data_5E8J # _model_server_result.job_id qGbnw7gbCp5DwBamBfikTg _model_server_result.datetime_utc '2024-11-19 23:12:29' _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 5e8j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":502}' # _entry.id 5E8J # _exptl.entry_id 5E8J _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90.06 _cell.angle_beta 92.41 _cell.angle_gamma 115.41 _cell.entry_id 5E8J _cell.length_a 49.147 _cell.length_b 50.487 _cell.length_c 84.579 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5E8J _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,H,J 1 1 B,D,G,I,K 2 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 F N N ? 4 G N N # _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 ? # 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 SAH sing 290 n n N HN1 SAH sing 291 n n N HN2 SAH sing 292 n n CA CB SAH sing 293 n n CA C SAH sing 294 n n CA HA SAH sing 295 n n CB CG SAH sing 296 n n CB HB1 SAH sing 297 n n CB HB2 SAH sing 298 n n CG SD SAH sing 299 n n CG HG1 SAH sing 300 n n CG HG2 SAH sing 301 n n SD C5' SAH sing 302 n n C O SAH doub 303 n n C OXT SAH sing 304 n n OXT HXT SAH sing 305 n n C5' C4' SAH sing 306 n n C5' "H5'1" SAH sing 307 n n C5' "H5'2" SAH sing 308 n n C4' O4' SAH sing 309 n n C4' C3' SAH sing 310 n n C4' H4' SAH sing 311 n n O4' C1' SAH sing 312 n n C3' O3' SAH sing 313 n n C3' C2' SAH sing 314 n n C3' H3' SAH sing 315 n n O3' HO3' SAH sing 316 n n C2' O2' SAH sing 317 n n C2' C1' SAH sing 318 n n C2' H2' SAH sing 319 n n O2' HO2' SAH sing 320 n n C1' N9 SAH sing 321 n n C1' H1' SAH sing 322 n n N9 C8 SAH sing 323 n y N9 C4 SAH sing 324 n y C8 N7 SAH doub 325 n y C8 H8 SAH sing 326 n n N7 C5 SAH sing 327 n y C5 C6 SAH sing 328 n y C5 C4 SAH doub 329 n y C6 N6 SAH sing 330 n n C6 N1 SAH doub 331 n y N6 HN61 SAH sing 332 n n N6 HN62 SAH sing 333 n n N1 C2 SAH sing 334 n y C2 N3 SAH doub 335 n y C2 H2 SAH sing 336 n n N3 C4 SAH sing 337 n y # _atom_sites.entry_id 5E8J _atom_sites.fract_transf_matrix[1][1] 0.020347 _atom_sites.fract_transf_matrix[1][2] 0.009668 _atom_sites.fract_transf_matrix[1][3] 0.001062 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021929 _atom_sites.fract_transf_matrix[2][3] 0.000466 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.011836 _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 3 GOL A 1 501 1 GOL GOL . F 4 SAH A 1 502 1 SAH SAH . G 4 SAH B 1 501 2 SAH SAH . H 5 HOH A 1 601 191 HOH HOH . H 5 HOH A 2 602 156 HOH HOH . H 5 HOH A 3 603 21 HOH HOH . H 5 HOH A 4 604 263 HOH HOH . H 5 HOH A 5 605 23 HOH HOH . H 5 HOH A 6 606 187 HOH HOH . H 5 HOH A 7 607 67 HOH HOH . H 5 HOH A 8 608 57 HOH HOH . H 5 HOH A 9 609 128 HOH HOH . H 5 HOH A 10 610 8 HOH HOH . H 5 HOH A 11 611 77 HOH HOH . H 5 HOH A 12 612 186 HOH HOH . H 5 HOH A 13 613 73 HOH HOH . H 5 HOH A 14 614 212 HOH HOH . H 5 HOH A 15 615 257 HOH HOH . H 5 HOH A 16 616 14 HOH HOH . H 5 HOH A 17 617 254 HOH HOH . H 5 HOH A 18 618 39 HOH HOH . H 5 HOH A 19 619 55 HOH HOH . H 5 HOH A 20 620 304 HOH HOH . H 5 HOH A 21 621 76 HOH HOH . H 5 HOH A 22 622 120 HOH HOH . H 5 HOH A 23 623 26 HOH HOH . H 5 HOH A 24 624 168 HOH HOH . H 5 HOH A 25 625 59 HOH HOH . H 5 HOH A 26 626 170 HOH HOH . H 5 HOH A 27 627 54 HOH HOH . H 5 HOH A 28 628 202 HOH HOH . H 5 HOH A 29 629 199 HOH HOH . H 5 HOH A 30 630 122 HOH HOH . H 5 HOH A 31 631 18 HOH HOH . H 5 HOH A 32 632 24 HOH HOH . H 5 HOH A 33 633 133 HOH HOH . H 5 HOH A 34 634 100 HOH HOH . H 5 HOH A 35 635 29 HOH HOH . H 5 HOH A 36 636 111 HOH HOH . H 5 HOH A 37 637 5 HOH HOH . H 5 HOH A 38 638 210 HOH HOH . H 5 HOH A 39 639 252 HOH HOH . H 5 HOH A 40 640 306 HOH HOH . H 5 HOH A 41 641 119 HOH HOH . H 5 HOH A 42 642 282 HOH HOH . H 5 HOH A 43 643 38 HOH HOH . H 5 HOH A 44 644 297 HOH HOH . H 5 HOH A 45 645 82 HOH HOH . H 5 HOH A 46 646 235 HOH HOH . H 5 HOH A 47 647 4 HOH HOH . H 5 HOH A 48 648 3 HOH HOH . H 5 HOH A 49 649 56 HOH HOH . H 5 HOH A 50 650 104 HOH HOH . H 5 HOH A 51 651 19 HOH HOH . H 5 HOH A 52 652 223 HOH HOH . H 5 HOH A 53 653 40 HOH HOH . H 5 HOH A 54 654 164 HOH HOH . H 5 HOH A 55 655 106 HOH HOH . H 5 HOH A 56 656 239 HOH HOH . H 5 HOH A 57 657 60 HOH HOH . H 5 HOH A 58 658 146 HOH HOH . H 5 HOH A 59 659 256 HOH HOH . H 5 HOH A 60 660 273 HOH HOH . H 5 HOH A 61 661 214 HOH HOH . H 5 HOH A 62 662 295 HOH HOH . H 5 HOH A 63 663 272 HOH HOH . H 5 HOH A 64 664 283 HOH HOH . H 5 HOH A 65 665 203 HOH HOH . H 5 HOH A 66 666 163 HOH HOH . H 5 HOH A 67 667 72 HOH HOH . H 5 HOH A 68 668 229 HOH HOH . H 5 HOH A 69 669 2 HOH HOH . H 5 HOH A 70 670 258 HOH HOH . H 5 HOH A 71 671 143 HOH HOH . H 5 HOH A 72 672 260 HOH HOH . H 5 HOH A 73 673 208 HOH HOH . H 5 HOH A 74 674 290 HOH HOH . H 5 HOH A 75 675 96 HOH HOH . H 5 HOH A 76 676 250 HOH HOH . H 5 HOH A 77 677 268 HOH HOH . H 5 HOH A 78 678 194 HOH HOH . H 5 HOH A 79 679 300 HOH HOH . H 5 HOH A 80 680 255 HOH HOH . H 5 HOH A 81 681 244 HOH HOH . H 5 HOH A 82 682 298 HOH HOH . H 5 HOH A 83 683 237 HOH HOH . H 5 HOH A 84 684 157 HOH HOH . H 5 HOH A 85 685 303 HOH HOH . H 5 HOH A 86 686 138 HOH HOH . H 5 HOH A 87 687 294 HOH HOH . H 5 HOH A 88 688 162 HOH HOH . H 5 HOH A 89 689 113 HOH HOH . H 5 HOH A 90 690 200 HOH HOH . H 5 HOH A 91 691 299 HOH HOH . H 5 HOH A 92 692 209 HOH HOH . H 5 HOH A 93 693 305 HOH HOH . H 5 HOH A 94 694 281 HOH HOH . H 5 HOH A 95 695 193 HOH HOH . H 5 HOH A 96 696 185 HOH HOH . H 5 HOH A 97 697 102 HOH HOH . H 5 HOH A 98 698 166 HOH HOH . H 5 HOH A 99 699 296 HOH HOH . H 5 HOH A 100 700 271 HOH HOH . H 5 HOH A 101 701 224 HOH HOH . H 5 HOH A 102 702 184 HOH HOH . I 5 HOH B 1 601 134 HOH HOH . I 5 HOH B 2 602 13 HOH HOH . I 5 HOH B 3 603 36 HOH HOH . I 5 HOH B 4 604 6 HOH HOH . I 5 HOH B 5 605 247 HOH HOH . I 5 HOH B 6 606 222 HOH HOH . I 5 HOH B 7 607 179 HOH HOH . I 5 HOH B 8 608 130 HOH HOH . I 5 HOH B 9 609 66 HOH HOH . I 5 HOH B 10 610 172 HOH HOH . I 5 HOH B 11 611 107 HOH HOH . I 5 HOH B 12 612 110 HOH HOH . I 5 HOH B 13 613 126 HOH HOH . I 5 HOH B 14 614 62 HOH HOH . I 5 HOH B 15 615 1 HOH HOH . I 5 HOH B 16 616 101 HOH HOH . I 5 HOH B 17 617 151 HOH HOH . I 5 HOH B 18 618 45 HOH HOH . I 5 HOH B 19 619 232 HOH HOH . I 5 HOH B 20 620 30 HOH HOH . I 5 HOH B 21 621 171 HOH HOH . I 5 HOH B 22 622 48 HOH HOH . I 5 HOH B 23 623 68 HOH HOH . I 5 HOH B 24 624 53 HOH HOH . I 5 HOH B 25 625 64 HOH HOH . I 5 HOH B 26 626 88 HOH HOH . I 5 HOH B 27 627 129 HOH HOH . I 5 HOH B 28 628 75 HOH HOH . I 5 HOH B 29 629 7 HOH HOH . I 5 HOH B 30 630 177 HOH HOH . I 5 HOH B 31 631 15 HOH HOH . I 5 HOH B 32 632 248 HOH HOH . I 5 HOH B 33 633 22 HOH HOH . I 5 HOH B 34 634 221 HOH HOH . I 5 HOH B 35 635 93 HOH HOH . I 5 HOH B 36 636 16 HOH HOH . I 5 HOH B 37 637 51 HOH HOH . I 5 HOH B 38 638 10 HOH HOH . I 5 HOH B 39 639 207 HOH HOH . I 5 HOH B 40 640 9 HOH HOH . I 5 HOH B 41 641 284 HOH HOH . I 5 HOH B 42 642 79 HOH HOH . I 5 HOH B 43 643 20 HOH HOH . I 5 HOH B 44 644 37 HOH HOH . I 5 HOH B 45 645 148 HOH HOH . I 5 HOH B 46 646 253 HOH HOH . I 5 HOH B 47 647 74 HOH HOH . I 5 HOH B 48 648 279 HOH HOH . I 5 HOH B 49 649 301 HOH HOH . I 5 HOH B 50 650 34 HOH HOH . I 5 HOH B 51 651 180 HOH HOH . I 5 HOH B 52 652 141 HOH HOH . I 5 HOH B 53 653 144 HOH HOH . I 5 HOH B 54 654 35 HOH HOH . I 5 HOH B 55 655 28 HOH HOH . I 5 HOH B 56 656 242 HOH HOH . I 5 HOH B 57 657 105 HOH HOH . I 5 HOH B 58 658 86 HOH HOH . I 5 HOH B 59 659 169 HOH HOH . I 5 HOH B 60 660 136 HOH HOH . I 5 HOH B 61 661 69 HOH HOH . I 5 HOH B 62 662 44 HOH HOH . I 5 HOH B 63 663 264 HOH HOH . I 5 HOH B 64 664 280 HOH HOH . I 5 HOH B 65 665 289 HOH HOH . I 5 HOH B 66 666 277 HOH HOH . I 5 HOH B 67 667 285 HOH HOH . I 5 HOH B 68 668 230 HOH HOH . I 5 HOH B 69 669 286 HOH HOH . I 5 HOH B 70 670 70 HOH HOH . I 5 HOH B 71 671 293 HOH HOH . I 5 HOH B 72 672 204 HOH HOH . I 5 HOH B 73 673 236 HOH HOH . I 5 HOH B 74 674 259 HOH HOH . I 5 HOH B 75 675 245 HOH HOH . I 5 HOH B 76 676 243 HOH HOH . I 5 HOH B 77 677 176 HOH HOH . I 5 HOH B 78 678 275 HOH HOH . J 5 HOH C 1 101 115 HOH HOH . J 5 HOH C 2 102 167 HOH HOH . J 5 HOH C 3 103 109 HOH HOH . J 5 HOH C 4 104 42 HOH HOH . J 5 HOH C 5 105 266 HOH HOH . J 5 HOH C 6 106 165 HOH HOH . J 5 HOH C 7 107 58 HOH HOH . J 5 HOH C 8 108 90 HOH HOH . J 5 HOH C 9 109 32 HOH HOH . J 5 HOH C 10 110 17 HOH HOH . J 5 HOH C 11 111 41 HOH HOH . J 5 HOH C 12 112 270 HOH HOH . J 5 HOH C 13 113 27 HOH HOH . J 5 HOH C 14 114 98 HOH HOH . J 5 HOH C 15 115 227 HOH HOH . J 5 HOH C 16 116 291 HOH HOH . J 5 HOH C 17 117 173 HOH HOH . J 5 HOH C 18 118 174 HOH HOH . J 5 HOH C 19 119 302 HOH HOH . J 5 HOH C 20 120 154 HOH HOH . K 5 HOH D 1 101 251 HOH HOH . K 5 HOH D 2 102 152 HOH HOH . K 5 HOH D 3 103 189 HOH HOH . K 5 HOH D 4 104 241 HOH HOH . K 5 HOH D 5 105 238 HOH HOH . K 5 HOH D 6 106 78 HOH HOH . K 5 HOH D 7 107 97 HOH HOH . K 5 HOH D 8 108 31 HOH HOH . K 5 HOH D 9 109 81 HOH HOH . K 5 HOH D 10 110 43 HOH HOH . K 5 HOH D 11 111 265 HOH HOH . K 5 HOH D 12 112 33 HOH HOH . K 5 HOH D 13 113 50 HOH HOH . K 5 HOH D 14 114 11 HOH HOH . K 5 HOH D 15 115 61 HOH HOH . K 5 HOH D 16 116 25 HOH HOH . K 5 HOH D 17 117 71 HOH HOH . K 5 HOH D 18 118 161 HOH HOH . K 5 HOH D 19 119 287 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 0.957 -4.131 -4.607 1 15.37 ? N SAH 502 A 1 HETATM 2 C CA SAH . . . F 4 1.365 -4.566 -5.924 1 15.8 ? CA SAH 502 A 1 HETATM 3 C CB SAH . . . F 4 0.165 -5.013 -6.731 1 16.12 ? CB SAH 502 A 1 HETATM 4 C CG SAH . . . F 4 -1.07 -4.041 -6.656 1 15.99 ? CG SAH 502 A 1 HETATM 5 S SD SAH . . . F 4 -2.534 -4.886 -7.328 1 16.58 ? SD SAH 502 A 1 HETATM 6 C C SAH . . . F 4 2.076 -3.404 -6.669 1 15.81 ? C SAH 502 A 1 HETATM 7 O O SAH . . . F 4 2.887 -3.669 -7.614 1 20.31 -1 O SAH 502 A 1 HETATM 8 O OXT SAH . . . F 4 1.865 -2.249 -6.355 1 15.52 ? OXT SAH 502 A 1 HETATM 9 C C5' SAH . . . F 4 -3.599 -5.458 -5.912 1 16.8 ? C5' SAH 502 A 1 HETATM 10 C C4' SAH . . . F 4 -2.982 -6.76 -5.24 1 25.04 ? C4' SAH 502 A 1 HETATM 11 O O4' SAH . . . F 4 -3.531 -6.947 -4.1 1 25.14 ? O4' SAH 502 A 1 HETATM 12 C C3' SAH . . . F 4 -3.318 -8.015 -6.094 1 16.78 ? C3' SAH 502 A 1 HETATM 13 O O3' SAH . . . F 4 -2.17 -8.66 -6.465 1 16.87 ? O3' SAH 502 A 1 HETATM 14 C C2' SAH . . . F 4 -4.152 -8.905 -5.179 1 16.7 ? C2' SAH 502 A 1 HETATM 15 O O2' SAH . . . F 4 -3.814 -10.371 -5.427 1 20.46 ? O2' SAH 502 A 1 HETATM 16 C C1' SAH . . . F 4 -3.791 -8.543 -3.983 1 16.27 ? C1' SAH 502 A 1 HETATM 17 N N9 SAH . . . F 4 -4.784 -8.807 -2.958 1 16.6 ? N9 SAH 502 A 1 HETATM 18 C C8 SAH . . . F 4 -6.058 -8.442 -2.967 1 16.63 ? C8 SAH 502 A 1 HETATM 19 N N7 SAH . . . F 4 -6.65 -8.859 -1.846 1 23.3 ? N7 SAH 502 A 1 HETATM 20 C C5 SAH . . . F 4 -5.727 -9.497 -1.105 1 22.85 ? C5 SAH 502 A 1 HETATM 21 C C6 SAH . . . F 4 -5.751 -10.138 0.147 1 21.15 ? C6 SAH 502 A 1 HETATM 22 N N6 SAH . . . F 4 -6.926 -10.191 0.88 1 15.7 ? N6 SAH 502 A 1 HETATM 23 N N1 SAH . . . F 4 -4.656 -10.679 0.61 1 22.69 ? N1 SAH 502 A 1 HETATM 24 C C2 SAH . . . F 4 -3.523 -10.637 -0.077 1 20.1 ? C2 SAH 502 A 1 HETATM 25 N N3 SAH . . . F 4 -3.465 -10.038 -1.269 1 16.99 ? N3 SAH 502 A 1 HETATM 26 C C4 SAH . . . F 4 -4.536 -9.469 -1.798 1 18.84 ? C4 SAH 502 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #