data_1XDS # _model_server_result.job_id wTOuDtqECaaSOzCbs4ZNKA _model_server_result.datetime_utc '2025-09-04 14:57:04' _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 1xds # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":5635}' # _entry.id 1XDS # _exptl.entry_id 1XDS _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 2 _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 120 _cell.entry_id 1XDS _cell.length_a 79.89 _cell.length_b 79.89 _cell.length_c 232.598 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XDS _symmetry.cell_setting trigonal _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _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 _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 ? 2 C N N ? 2 E N 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 covale ? covale1 A C PRO 30 A PRO 30 1_555 A N MSE 31 A MSE 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale2 A C MSE 31 A MSE 31 1_555 A N ALA 32 A ALA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale3 A C GLY 95 A GLY 95 1_555 A N MSE 96 A MSE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 A C MSE 96 A MSE 96 1_555 A N LEU 97 A LEU 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale5 A C LEU 162 A LEU 162 1_555 A N MSE 163 A MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale6 A C MSE 163 A MSE 163 1_555 A N SER 164 A SER 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? covale ? covale7 A C GLY 195 A GLY 195 1_555 A N MSE 196 A MSE 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale8 A C MSE 196 A MSE 196 1_555 A N LEU 197 A LEU 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale9 A C ARG 307 A ARG 307 1_555 A N MSE 308 A MSE 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale10 A C MSE 308 A MSE 308 1_555 A N LEU 309 A LEU 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale11 A C PHE 311 A PHE 311 1_555 A N MSE 312 A MSE 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale12 A C MSE 312 A MSE 312 1_555 A N GLY 313 A GLY 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale13 B C PRO 30 B PRO 30 1_555 B N MSE 31 B MSE 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale14 B C MSE 31 B MSE 31 1_555 B N ALA 32 B ALA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale15 B C GLY 95 B GLY 95 1_555 B N MSE 96 B MSE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 B C MSE 96 B MSE 96 1_555 B N LEU 97 B LEU 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale17 B C LEU 162 B LEU 162 1_555 B N MSE 163 B MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale18 B C MSE 163 B MSE 163 1_555 B N SER 164 B SER 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale19 B C GLY 195 B GLY 195 1_555 B N MSE 196 B MSE 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale20 B C MSE 196 B MSE 196 1_555 B N LEU 197 B LEU 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale21 B C ARG 307 B ARG 307 1_555 B N MSE 308 B MSE 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale22 B C MSE 308 B MSE 308 1_555 B N LEU 309 B LEU 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale23 B C PHE 311 B PHE 311 1_555 B N MSE 312 B MSE 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale24 B C MSE 312 B MSE 312 1_555 B N GLY 313 B GLY 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? # _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 408 n n N HN1 SAM sing 409 n n N HN2 SAM sing 410 n n CA C SAM sing 411 n n CA CB SAM sing 412 n n CA HA SAM sing 413 n n C O SAM doub 414 n n C OXT SAM sing 415 n n CB CG SAM sing 416 n n CB HB1 SAM sing 417 n n CB HB2 SAM sing 418 n n CG SD SAM sing 419 n n CG HG1 SAM sing 420 n n CG HG2 SAM sing 421 n n SD CE SAM sing 422 n n SD C5' SAM sing 423 n n CE HE1 SAM sing 424 n n CE HE2 SAM sing 425 n n CE HE3 SAM sing 426 n n C5' C4' SAM sing 427 n n C5' "H5'1" SAM sing 428 n n C5' "H5'2" SAM sing 429 n n C4' O4' SAM sing 430 n n C4' C3' SAM sing 431 n n C4' H4' SAM sing 432 n n O4' C1' SAM sing 433 n n C3' O3' SAM sing 434 n n C3' C2' SAM sing 435 n n C3' H3' SAM sing 436 n n O3' HO3' SAM sing 437 n n C2' O2' SAM sing 438 n n C2' C1' SAM sing 439 n n C2' H2' SAM sing 440 n n O2' HO2' SAM sing 441 n n C1' N9 SAM sing 442 n n C1' H1' SAM sing 443 n n N9 C8 SAM sing 444 n y N9 C4 SAM sing 445 n y C8 N7 SAM doub 446 n y C8 H8 SAM sing 447 n n N7 C5 SAM sing 448 n y C5 C6 SAM sing 449 n y C5 C4 SAM doub 450 n y C6 N6 SAM sing 451 n n C6 N1 SAM doub 452 n y N6 HN61 SAM sing 453 n n N6 HN62 SAM sing 454 n n N1 C2 SAM sing 455 n y C2 N3 SAM doub 456 n y C2 H2 SAM sing 457 n n N3 C4 SAM sing 458 n y # _atom_sites.entry_id 1XDS _atom_sites.fract_transf_matrix[1][1] 0.012517 _atom_sites.fract_transf_matrix[1][2] 0.007227 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014454 _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] 0.004299 _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 2 SAM A 1 5635 5635 SAM SAM . D 3 DRA A 1 5600 5600 DRA DRA . E 2 SAM B 1 9635 9635 SAM SAM . F 3 DRA B 1 9600 9600 DRA DRA . G 4 HOH A 1 5636 1 HOH HOH . G 4 HOH A 2 5637 2 HOH HOH . G 4 HOH A 3 5638 3 HOH HOH . G 4 HOH A 4 5639 4 HOH HOH . G 4 HOH A 5 5640 11 HOH HOH . G 4 HOH A 6 5641 13 HOH HOH . G 4 HOH A 7 5642 15 HOH HOH . G 4 HOH A 8 5643 21 HOH HOH . G 4 HOH A 9 5644 22 HOH HOH . G 4 HOH A 10 5645 23 HOH HOH . G 4 HOH A 11 5646 24 HOH HOH . G 4 HOH A 12 5647 27 HOH HOH . G 4 HOH A 13 5648 32 HOH HOH . G 4 HOH A 14 5649 33 HOH HOH . G 4 HOH A 15 5650 34 HOH HOH . G 4 HOH A 16 5651 37 HOH HOH . G 4 HOH A 17 5652 44 HOH HOH . G 4 HOH A 18 5653 45 HOH HOH . G 4 HOH A 19 5654 46 HOH HOH . G 4 HOH A 20 5655 47 HOH HOH . G 4 HOH A 21 5656 51 HOH HOH . G 4 HOH A 22 5657 55 HOH HOH . G 4 HOH A 23 5658 57 HOH HOH . G 4 HOH A 24 5659 64 HOH HOH . G 4 HOH A 25 5660 71 HOH HOH . G 4 HOH A 26 5661 78 HOH HOH . G 4 HOH A 27 5662 79 HOH HOH . G 4 HOH A 28 5663 80 HOH HOH . G 4 HOH A 29 5664 81 HOH HOH . G 4 HOH A 30 5665 82 HOH HOH . G 4 HOH A 31 5666 85 HOH HOH . G 4 HOH A 32 5667 93 HOH HOH . G 4 HOH A 33 5668 94 HOH HOH . G 4 HOH A 34 5669 97 HOH HOH . G 4 HOH A 35 5670 98 HOH HOH . G 4 HOH A 36 5671 106 HOH HOH . G 4 HOH A 37 5672 107 HOH HOH . G 4 HOH A 38 5673 112 HOH HOH . G 4 HOH A 39 5674 115 HOH HOH . G 4 HOH A 40 5675 124 HOH HOH . G 4 HOH A 41 5676 125 HOH HOH . G 4 HOH A 42 5677 126 HOH HOH . G 4 HOH A 43 5678 131 HOH HOH . G 4 HOH A 44 5679 140 HOH HOH . G 4 HOH A 45 5680 165 HOH HOH . G 4 HOH A 46 5681 173 HOH HOH . G 4 HOH A 47 5682 183 HOH HOH . G 4 HOH A 48 5683 185 HOH HOH . G 4 HOH A 49 5684 186 HOH HOH . G 4 HOH A 50 5685 190 HOH HOH . G 4 HOH A 51 5686 192 HOH HOH . G 4 HOH A 52 5687 193 HOH HOH . G 4 HOH A 53 5688 195 HOH HOH . G 4 HOH A 54 5689 207 HOH HOH . G 4 HOH A 55 5690 217 HOH HOH . G 4 HOH A 56 5691 219 HOH HOH . H 4 HOH B 1 9636 5 HOH HOH . H 4 HOH B 2 9637 6 HOH HOH . H 4 HOH B 3 9638 7 HOH HOH . H 4 HOH B 4 9639 8 HOH HOH . H 4 HOH B 5 9640 9 HOH HOH . H 4 HOH B 6 9641 10 HOH HOH . H 4 HOH B 7 9642 12 HOH HOH . H 4 HOH B 8 9643 14 HOH HOH . H 4 HOH B 9 9644 18 HOH HOH . H 4 HOH B 10 9645 19 HOH HOH . H 4 HOH B 11 9646 25 HOH HOH . H 4 HOH B 12 9647 28 HOH HOH . H 4 HOH B 13 9648 29 HOH HOH . H 4 HOH B 14 9649 31 HOH HOH . H 4 HOH B 15 9650 35 HOH HOH . H 4 HOH B 16 9651 38 HOH HOH . H 4 HOH B 17 9652 39 HOH HOH . H 4 HOH B 18 9653 41 HOH HOH . H 4 HOH B 19 9654 49 HOH HOH . H 4 HOH B 20 9655 50 HOH HOH . H 4 HOH B 21 9656 53 HOH HOH . H 4 HOH B 22 9657 62 HOH HOH . H 4 HOH B 23 9658 63 HOH HOH . H 4 HOH B 24 9659 65 HOH HOH . H 4 HOH B 25 9660 67 HOH HOH . H 4 HOH B 26 9661 68 HOH HOH . H 4 HOH B 27 9662 70 HOH HOH . H 4 HOH B 28 9663 73 HOH HOH . H 4 HOH B 29 9664 75 HOH HOH . H 4 HOH B 30 9665 76 HOH HOH . H 4 HOH B 31 9666 86 HOH HOH . H 4 HOH B 32 9667 105 HOH HOH . H 4 HOH B 33 9668 110 HOH HOH . H 4 HOH B 34 9669 111 HOH HOH . H 4 HOH B 35 9670 114 HOH HOH . H 4 HOH B 36 9671 119 HOH HOH . H 4 HOH B 37 9672 120 HOH HOH . H 4 HOH B 38 9673 121 HOH HOH . H 4 HOH B 39 9674 123 HOH HOH . H 4 HOH B 40 9675 134 HOH HOH . H 4 HOH B 41 9676 145 HOH HOH . H 4 HOH B 42 9677 154 HOH HOH . H 4 HOH B 43 9678 170 HOH HOH . H 4 HOH B 44 9679 200 HOH HOH . H 4 HOH B 45 9680 203 HOH HOH . H 4 HOH B 46 9681 208 HOH HOH . H 4 HOH B 47 9682 210 HOH HOH . H 4 HOH B 48 9683 212 HOH HOH . H 4 HOH B 49 9684 213 HOH HOH . H 4 HOH B 50 9685 214 HOH HOH . H 4 HOH B 51 9686 215 HOH HOH . H 4 HOH B 52 9687 216 HOH HOH . H 4 HOH B 53 9688 218 HOH HOH . H 4 HOH B 54 9689 222 HOH HOH . H 4 HOH B 55 9690 226 HOH HOH . H 4 HOH B 56 9691 227 HOH HOH . H 4 HOH B 57 9692 228 HOH HOH . H 4 HOH B 58 9693 229 HOH HOH . H 4 HOH B 59 9694 231 HOH HOH . H 4 HOH B 60 9695 232 HOH HOH . H 4 HOH B 61 9696 233 HOH HOH . H 4 HOH B 62 9697 234 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 . . . C 2 46.224 44.988 115.925 1 37.39 ? N SAM 5635 A 1 HETATM 2 C CA SAM . . . C 2 45.188 44.13 115.371 1 37.46 ? CA SAM 5635 A 1 HETATM 3 C C SAM . . . C 2 45.291 42.7 115.862 1 38.11 ? C SAM 5635 A 1 HETATM 4 O O SAM . . . C 2 46.409 42.155 115.99 1 37.41 ? O SAM 5635 A 1 HETATM 5 O OXT SAM . . . C 2 44.234 42.072 116.118 1 38.96 ? OXT SAM 5635 A 1 HETATM 6 C CB SAM . . . C 2 45.377 44.16 113.865 1 37.18 ? CB SAM 5635 A 1 HETATM 7 C CG SAM . . . C 2 44.092 43.892 113.134 1 36.69 ? CG SAM 5635 A 1 HETATM 8 S SD SAM . . . C 2 44.275 43.993 111.479 1 36.25 ? SD SAM 5635 A 1 HETATM 9 C CE SAM . . . C 2 45.269 42.747 111.001 1 38.02 ? CE SAM 5635 A 1 HETATM 10 C C5' SAM . . . C 2 44.77 45.467 110.843 1 33.79 ? C5' SAM 5635 A 1 HETATM 11 C C4' SAM . . . C 2 43.914 46.586 111.422 1 31.08 ? C4' SAM 5635 A 1 HETATM 12 O O4' SAM . . . C 2 44.345 47.907 111.079 1 30.16 ? O4' SAM 5635 A 1 HETATM 13 C C3' SAM . . . C 2 42.417 46.52 111.081 1 31.96 ? C3' SAM 5635 A 1 HETATM 14 O O3' SAM . . . C 2 41.716 46.256 112.284 1 31.19 ? O3' SAM 5635 A 1 HETATM 15 C C2' SAM . . . C 2 42.01 47.89 110.542 1 30.05 ? C2' SAM 5635 A 1 HETATM 16 O O2' SAM . . . C 2 40.876 48.496 111.086 1 30.55 ? O2' SAM 5635 A 1 HETATM 17 C C1' SAM . . . C 2 43.229 48.75 110.777 1 29.94 ? C1' SAM 5635 A 1 HETATM 18 N N9 SAM . . . C 2 43.426 49.878 109.836 1 28.57 ? N9 SAM 5635 A 1 HETATM 19 C C8 SAM . . . C 2 43.54 49.897 108.489 1 27.14 ? C8 SAM 5635 A 1 HETATM 20 N N7 SAM . . . C 2 43.714 51.161 108.011 1 26.23 ? N7 SAM 5635 A 1 HETATM 21 C C5 SAM . . . C 2 43.709 51.97 109.079 1 28.26 ? C5 SAM 5635 A 1 HETATM 22 C C6 SAM . . . C 2 43.821 53.316 109.365 1 28.3 ? C6 SAM 5635 A 1 HETATM 23 N N6 SAM . . . C 2 43.994 54.134 108.317 1 28.7 ? N6 SAM 5635 A 1 HETATM 24 N N1 SAM . . . C 2 43.744 53.791 110.652 1 26.63 ? N1 SAM 5635 A 1 HETATM 25 C C2 SAM . . . C 2 43.555 52.989 111.713 1 26.41 ? C2 SAM 5635 A 1 HETATM 26 N N3 SAM . . . C 2 43.421 51.655 111.57 1 26.53 ? N3 SAM 5635 A 1 HETATM 27 C C4 SAM . . . C 2 43.502 51.123 110.23 1 27.04 ? C4 SAM 5635 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #