data_5NFJ # _model_server_result.job_id F-YyG3eQ1EAO5f6MQbacgQ _model_server_result.datetime_utc '2024-11-21 13:34:52' _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 5nfj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 5NFJ # _exptl.entry_id 5NFJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 5NFJ _cell.length_a 82.64 _cell.length_b 82.64 _cell.length_c 148.62 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NFJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,H,I,R 1 1 B,J,K,L,M,N,O,S 2 1 C,P,Q,T 3 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 ? 2 D N N ? 2 J N N ? 2 P N N # _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 299 n n N HN1 SAM sing 300 n n N HN2 SAM sing 301 n n CA C SAM sing 302 n n CA CB SAM sing 303 n n CA HA SAM sing 304 n n C O SAM doub 305 n n C OXT SAM sing 306 n n CB CG SAM sing 307 n n CB HB1 SAM sing 308 n n CB HB2 SAM sing 309 n n CG SD SAM sing 310 n n CG HG1 SAM sing 311 n n CG HG2 SAM sing 312 n n SD CE SAM sing 313 n n SD C5' SAM sing 314 n n CE HE1 SAM sing 315 n n CE HE2 SAM sing 316 n n CE HE3 SAM sing 317 n n C5' C4' SAM sing 318 n n C5' "H5'1" SAM sing 319 n n C5' "H5'2" SAM sing 320 n n C4' O4' SAM sing 321 n n C4' C3' SAM sing 322 n n C4' H4' SAM sing 323 n n O4' C1' SAM sing 324 n n C3' O3' SAM sing 325 n n C3' C2' SAM sing 326 n n C3' H3' SAM sing 327 n n O3' HO3' SAM sing 328 n n C2' O2' SAM sing 329 n n C2' C1' SAM sing 330 n n C2' H2' SAM sing 331 n n O2' HO2' SAM sing 332 n n C1' N9 SAM sing 333 n n C1' H1' SAM sing 334 n n N9 C8 SAM sing 335 n y N9 C4 SAM sing 336 n y C8 N7 SAM doub 337 n y C8 H8 SAM sing 338 n n N7 C5 SAM sing 339 n y C5 C6 SAM sing 340 n y C5 C4 SAM doub 341 n y C6 N6 SAM sing 342 n n C6 N1 SAM doub 343 n y N6 HN61 SAM sing 344 n n N6 HN62 SAM sing 345 n n N1 C2 SAM sing 346 n y C2 N3 SAM doub 347 n y C2 H2 SAM sing 348 n n N3 C4 SAM sing 349 n y # _atom_sites.entry_id 5NFJ _atom_sites.fract_transf_matrix[1][1] 0.012101 _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] 0.012101 _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] 0.006729 _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 D 2 SAM A 1 501 500 SAM SAM . E 3 GOL A 1 502 1 GOL GOL . F 3 GOL A 1 503 2 GOL GOL . G 3 GOL A 1 504 3 GOL GOL . H 4 EDO A 1 505 2 EDO EDO . I 4 EDO A 1 506 5 EDO EDO . J 2 SAM B 1 501 500 SAM SAM . K 3 GOL B 1 502 4 GOL GOL . L 3 GOL B 1 503 5 GOL GOL . M 3 GOL B 1 504 8 GOL GOL . N 4 EDO B 1 505 6 EDO EDO . O 4 EDO B 1 506 7 EDO EDO . P 2 SAM C 1 501 500 SAM SAM . Q 3 GOL C 1 502 6 GOL GOL . R 5 HOH A 1 601 224 HOH HOH . R 5 HOH A 2 602 122 HOH HOH . R 5 HOH A 3 603 187 HOH HOH . R 5 HOH A 4 604 134 HOH HOH . R 5 HOH A 5 605 157 HOH HOH . R 5 HOH A 6 606 253 HOH HOH . R 5 HOH A 7 607 82 HOH HOH . R 5 HOH A 8 608 256 HOH HOH . R 5 HOH A 9 609 89 HOH HOH . R 5 HOH A 10 610 81 HOH HOH . R 5 HOH A 11 611 250 HOH HOH . R 5 HOH A 12 612 24 HOH HOH . R 5 HOH A 13 613 104 HOH HOH . R 5 HOH A 14 614 88 HOH HOH . R 5 HOH A 15 615 19 HOH HOH . R 5 HOH A 16 616 54 HOH HOH . R 5 HOH A 17 617 26 HOH HOH . R 5 HOH A 18 618 144 HOH HOH . R 5 HOH A 19 619 105 HOH HOH . R 5 HOH A 20 620 127 HOH HOH . R 5 HOH A 21 621 43 HOH HOH . R 5 HOH A 22 622 23 HOH HOH . R 5 HOH A 23 623 219 HOH HOH . R 5 HOH A 24 624 58 HOH HOH . R 5 HOH A 25 625 174 HOH HOH . R 5 HOH A 26 626 178 HOH HOH . R 5 HOH A 27 627 216 HOH HOH . R 5 HOH A 28 628 197 HOH HOH . R 5 HOH A 29 629 101 HOH HOH . R 5 HOH A 30 630 184 HOH HOH . R 5 HOH A 31 631 152 HOH HOH . R 5 HOH A 32 632 133 HOH HOH . R 5 HOH A 33 633 177 HOH HOH . R 5 HOH A 34 634 191 HOH HOH . R 5 HOH A 35 635 215 HOH HOH . R 5 HOH A 36 636 9 HOH HOH . R 5 HOH A 37 637 151 HOH HOH . R 5 HOH A 38 638 27 HOH HOH . R 5 HOH A 39 639 123 HOH HOH . R 5 HOH A 40 640 188 HOH HOH . R 5 HOH A 41 641 70 HOH HOH . R 5 HOH A 42 642 69 HOH HOH . R 5 HOH A 43 643 97 HOH HOH . R 5 HOH A 44 644 66 HOH HOH . R 5 HOH A 45 645 41 HOH HOH . R 5 HOH A 46 646 17 HOH HOH . R 5 HOH A 47 647 158 HOH HOH . R 5 HOH A 48 648 20 HOH HOH . R 5 HOH A 49 649 49 HOH HOH . R 5 HOH A 50 650 207 HOH HOH . R 5 HOH A 51 651 222 HOH HOH . R 5 HOH A 52 652 220 HOH HOH . R 5 HOH A 53 653 154 HOH HOH . R 5 HOH A 54 654 159 HOH HOH . R 5 HOH A 55 655 285 HOH HOH . R 5 HOH A 56 656 129 HOH HOH . R 5 HOH A 57 657 185 HOH HOH . R 5 HOH A 58 658 143 HOH HOH . R 5 HOH A 59 659 249 HOH HOH . R 5 HOH A 60 660 34 HOH HOH . R 5 HOH A 61 661 95 HOH HOH . R 5 HOH A 62 662 284 HOH HOH . R 5 HOH A 63 663 77 HOH HOH . R 5 HOH A 64 664 227 HOH HOH . S 5 HOH B 1 601 228 HOH HOH . S 5 HOH B 2 602 140 HOH HOH . S 5 HOH B 3 603 18 HOH HOH . S 5 HOH B 4 604 221 HOH HOH . S 5 HOH B 5 605 35 HOH HOH . S 5 HOH B 6 606 114 HOH HOH . S 5 HOH B 7 607 102 HOH HOH . S 5 HOH B 8 608 31 HOH HOH . S 5 HOH B 9 609 64 HOH HOH . S 5 HOH B 10 610 109 HOH HOH . S 5 HOH B 11 611 11 HOH HOH . S 5 HOH B 12 612 25 HOH HOH . S 5 HOH B 13 613 121 HOH HOH . S 5 HOH B 14 614 113 HOH HOH . S 5 HOH B 15 615 111 HOH HOH . S 5 HOH B 16 616 67 HOH HOH . S 5 HOH B 17 617 155 HOH HOH . S 5 HOH B 18 618 48 HOH HOH . S 5 HOH B 19 619 46 HOH HOH . S 5 HOH B 20 620 73 HOH HOH . S 5 HOH B 21 621 45 HOH HOH . S 5 HOH B 22 622 167 HOH HOH . S 5 HOH B 23 623 116 HOH HOH . S 5 HOH B 24 624 280 HOH HOH . S 5 HOH B 25 625 118 HOH HOH . S 5 HOH B 26 626 93 HOH HOH . S 5 HOH B 27 627 136 HOH HOH . S 5 HOH B 28 628 163 HOH HOH . S 5 HOH B 29 629 22 HOH HOH . S 5 HOH B 30 630 13 HOH HOH . S 5 HOH B 31 631 29 HOH HOH . S 5 HOH B 32 632 14 HOH HOH . S 5 HOH B 33 633 166 HOH HOH . S 5 HOH B 34 634 52 HOH HOH . S 5 HOH B 35 635 37 HOH HOH . S 5 HOH B 36 636 80 HOH HOH . S 5 HOH B 37 637 234 HOH HOH . S 5 HOH B 38 638 62 HOH HOH . S 5 HOH B 39 639 1 HOH HOH . S 5 HOH B 40 640 33 HOH HOH . S 5 HOH B 41 641 164 HOH HOH . S 5 HOH B 42 642 145 HOH HOH . S 5 HOH B 43 643 126 HOH HOH . S 5 HOH B 44 644 21 HOH HOH . S 5 HOH B 45 645 175 HOH HOH . S 5 HOH B 46 646 268 HOH HOH . S 5 HOH B 47 647 61 HOH HOH . S 5 HOH B 48 648 38 HOH HOH . S 5 HOH B 49 649 40 HOH HOH . S 5 HOH B 50 650 30 HOH HOH . S 5 HOH B 51 651 115 HOH HOH . S 5 HOH B 52 652 258 HOH HOH . S 5 HOH B 53 653 50 HOH HOH . S 5 HOH B 54 654 12 HOH HOH . S 5 HOH B 55 655 135 HOH HOH . S 5 HOH B 56 656 90 HOH HOH . S 5 HOH B 57 657 71 HOH HOH . S 5 HOH B 58 658 195 HOH HOH . S 5 HOH B 59 659 2 HOH HOH . S 5 HOH B 60 660 72 HOH HOH . S 5 HOH B 61 661 56 HOH HOH . S 5 HOH B 62 662 84 HOH HOH . S 5 HOH B 63 663 94 HOH HOH . S 5 HOH B 64 664 203 HOH HOH . S 5 HOH B 65 665 8 HOH HOH . S 5 HOH B 66 666 156 HOH HOH . S 5 HOH B 67 667 99 HOH HOH . S 5 HOH B 68 668 32 HOH HOH . S 5 HOH B 69 669 53 HOH HOH . S 5 HOH B 70 670 248 HOH HOH . S 5 HOH B 71 671 149 HOH HOH . S 5 HOH B 72 672 179 HOH HOH . S 5 HOH B 73 673 230 HOH HOH . S 5 HOH B 74 674 190 HOH HOH . S 5 HOH B 75 675 173 HOH HOH . S 5 HOH B 76 676 247 HOH HOH . S 5 HOH B 77 677 100 HOH HOH . S 5 HOH B 78 678 110 HOH HOH . S 5 HOH B 79 679 176 HOH HOH . S 5 HOH B 80 680 108 HOH HOH . S 5 HOH B 81 681 85 HOH HOH . S 5 HOH B 82 682 254 HOH HOH . S 5 HOH B 83 683 264 HOH HOH . S 5 HOH B 84 684 147 HOH HOH . S 5 HOH B 85 685 172 HOH HOH . S 5 HOH B 86 686 112 HOH HOH . S 5 HOH B 87 687 165 HOH HOH . S 5 HOH B 88 688 266 HOH HOH . T 5 HOH C 1 601 252 HOH HOH . T 5 HOH C 2 602 245 HOH HOH . T 5 HOH C 3 603 3 HOH HOH . T 5 HOH C 4 604 42 HOH HOH . T 5 HOH C 5 605 186 HOH HOH . T 5 HOH C 6 606 59 HOH HOH . T 5 HOH C 7 607 16 HOH HOH . T 5 HOH C 8 608 153 HOH HOH . T 5 HOH C 9 609 146 HOH HOH . T 5 HOH C 10 610 87 HOH HOH . T 5 HOH C 11 611 160 HOH HOH . T 5 HOH C 12 612 57 HOH HOH . T 5 HOH C 13 613 181 HOH HOH . T 5 HOH C 14 614 120 HOH HOH . T 5 HOH C 15 615 10 HOH HOH . T 5 HOH C 16 616 161 HOH HOH . T 5 HOH C 17 617 189 HOH HOH . T 5 HOH C 18 618 79 HOH HOH . T 5 HOH C 19 619 92 HOH HOH . T 5 HOH C 20 620 28 HOH HOH . T 5 HOH C 21 621 150 HOH HOH . T 5 HOH C 22 622 106 HOH HOH . T 5 HOH C 23 623 47 HOH HOH . T 5 HOH C 24 624 117 HOH HOH . T 5 HOH C 25 625 36 HOH HOH . T 5 HOH C 26 626 119 HOH HOH . T 5 HOH C 27 627 15 HOH HOH . T 5 HOH C 28 628 265 HOH HOH . T 5 HOH C 29 629 39 HOH HOH . T 5 HOH C 30 630 255 HOH HOH . T 5 HOH C 31 631 180 HOH HOH . T 5 HOH C 32 632 4 HOH HOH . T 5 HOH C 33 633 214 HOH HOH . T 5 HOH C 34 634 7 HOH HOH . T 5 HOH C 35 635 55 HOH HOH . T 5 HOH C 36 636 274 HOH HOH . T 5 HOH C 37 637 51 HOH HOH . T 5 HOH C 38 638 60 HOH HOH . T 5 HOH C 39 639 276 HOH HOH . T 5 HOH C 40 640 75 HOH HOH . T 5 HOH C 41 641 83 HOH HOH . T 5 HOH C 42 642 68 HOH HOH . T 5 HOH C 43 643 63 HOH HOH . T 5 HOH C 44 644 132 HOH HOH . T 5 HOH C 45 645 168 HOH HOH . T 5 HOH C 46 646 78 HOH HOH . T 5 HOH C 47 647 5 HOH HOH . T 5 HOH C 48 648 103 HOH HOH . T 5 HOH C 49 649 130 HOH HOH . T 5 HOH C 50 650 96 HOH HOH . T 5 HOH C 51 651 107 HOH HOH . T 5 HOH C 52 652 162 HOH HOH . T 5 HOH C 53 653 98 HOH HOH . T 5 HOH C 54 654 91 HOH HOH . T 5 HOH C 55 655 202 HOH HOH . T 5 HOH C 56 656 6 HOH HOH . T 5 HOH C 57 657 44 HOH HOH . T 5 HOH C 58 658 212 HOH HOH . T 5 HOH C 59 659 194 HOH HOH . T 5 HOH C 60 660 142 HOH HOH . T 5 HOH C 61 661 237 HOH HOH . T 5 HOH C 62 662 128 HOH HOH . T 5 HOH C 63 663 200 HOH HOH . T 5 HOH C 64 664 86 HOH HOH . T 5 HOH C 65 665 148 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 . . . D 2 -8.54 48.415 -15.863 1 51.6 ? N SAM 501 A 1 HETATM 2 C CA SAM . . . D 2 -9.08 47.058 -15.919 1 63.21 ? CA SAM 501 A 1 HETATM 3 C C SAM . . . D 2 -10.411 47.095 -16.685 1 66.5 ? C SAM 501 A 1 HETATM 4 O O SAM . . . D 2 -10.579 47.978 -17.594 1 51.61 ? O SAM 501 A 1 HETATM 5 O OXT SAM . . . D 2 -11.311 46.263 -16.375 1 56.51 ? OXT SAM 501 A 1 HETATM 6 C CB SAM . . . D 2 -9.213 46.435 -14.502 1 52.32 ? CB SAM 501 A 1 HETATM 7 C CG SAM . . . D 2 -8.969 44.905 -14.568 1 55.74 ? CG SAM 501 A 1 HETATM 8 S SD SAM . . . D 2 -9.315 43.974 -13.153 1 52.36 ? SD SAM 501 A 1 HETATM 9 C CE SAM . . . D 2 -7.819 44.035 -12.387 1 49.6 ? CE SAM 501 A 1 HETATM 10 C C5' SAM . . . D 2 -9.659 42.357 -13.67 1 51.81 ? C5' SAM 501 A 1 HETATM 11 C C4' SAM . . . D 2 -11.032 41.966 -14.226 1 42.15 ? C4' SAM 501 A 1 HETATM 12 O O4' SAM . . . D 2 -11.903 41.456 -13.22 1 38.77 ? O4' SAM 501 A 1 HETATM 13 C C3' SAM . . . D 2 -11.872 43.071 -14.942 1 40.37 ? C3' SAM 501 A 1 HETATM 14 O O3' SAM . . . D 2 -11.626 43.04 -16.337 1 47.42 ? O3' SAM 501 A 1 HETATM 15 C C2' SAM . . . D 2 -13.264 42.714 -14.655 1 40.64 ? C2' SAM 501 A 1 HETATM 16 O O2' SAM . . . D 2 -13.734 41.773 -15.619 1 42.1 ? O2' SAM 501 A 1 HETATM 17 C C1' SAM . . . D 2 -13.22 41.993 -13.307 1 42.6 ? C1' SAM 501 A 1 HETATM 18 N N9 SAM . . . D 2 -13.495 42.857 -12.125 1 40.18 ? N9 SAM 501 A 1 HETATM 19 C C8 SAM . . . D 2 -12.571 43.246 -11.228 1 43.48 ? C8 SAM 501 A 1 HETATM 20 N N7 SAM . . . D 2 -13.148 43.935 -10.243 1 41.97 ? N7 SAM 501 A 1 HETATM 21 C C5 SAM . . . D 2 -14.47 43.983 -10.503 1 41.2 ? C5 SAM 501 A 1 HETATM 22 C C6 SAM . . . D 2 -15.63 44.655 -9.904 1 39.05 ? C6 SAM 501 A 1 HETATM 23 N N6 SAM . . . D 2 -15.474 45.353 -8.741 1 45.4 ? N6 SAM 501 A 1 HETATM 24 N N1 SAM . . . D 2 -16.834 44.505 -10.492 1 42.29 ? N1 SAM 501 A 1 HETATM 25 C C2 SAM . . . D 2 -16.957 43.787 -11.641 1 45.01 ? C2 SAM 501 A 1 HETATM 26 N N3 SAM . . . D 2 -15.913 43.237 -12.274 1 43.13 ? N3 SAM 501 A 1 HETATM 27 C C4 SAM . . . D 2 -14.678 43.282 -11.747 1 39.03 ? C4 SAM 501 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #