data_1XVA # _model_server_result.job_id BE4tNdVPnnoacpDeFkwZ8A _model_server_result.datetime_utc '2024-12-03 06:37:47' _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 1xva # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":293}' # _entry.id 1XVA # _exptl.entry_id 1XVA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 3 _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 90 _cell.entry_id 1XVA _cell.length_a 86.4 _cell.length_b 175.7 _cell.length_c 45.5 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XVA _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,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_765 -x+2,-y+1,z -1 0 0 0 -1 0 0 0 1 172.8 175.7 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F 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 283 n n N HN1 SAM sing 284 n n N HN2 SAM sing 285 n n CA C SAM sing 286 n n CA CB SAM sing 287 n n CA HA SAM sing 288 n n C O SAM doub 289 n n C OXT SAM sing 290 n n CB CG SAM sing 291 n n CB HB1 SAM sing 292 n n CB HB2 SAM sing 293 n n CG SD SAM sing 294 n n CG HG1 SAM sing 295 n n CG HG2 SAM sing 296 n n SD CE SAM sing 297 n n SD C5' SAM sing 298 n n CE HE1 SAM sing 299 n n CE HE2 SAM sing 300 n n CE HE3 SAM sing 301 n n C5' C4' SAM sing 302 n n C5' "H5'1" SAM sing 303 n n C5' "H5'2" SAM sing 304 n n C4' O4' SAM sing 305 n n C4' C3' SAM sing 306 n n C4' H4' SAM sing 307 n n O4' C1' SAM sing 308 n n C3' O3' SAM sing 309 n n C3' C2' SAM sing 310 n n C3' H3' SAM sing 311 n n O3' HO3' SAM sing 312 n n C2' O2' SAM sing 313 n n C2' C1' SAM sing 314 n n C2' H2' SAM sing 315 n n O2' HO2' SAM sing 316 n n C1' N9 SAM sing 317 n n C1' H1' SAM sing 318 n n N9 C8 SAM sing 319 n y N9 C4 SAM sing 320 n y C8 N7 SAM doub 321 n y C8 H8 SAM sing 322 n n N7 C5 SAM sing 323 n y C5 C6 SAM sing 324 n y C5 C4 SAM doub 325 n y C6 N6 SAM sing 326 n n C6 N1 SAM doub 327 n y N6 HN61 SAM sing 328 n n N6 HN62 SAM sing 329 n n N1 C2 SAM sing 330 n y C2 N3 SAM doub 331 n y C2 H2 SAM sing 332 n n N3 C4 SAM sing 333 n y # _atom_sites.entry_id 1XVA _atom_sites.fract_transf_matrix[1][1] 0.011574 _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] 0.005692 _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] 0.021978 _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 ACT A 1 294 294 ACT ACT . D 3 SAM A 1 293 293 SAM SAM . E 2 ACT B 1 294 294 ACT ACT . F 3 SAM B 1 293 293 SAM SAM . G 4 HOH A 1 295 1 HOH HOH . G 4 HOH A 2 296 2 HOH HOH . G 4 HOH A 3 297 3 HOH HOH . G 4 HOH A 4 298 5 HOH HOH . G 4 HOH A 5 299 7 HOH HOH . G 4 HOH A 6 300 8 HOH HOH . G 4 HOH A 7 301 10 HOH HOH . G 4 HOH A 8 302 11 HOH HOH . G 4 HOH A 9 303 16 HOH HOH . G 4 HOH A 10 304 17 HOH HOH . G 4 HOH A 11 305 18 HOH HOH . G 4 HOH A 12 306 19 HOH HOH . G 4 HOH A 13 307 20 HOH HOH . G 4 HOH A 14 308 22 HOH HOH . G 4 HOH A 15 309 23 HOH HOH . G 4 HOH A 16 310 25 HOH HOH . G 4 HOH A 17 311 26 HOH HOH . G 4 HOH A 18 312 27 HOH HOH . G 4 HOH A 19 313 29 HOH HOH . G 4 HOH A 20 314 30 HOH HOH . G 4 HOH A 21 315 31 HOH HOH . G 4 HOH A 22 316 32 HOH HOH . G 4 HOH A 23 317 33 HOH HOH . G 4 HOH A 24 318 36 HOH HOH . G 4 HOH A 25 319 37 HOH HOH . G 4 HOH A 26 320 40 HOH HOH . G 4 HOH A 27 321 41 HOH HOH . G 4 HOH A 28 322 45 HOH HOH . G 4 HOH A 29 323 46 HOH HOH . G 4 HOH A 30 324 48 HOH HOH . G 4 HOH A 31 325 49 HOH HOH . G 4 HOH A 32 326 51 HOH HOH . G 4 HOH A 33 327 52 HOH HOH . G 4 HOH A 34 328 54 HOH HOH . G 4 HOH A 35 329 57 HOH HOH . G 4 HOH A 36 330 58 HOH HOH . G 4 HOH A 37 331 59 HOH HOH . G 4 HOH A 38 332 60 HOH HOH . G 4 HOH A 39 333 61 HOH HOH . G 4 HOH A 40 334 63 HOH HOH . G 4 HOH A 41 335 64 HOH HOH . G 4 HOH A 42 336 65 HOH HOH . G 4 HOH A 43 337 67 HOH HOH . G 4 HOH A 44 338 68 HOH HOH . G 4 HOH A 45 339 69 HOH HOH . G 4 HOH A 46 340 70 HOH HOH . G 4 HOH A 47 341 72 HOH HOH . G 4 HOH A 48 342 75 HOH HOH . G 4 HOH A 49 343 76 HOH HOH . G 4 HOH A 50 344 77 HOH HOH . G 4 HOH A 51 345 79 HOH HOH . G 4 HOH A 52 346 80 HOH HOH . G 4 HOH A 53 347 86 HOH HOH . G 4 HOH A 54 348 87 HOH HOH . G 4 HOH A 55 349 88 HOH HOH . G 4 HOH A 56 350 89 HOH HOH . G 4 HOH A 57 351 90 HOH HOH . G 4 HOH A 58 352 93 HOH HOH . G 4 HOH A 59 353 94 HOH HOH . H 4 HOH B 1 295 4 HOH HOH . H 4 HOH B 2 296 6 HOH HOH . H 4 HOH B 3 297 9 HOH HOH . H 4 HOH B 4 298 12 HOH HOH . H 4 HOH B 5 299 13 HOH HOH . H 4 HOH B 6 300 14 HOH HOH . H 4 HOH B 7 301 15 HOH HOH . H 4 HOH B 8 302 21 HOH HOH . H 4 HOH B 9 303 24 HOH HOH . H 4 HOH B 10 304 28 HOH HOH . H 4 HOH B 11 305 34 HOH HOH . H 4 HOH B 12 306 35 HOH HOH . H 4 HOH B 13 307 38 HOH HOH . H 4 HOH B 14 308 39 HOH HOH . H 4 HOH B 15 309 42 HOH HOH . H 4 HOH B 16 310 43 HOH HOH . H 4 HOH B 17 311 44 HOH HOH . H 4 HOH B 18 312 47 HOH HOH . H 4 HOH B 19 313 50 HOH HOH . H 4 HOH B 20 314 53 HOH HOH . H 4 HOH B 21 315 55 HOH HOH . H 4 HOH B 22 316 56 HOH HOH . H 4 HOH B 23 317 62 HOH HOH . H 4 HOH B 24 318 66 HOH HOH . H 4 HOH B 25 319 71 HOH HOH . H 4 HOH B 26 320 73 HOH HOH . H 4 HOH B 27 321 74 HOH HOH . H 4 HOH B 28 322 78 HOH HOH . H 4 HOH B 29 323 81 HOH HOH . H 4 HOH B 30 324 82 HOH HOH . H 4 HOH B 31 325 83 HOH HOH . H 4 HOH B 32 326 84 HOH HOH . H 4 HOH B 33 327 85 HOH HOH . H 4 HOH B 34 328 91 HOH HOH . H 4 HOH B 35 329 92 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 3 61.528 67.488 7.56 1 45.04 ? N SAM 293 A 1 HETATM 2 C CA SAM . . . D 3 61.353 68.9 7.24 1 43.23 ? CA SAM 293 A 1 HETATM 3 C C SAM . . . D 3 61.499 69.037 5.716 1 44.19 ? C SAM 293 A 1 HETATM 4 O O SAM . . . D 3 60.561 68.693 4.977 1 44.14 ? O SAM 293 A 1 HETATM 5 O OXT SAM . . . D 3 62.43 69.659 5.212 1 45.33 ? OXT SAM 293 A 1 HETATM 6 C CB SAM . . . D 3 62.409 69.71 8.012 1 44.38 ? CB SAM 293 A 1 HETATM 7 C CG SAM . . . D 3 61.927 70.808 8.974 1 43.77 ? CG SAM 293 A 1 HETATM 8 S SD SAM . . . D 3 63.273 71.731 9.793 1 59.97 ? SD SAM 293 A 1 HETATM 9 C CE SAM . . . D 3 63.878 70.657 11.085 1 46.38 ? CE SAM 293 A 1 HETATM 10 C C5' SAM . . . D 3 62.463 73.035 10.787 1 44.09 ? C5' SAM 293 A 1 HETATM 11 C C4' SAM . . . D 3 61.83 73.945 9.872 1 45.66 ? C4' SAM 293 A 1 HETATM 12 O O4' SAM . . . D 3 60.84 74.781 10.592 1 44.57 ? O4' SAM 293 A 1 HETATM 13 C C3' SAM . . . D 3 62.951 74.918 9.295 1 46.16 ? C3' SAM 293 A 1 HETATM 14 O O3' SAM . . . D 3 62.961 74.937 7.829 1 43.23 ? O3' SAM 293 A 1 HETATM 15 C C2' SAM . . . D 3 62.55 76.288 9.822 1 46.98 ? C2' SAM 293 A 1 HETATM 16 O O2' SAM . . . D 3 62.783 77.271 8.836 1 48.14 ? O2' SAM 293 A 1 HETATM 17 C C1' SAM . . . D 3 61.048 76.139 10.102 1 46.1 ? C1' SAM 293 A 1 HETATM 18 N N9 SAM . . . D 3 60.408 77.309 10.84 1 48.29 ? N9 SAM 293 A 1 HETATM 19 C C8 SAM . . . D 3 59.92 78.44 10.189 1 45 ? C8 SAM 293 A 1 HETATM 20 N N7 SAM . . . D 3 59.502 79.378 10.988 1 46.15 ? N7 SAM 293 A 1 HETATM 21 C C5 SAM . . . D 3 59.712 78.857 12.277 1 44.9 ? C5 SAM 293 A 1 HETATM 22 C C6 SAM . . . D 3 59.392 79.355 13.564 1 46.45 ? C6 SAM 293 A 1 HETATM 23 N N6 SAM . . . D 3 58.865 80.571 13.745 1 44.7 ? N6 SAM 293 A 1 HETATM 24 N N1 SAM . . . D 3 59.638 78.566 14.633 1 45.07 ? N1 SAM 293 A 1 HETATM 25 C C2 SAM . . . D 3 60.188 77.369 14.433 1 43.82 ? C2 SAM 293 A 1 HETATM 26 N N3 SAM . . . D 3 60.547 76.788 13.293 1 44.81 ? N3 SAM 293 A 1 HETATM 27 C C4 SAM . . . D 3 60.279 77.596 12.218 1 46.18 ? C4 SAM 293 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 27 #