data_2HMY # _model_server_result.job_id 4hvlc2wgvYcIxOGeBKnthA _model_server_result.datetime_utc '2025-03-01 10:23:12' _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 2hmy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":328}' # _entry.id 2HMY # _exptl.entry_id 2HMY _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103 _cell.angle_gamma 90 _cell.entry_id 2HMY _cell.length_a 55.3 _cell.length_b 74.68 _cell.length_c 90.96 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2HMY _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 277 n n N HN1 SAM sing 278 n n N HN2 SAM sing 279 n n CA C SAM sing 280 n n CA CB SAM sing 281 n n CA HA SAM sing 282 n n C O SAM doub 283 n n C OXT SAM sing 284 n n CB CG SAM sing 285 n n CB HB1 SAM sing 286 n n CB HB2 SAM sing 287 n n CG SD SAM sing 288 n n CG HG1 SAM sing 289 n n CG HG2 SAM sing 290 n n SD CE SAM sing 291 n n SD C5' SAM sing 292 n n CE HE1 SAM sing 293 n n CE HE2 SAM sing 294 n n CE HE3 SAM sing 295 n n C5' C4' SAM sing 296 n n C5' "H5'1" SAM sing 297 n n C5' "H5'2" SAM sing 298 n n C4' O4' SAM sing 299 n n C4' C3' SAM sing 300 n n C4' H4' SAM sing 301 n n O4' C1' SAM sing 302 n n C3' O3' SAM sing 303 n n C3' C2' SAM sing 304 n n C3' H3' SAM sing 305 n n O3' HO3' SAM sing 306 n n C2' O2' SAM sing 307 n n C2' C1' SAM sing 308 n n C2' H2' SAM sing 309 n n O2' HO2' SAM sing 310 n n C1' N9 SAM sing 311 n n C1' H1' SAM sing 312 n n N9 C8 SAM sing 313 n y N9 C4 SAM sing 314 n y C8 N7 SAM doub 315 n y C8 H8 SAM sing 316 n n N7 C5 SAM sing 317 n y C5 C6 SAM sing 318 n y C5 C4 SAM doub 319 n y C6 N6 SAM sing 320 n n C6 N1 SAM doub 321 n y N6 HN61 SAM sing 322 n n N6 HN62 SAM sing 323 n n N1 C2 SAM sing 324 n y C2 N3 SAM doub 325 n y C2 H2 SAM sing 326 n n N3 C4 SAM sing 327 n y # _atom_sites.entry_id 2HMY _atom_sites.fract_transf_matrix[1][1] 0.018083 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004175 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01339 _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] 0.011283 _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 B 2 SAM B 1 328 328 SAM SAM . C 3 HOH B 1 329 3 HOH HOH . C 3 HOH B 2 330 4 HOH HOH . C 3 HOH B 3 331 10 HOH HOH . C 3 HOH B 4 332 11 HOH HOH . C 3 HOH B 5 333 14 HOH HOH . C 3 HOH B 6 334 15 HOH HOH . C 3 HOH B 7 335 16 HOH HOH . C 3 HOH B 8 336 20 HOH HOH . C 3 HOH B 9 337 21 HOH HOH . C 3 HOH B 10 338 22 HOH HOH . C 3 HOH B 11 339 23 HOH HOH . C 3 HOH B 12 340 27 HOH HOH . C 3 HOH B 13 341 31 HOH HOH . C 3 HOH B 14 342 32 HOH HOH . C 3 HOH B 15 343 33 HOH HOH . C 3 HOH B 16 344 34 HOH HOH . C 3 HOH B 17 345 35 HOH HOH . C 3 HOH B 18 346 36 HOH HOH . C 3 HOH B 19 347 37 HOH HOH . C 3 HOH B 20 348 38 HOH HOH . C 3 HOH B 21 349 39 HOH HOH . C 3 HOH B 22 350 40 HOH HOH . C 3 HOH B 23 351 42 HOH HOH . C 3 HOH B 24 352 43 HOH HOH . C 3 HOH B 25 353 44 HOH HOH . C 3 HOH B 26 354 45 HOH HOH . C 3 HOH B 27 355 46 HOH HOH . C 3 HOH B 28 356 50 HOH HOH . C 3 HOH B 29 357 51 HOH HOH . C 3 HOH B 30 358 52 HOH HOH . C 3 HOH B 31 359 53 HOH HOH . C 3 HOH B 32 360 54 HOH HOH . C 3 HOH B 33 361 55 HOH HOH . C 3 HOH B 34 362 60 HOH HOH . C 3 HOH B 35 363 61 HOH HOH . C 3 HOH B 36 364 66 HOH HOH . C 3 HOH B 37 365 68 HOH HOH . C 3 HOH B 38 366 70 HOH HOH . C 3 HOH B 39 367 74 HOH HOH . C 3 HOH B 40 368 75 HOH HOH . C 3 HOH B 41 369 76 HOH HOH . C 3 HOH B 42 370 77 HOH HOH . C 3 HOH B 43 371 78 HOH HOH . C 3 HOH B 44 372 79 HOH HOH . C 3 HOH B 45 373 80 HOH HOH . C 3 HOH B 46 374 81 HOH HOH . C 3 HOH B 47 375 82 HOH HOH . C 3 HOH B 48 376 83 HOH HOH . C 3 HOH B 49 377 90 HOH HOH . C 3 HOH B 50 378 91 HOH HOH . C 3 HOH B 51 379 92 HOH HOH . C 3 HOH B 52 380 93 HOH HOH . C 3 HOH B 53 381 94 HOH HOH . C 3 HOH B 54 382 95 HOH HOH . C 3 HOH B 55 383 96 HOH HOH . C 3 HOH B 56 384 97 HOH HOH . C 3 HOH B 57 385 102 HOH HOH . C 3 HOH B 58 386 103 HOH HOH . C 3 HOH B 59 387 104 HOH HOH . C 3 HOH B 60 388 106 HOH HOH . C 3 HOH B 61 389 107 HOH HOH . C 3 HOH B 62 390 108 HOH HOH . C 3 HOH B 63 391 109 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 . . . B 2 7.846 -0.557 65.565 1 12.18 ? N SAM 328 B 1 HETATM 2 C CA SAM . . . B 2 7.15 -1.506 64.698 1 15.69 ? CA SAM 328 B 1 HETATM 3 C C SAM . . . B 2 8.267 -1.83 63.716 1 17.18 ? C SAM 328 B 1 HETATM 4 O O SAM . . . B 2 9.452 -1.379 64.005 1 15.63 ? O SAM 328 B 1 HETATM 5 O OXT SAM . . . B 2 7.993 -2.079 62.464 1 23.54 ? OXT SAM 328 B 1 HETATM 6 C CB SAM . . . B 2 6.012 -0.735 64.005 1 13.75 ? CB SAM 328 B 1 HETATM 7 C CG SAM . . . B 2 4.974 -1.575 63.263 1 4.31 ? CG SAM 328 B 1 HETATM 8 S SD SAM . . . B 2 3.635 -0.407 62.804 1 6.46 ? SD SAM 328 B 1 HETATM 9 C CE SAM . . . B 2 3.048 1.296 62.927 1 2 ? CE SAM 328 B 1 HETATM 10 C C5' SAM . . . B 2 2.039 -1.149 63.096 1 2 ? C5' SAM 328 B 1 HETATM 11 C C4' SAM . . . B 2 2.046 -2.696 62.854 1 8.78 ? C4' SAM 328 B 1 HETATM 12 O O4' SAM . . . B 2 0.7 -3.155 63.278 1 6.3 ? O4' SAM 328 B 1 HETATM 13 C C3' SAM . . . B 2 2.257 -3.232 61.39 1 10.68 ? C3' SAM 328 B 1 HETATM 14 O O3' SAM . . . B 2 3.227 -4.339 61.293 1 10.47 ? O3' SAM 328 B 1 HETATM 15 C C2' SAM . . . B 2 0.819 -3.918 61.267 1 11.97 ? C2' SAM 328 B 1 HETATM 16 O O2' SAM . . . B 2 0.899 -5.019 60.361 1 8.55 ? O2' SAM 328 B 1 HETATM 17 C C1' SAM . . . B 2 0.592 -4.485 62.714 1 7.45 ? C1' SAM 328 B 1 HETATM 18 N N9 SAM . . . B 2 -0.787 -4.944 62.885 1 7.01 ? N9 SAM 328 B 1 HETATM 19 C C8 SAM . . . B 2 -1.958 -4.196 62.548 1 2.06 ? C8 SAM 328 B 1 HETATM 20 N N7 SAM . . . B 2 -3.088 -4.814 62.944 1 8.88 ? N7 SAM 328 B 1 HETATM 21 C C5 SAM . . . B 2 -2.643 -6.054 63.588 1 5.8 ? C5 SAM 328 B 1 HETATM 22 C C6 SAM . . . B 2 -3.325 -7.152 64.186 1 5.2 ? C6 SAM 328 B 1 HETATM 23 N N6 SAM . . . B 2 -4.668 -7.267 64.285 1 2.73 ? N6 SAM 328 B 1 HETATM 24 N N1 SAM . . . B 2 -2.576 -8.184 64.658 1 7.19 ? N1 SAM 328 B 1 HETATM 25 C C2 SAM . . . B 2 -1.27 -8.104 64.527 1 2.79 ? C2 SAM 328 B 1 HETATM 26 N N3 SAM . . . B 2 -0.524 -7.134 63.996 1 3.89 ? N3 SAM 328 B 1 HETATM 27 C C4 SAM . . . B 2 -1.265 -6.128 63.541 1 4.23 ? C4 SAM 328 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #