 HOH HOH . V 7 HOH A 28 628 14 HOH HOH . V 7 HOH A 29 629 159 HOH HOH . V 7 HOH A 30 630 104 HOH HOH . V 7 HOH A 31 631 89 HOH HOH . V 7 HOH A 32 632 6 HOH HOH . V 7 HOH A 33 633 79 HOH HOH . V 7 HOH A 34 634 138 HOH HOH . V 7 HOH A 35 635 18 HOH HOH . V 7 HOH A 36 636 13 HOH HOH . V 7 HOH A 37 637 31 HOH HOH . V 7 HOH A 38 638 117 HOH HOH . V 7 HOH A 39 639 135 HOH HOH . V 7 HOH A 40 640 64 HOH HOH . V 7 HOH A 41 641 34 HOH HOH . V 7 HOH A 42 642 8 HOH HOH . V 7 HOH A 43 643 93 HOH HOH . V 7 HOH A 44 644 154 HOH HOH . V 7 HOH A 45 645 119 HOH HOH . V 7 HOH A 46 646 97 HOH HOH . V 7 HOH A 47 647 128 HOH HOH . V 7 HOH A 48 648 11 HOH HOH . V 7 HOH A 49 649 63 HOH HOH . V 7 HOH A 50 650 25 HOH HOH . V 7 HOH A 51 651 111 HOH HOH . V 7 HOH A 52 652 162 HOH HOH . V 7 HOH A 53 653 121 HOH HOH . V 7 HOH A 54 654 42 HOH HOH . V 7 HOH A 55 655 21 HOH HOH . V 7 HOH A 56 656 115 HOH HOH . V 7 HOH A 57 657 58 HOH HOH . V 7 HOH A 58 658 99 HOH HOH . V 7 HOH A 59 659 70 HOH HOH . V 7 HOH A 60 660 59 HOH HOH . W 7 HOH B 1 601 113 HOH HOH . W 7 HOH B 2 602 54 HOH HOH . W 7 HOH B 3 603 78 HOH HOH . W 7 HOH B 4 604 105 HOH HOH . W 7 HOH B 5 605 160 HOH HOH . W 7 HOH B 6 606 164 HOH HOH . W 7 HOH B 7 607 55 HOH HOH . W 7 HOH B 8 608 87 HOH HOH . W 7 HOH B 9 609 41 HOH HOH . W 7 HOH B 10 610 15 HOH HOH . W 7 HOH B 11 611 125 HOH HOH . W 7 HOH B 12 612 44 HOH HOH . W 7 HOH B 13 613 82 HOH HOH . W 7 HOH B 14 614 5 HOH HOH . W 7 HOH B 15 615 109 HOH HOH . W 7 HOH B 16 616 132 HOH HOH . W 7 HOH B 17 617 48 HOH HOH . W 7 HOH B 18 618 16 HOH HOH . W 7 HOH B 19 619 46 HOH HOH . W 7 HOH B 20 620 163 HOH HOH . W 7 HOH B 21 621 149 HOH HOH . W 7 HOH B 22 622 116 HOH HOH . W 7 HOH B 23 623 94 HOH HOH . W 7 HOH B 24 624 98 HOH HOH . W 7 HOH B 25 625 133 HOH HOH . W 7 HOH B 26 626 118 HOH HOH . W 7 HOH B 27 627 23 HOH HOH . W 7 HOH B 28 628 145 HOH HOH . W 7 HOH B 29 629 67 HOH HOH . W 7 HOH B 30 630 56 HOH HOH . X 7 HOH C 1 601 131 HOH HOH . X 7 HOH C 2 602 50 HOH HOH . X 7 HOH C 3 603 126 HOH HOH . X 7 HOH C 4 604 127 HOH HOH . X 7 HOH C 5 605 158 HOH HOH . X 7 HOH C 6 606 65 HOH HOH . X 7 HOH C 7 607 53 HOH HOH . X 7 HOH C 8 608 76 HOH HOH . X 7 HOH C 9 609 157 HOH HOH . X 7 HOH C 10 610 146 HOH HOH . X 7 HOH C 11 611 96 HOH HOH . X 7 HOH C 12 612 71 HOH HOH . X 7 HOH C 13 613 52 HOH HOH . X 7 HOH C 14 614 81 HOH HOH . X 7 HOH C 15 615 124 HOH HOH . X 7 HOH C 16 616 37 HOH HOH . X 7 HOH C 17 617 165 HOH HOH . X 7 HOH C 18 618 136 HOH HOH . X 7 HOH C 19 619 110 HOH HOH . X 7 HOH C 20 620 150 HOH HOH . X 7 HOH C 21 621 45 HOH HOH . X 7 HOH C 22 622 148 HOH HOH . X 7 HOH C 23 623 57 HOH HOH . X 7 HOH C 24 624 38 HOH HOH . X 7 HOH C 25 625 20 HOH HOH . X 7 HOH C 26 626 120 HOH HOH . X 7 HOH C 27 627 9 HOH HOH . X 7 HOH C 28 628 61 HOH HOH . X 7 HOH C 29 629 139 HOH HOH . X 7 HOH C 30 630 74 HOH HOH . X 7 HOH C 31 631 80 HOH HOH . X 7 HOH C 32 632 26 HOH HOH . X 7 HOH C 33 633 147 HOH HOH . X 7 HOH C 34 634 17 HOH HOH . X 7 HOH C 35 635 130 HOH HOH . X 7 HOH C 36 636 92 HOH HOH . X 7 HOH C 37 637 28 HOH HOH . X 7 HOH C 38 638 91 HOH HOH . X 7 HOH C 39 639 27 HOH HOH . X 7 HOH C 40 640 60 HOH HOH . X 7 HOH C 41 641 30 HOH HOH . X 7 HOH C 42 642 10 HOH HOH . X 7 HOH C 43 643 129 HOH HOH . Y 7 HOH D 1 601 86 HOH HOH . Y 7 HOH D 2 602 12 HOH HOH . Y 7 HOH D 3 603 123 HOH HOH . Y 7 HOH D 4 604 73 HOH HOH . Y 7 HOH D 5 605 153 HOH HOH . Y 7 HOH D 6 606 51 HOH HOH . Y 7 HOH D 7 607 2 HOH HOH . Y 7 HOH D 8 608 102 HOH HOH . Y 7 HOH D 9 609 1 HOH HOH . Y 7 HOH D 10 610 72 HOH HOH . Y 7 HOH D 11 611 4 HOH HOH . Y 7 HOH D 12 612 66 HOH HOH . Y 7 HOH D 13 613 112 HOH HOH . Y 7 HOH D 14 614 40 HOH HOH . Y 7 HOH D 15 615 142 HOH HOH . Y 7 HOH D 16 616 83 HOH HOH . Y 7 HOH D 17 617 140 HOH HOH . Y 7 HOH D 18 618 33 HOH HOH . Y 7 HOH D 19 619 143 HOH HOH . Y 7 HOH D 20 620 141 HOH HOH . Y 7 HOH D 21 621 69 HOH HOH . Y 7 HOH D 22 622 22 HOH HOH . Y 7 HOH D 23 623 24 HOH HOH . Y 7 HOH D 24 624 47 HOH HOH . Y 7 HOH D 25 625 103 HOH HOH . Y 7 HOH D 26 626 144 HOH HOH . Y 7 HOH D 27 627 101 HOH HOH . Y 7 HOH D 28 628 77 HOH HOH . Y 7 HOH D 29 629 75 HOH HOH . Y 7 HOH D 30 630 161 HOH HOH . Y 7 HOH D 31 631 151 HOH HOH . Y 7 HOH D 32 632 62 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 SAO . . . S 5 22.862 38.335 174.348 1 75.26 ? N SAO 504 C 1 HETATM 2 C CA SAO . . . S 5 24.002 37.477 173.922 1 74.6 ? CA SAO 504 C 1 HETATM 3 C CB SAO . . . S 5 24.841 37.034 175.124 1 73.75 ? CB SAO 504 C 1 HETATM 4 C CG SAO . . . S 5 24.099 36.148 176.118 1 73.24 ? CG SAO 504 C 1 HETATM 5 S SD SAO . . . S 5 25.396 35.474 177.204 1 73.84 ? SD SAO 504 C 1 HETATM 6 C C SAO . . . S 5 23.471 36.279 173.134 1 73.66 ? C SAO 504 C 1 HETATM 7 O O SAO . . . S 5 24.239 35.768 172.287 1 73.28 ? O SAO 504 C 1 HETATM 8 O OXT SAO . . . S 5 22.31 35.889 173.392 1 72.1 ? OXT SAO 504 C 1 HETATM 9 C C5' SAO . . . S 5 25.409 36.605 178.62 1 70.58 ? C5' SAO 504 C 1 HETATM 10 C C4' SAO . . . S 5 26.221 37.846 178.299 1 69.81 ? C4' SAO 504 C 1 HETATM 11 O O4' SAO . . . S 5 25.971 38.849 179.307 1 68.47 ? O4' SAO 504 C 1 HETATM 12 C C3' SAO . . . S 5 27.737 37.62 178.274 1 69.96 ? C3' SAO 504 C 1 HETATM 13 O O3' SAO . . . S 5 28.319 38.253 177.143 1 70.86 ? O3' SAO 504 C 1 HETATM 14 C C2' SAO . . . S 5 28.215 38.259 179.583 1 67.33 ? C2' SAO 504 C 1 HETATM 15 O O2' SAO . . . S 5 29.531 38.791 179.468 1 65.14 ? O2' SAO 504 C 1 HETATM 16 C C1' SAO . . . S 5 27.199 39.381 179.75 1 67.81 ? C1' SAO 504 C 1 HETATM 17 N N9 SAO . . . S 5 27.017 39.852 181.12 1 67.17 ? N9 SAO 504 C 1 HETATM 18 C C8 SAO . . . S 5 26.856 39.095 182.246 1 64.58 ? C8 SAO 504 C 1 HETATM 19 N N7 SAO . . . S 5 26.608 39.788 183.334 1 63.4 ? N7 SAO 504 C 1 HETATM 20 C C5 SAO . . . S 5 26.616 41.098 182.885 1 65.51 ? C5 SAO 504 C 1 HETATM 21 C C6 SAO . . . S 5 26.408 42.327 183.548 1 66.23 ? C6 SAO 504 C 1 HETATM 22 N N6 SAO . . . S 5 26.115 42.429 184.847 1 64.92 ? N6 SAO 504 C 1 HETATM 23 N N1 SAO . . . S 5 26.493 43.457 182.814 1 66.79 ? N1 SAO 504 C 1 HETATM 24 C C2 SAO . . . S 5 26.764 43.358 181.508 1 67.34 ? C2 SAO 504 C 1 HETATM 25 N N3 SAO . . . S 5 26.966 42.26 180.774 1 66.63 ? N3 SAO 504 C 1 HETATM 26 C C4 SAO . . . S 5 26.876 41.161 181.527 1 66.88 ? C4 SAO 504 C 1 HETATM 27 H H2 SAO . . . S 5 26.827 44.308 180.979 1 80.81 ? H2 SAO 504 C 1 HETATM 28 H HN2 SAO . . . S 5 22.129 37.668 174.569 1 90.31 ? HN2 SAO 504 C 1 HETATM 29 H H3 SAO . . . S 5 23.076 38.886 175.174 1 90.31 ? H3 SAO 504 C 1 HETATM 30 H HN1 SAO . . . S 5 22.532 38.96 173.62 1 90.31 ? HN1 SAO 504 C 1 HETATM 31 H HA SAO . . . S 5 24.631 38.048 173.24 1 89.53 ? HA SAO 504 C 1 HETATM 32 H HB1 SAO . . . S 5 25.183 37.934 175.632 1 88.49 ? HB1 SAO 504 C 1 HETATM 33 H HB2 SAO . . . S 5 25.763 36.557 174.795 1 88.49 ? HB2 SAO 504 C 1 HETATM 34 H HG2 SAO . . . S 5 23.368 36.704 176.702 1 87.89 ? HG2 SAO 504 C 1 HETATM 35 H HG1 SAO . . . S 5 23.556 35.328 175.65 1 87.89 ? HG1 SAO 504 C 1 HETATM 36 H "H5'2" SAO . . . S 5 25.806 36.088 179.492 1 84.7 ? "H5'2" SAO 504 C 1 HETATM 37 H "H5'1" SAO . . . S 5 24.379 36.846 178.878 1 84.7 ? "H5'1" SAO 504 C 1 HETATM 38 H H4' SAO . . . S 5 25.847 38.297 177.381 1 83.78 ? H4' SAO 504 C 1 HETATM 39 H H3' SAO . . . S 5 28.057 36.586 178.149 1 83.95 ? H3' SAO 504 C 1 HETATM 40 H HO3' SAO . . . S 5 28.283 39.237 177.273 1 85.04 ? HO3' SAO 504 C 1 HETATM 41 H H2' SAO . . . S 5 28.283 37.562 180.417 1 80.79 ? H2' SAO 504 C 1 HETATM 42 H HO2' SAO . . . S 5 29.566 39.458 178.734 1 78.16 ? HO2' SAO 504 C 1 HETATM 43 H H1' SAO . . . S 5 27.417 40.256 179.14 1 81.37 ? H1' SAO 504 C 1 HETATM 44 H H8 SAO . . . S 5 26.928 38.008 182.238 1 77.5 ? H8 SAO 504 C 1 HETATM 45 H HN61 SAO . . . S 5 26.03 41.595 185.419 1 77.91 ? HN61 SAO 504 C 1 HETATM 46 H HN62 SAO . . . S 5 25.973 43.332 185.29 1 77.91 ? HN62 SAO 504 C 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 46 #