data_5HIM # _model_server_result.job_id J7j0JuILE2KOIbULS2RdHw _model_server_result.datetime_utc '2024-11-29 15:44:39' _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 5him # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5HIM # _exptl.entry_id 5HIM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 90 _cell.angle_gamma 90 _cell.entry_id 5HIM _cell.length_a 51.975 _cell.length_b 121.219 _cell.length_c 131.686 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HIM _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,I,J _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 '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 301 n n N HN1 SAH sing 302 n n N HN2 SAH sing 303 n n CA CB SAH sing 304 n n CA C SAH sing 305 n n CA HA SAH sing 306 n n CB CG SAH sing 307 n n CB HB1 SAH sing 308 n n CB HB2 SAH sing 309 n n CG SD SAH sing 310 n n CG HG1 SAH sing 311 n n CG HG2 SAH sing 312 n n SD C5' SAH sing 313 n n C O SAH doub 314 n n C OXT SAH sing 315 n n OXT HXT SAH sing 316 n n C5' C4' SAH sing 317 n n C5' "H5'1" SAH sing 318 n n C5' "H5'2" SAH sing 319 n n C4' O4' SAH sing 320 n n C4' C3' SAH sing 321 n n C4' H4' SAH sing 322 n n O4' C1' SAH sing 323 n n C3' O3' SAH sing 324 n n C3' C2' SAH sing 325 n n C3' H3' SAH sing 326 n n O3' HO3' SAH sing 327 n n C2' O2' SAH sing 328 n n C2' C1' SAH sing 329 n n C2' H2' SAH sing 330 n n O2' HO2' SAH sing 331 n n C1' N9 SAH sing 332 n n C1' H1' SAH sing 333 n n N9 C8 SAH sing 334 n y N9 C4 SAH sing 335 n y C8 N7 SAH doub 336 n y C8 H8 SAH sing 337 n n N7 C5 SAH sing 338 n y C5 C6 SAH sing 339 n y C5 C4 SAH doub 340 n y C6 N6 SAH sing 341 n n C6 N1 SAH doub 342 n y N6 HN61 SAH sing 343 n n N6 HN62 SAH sing 344 n n N1 C2 SAH sing 345 n y C2 N3 SAH doub 346 n y C2 H2 SAH sing 347 n n N3 C4 SAH sing 348 n y # _atom_sites.entry_id 5HIM _atom_sites.fract_transf_matrix[1][1] 0.01924 _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] 0.00825 _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] 0.007594 _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 SAH A 1 301 1 SAH SAH . C 3 DMG A 1 302 1 DMG DMG . D 4 EDO A 1 303 1 EDO EDO . E 4 EDO A 1 304 2 EDO EDO . F 4 EDO A 1 305 3 EDO EDO . G 4 EDO A 1 306 4 EDO EDO . H 4 EDO A 1 307 5 EDO EDO . I 4 EDO A 1 308 6 EDO EDO . J 5 HOH A 1 401 12 HOH HOH . J 5 HOH A 2 402 24 HOH HOH . J 5 HOH A 3 403 44 HOH HOH . J 5 HOH A 4 404 47 HOH HOH . J 5 HOH A 5 405 62 HOH HOH . J 5 HOH A 6 406 15 HOH HOH . J 5 HOH A 7 407 77 HOH HOH . J 5 HOH A 8 408 14 HOH HOH . J 5 HOH A 9 409 61 HOH HOH . J 5 HOH A 10 410 30 HOH HOH . J 5 HOH A 11 411 28 HOH HOH . J 5 HOH A 12 412 2 HOH HOH . J 5 HOH A 13 413 22 HOH HOH . J 5 HOH A 14 414 20 HOH HOH . J 5 HOH A 15 415 58 HOH HOH . J 5 HOH A 16 416 9 HOH HOH . J 5 HOH A 17 417 57 HOH HOH . J 5 HOH A 18 418 37 HOH HOH . J 5 HOH A 19 419 54 HOH HOH . J 5 HOH A 20 420 38 HOH HOH . J 5 HOH A 21 421 25 HOH HOH . J 5 HOH A 22 422 5 HOH HOH . J 5 HOH A 23 423 69 HOH HOH . J 5 HOH A 24 424 8 HOH HOH . J 5 HOH A 25 425 35 HOH HOH . J 5 HOH A 26 426 3 HOH HOH . J 5 HOH A 27 427 1 HOH HOH . J 5 HOH A 28 428 17 HOH HOH . J 5 HOH A 29 429 48 HOH HOH . J 5 HOH A 30 430 27 HOH HOH . J 5 HOH A 31 431 11 HOH HOH . J 5 HOH A 32 432 13 HOH HOH . J 5 HOH A 33 433 56 HOH HOH . J 5 HOH A 34 434 7 HOH HOH . J 5 HOH A 35 435 31 HOH HOH . J 5 HOH A 36 436 43 HOH HOH . J 5 HOH A 37 437 29 HOH HOH . J 5 HOH A 38 438 10 HOH HOH . J 5 HOH A 39 439 46 HOH HOH . J 5 HOH A 40 440 53 HOH HOH . J 5 HOH A 41 441 34 HOH HOH . J 5 HOH A 42 442 16 HOH HOH . J 5 HOH A 43 443 68 HOH HOH . J 5 HOH A 44 444 39 HOH HOH . J 5 HOH A 45 445 55 HOH HOH . J 5 HOH A 46 446 42 HOH HOH . J 5 HOH A 47 447 33 HOH HOH . J 5 HOH A 48 448 26 HOH HOH . J 5 HOH A 49 449 63 HOH HOH . J 5 HOH A 50 450 18 HOH HOH . J 5 HOH A 51 451 23 HOH HOH . J 5 HOH A 52 452 21 HOH HOH . J 5 HOH A 53 453 4 HOH HOH . J 5 HOH A 54 454 72 HOH HOH . J 5 HOH A 55 455 19 HOH HOH . J 5 HOH A 56 456 65 HOH HOH . J 5 HOH A 57 457 45 HOH HOH . J 5 HOH A 58 458 32 HOH HOH . J 5 HOH A 59 459 64 HOH HOH . J 5 HOH A 60 460 50 HOH HOH . J 5 HOH A 61 461 67 HOH HOH . J 5 HOH A 62 462 74 HOH HOH . J 5 HOH A 63 463 40 HOH HOH . J 5 HOH A 64 464 52 HOH HOH . J 5 HOH A 65 465 66 HOH HOH . J 5 HOH A 66 466 70 HOH HOH . J 5 HOH A 67 467 78 HOH HOH . J 5 HOH A 68 468 71 HOH HOH . J 5 HOH A 69 469 41 HOH HOH . J 5 HOH A 70 470 59 HOH HOH . J 5 HOH A 71 471 73 HOH HOH . J 5 HOH A 72 472 6 HOH HOH . J 5 HOH A 73 473 76 HOH HOH . J 5 HOH A 74 474 75 HOH HOH . J 5 HOH A 75 475 49 HOH HOH . J 5 HOH A 76 476 36 HOH HOH . J 5 HOH A 77 477 51 HOH HOH . J 5 HOH A 78 478 60 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 . . . B 2 -5.391 -16.08 -21.86 1 39.62 ? N SAH 301 A 1 HETATM 2 C CA SAH . . . B 2 -5.195 -15.779 -23.25 1 46.57 ? CA SAH 301 A 1 HETATM 3 C CB SAH . . . B 2 -3.839 -16.171 -23.78 1 45.44 ? CB SAH 301 A 1 HETATM 4 C CG SAH . . . B 2 -3.17 -17.186 -22.921 1 40.09 ? CG SAH 301 A 1 HETATM 5 S SD SAH . . . B 2 -1.547 -17.59 -23.582 1 42.73 ? SD SAH 301 A 1 HETATM 6 C C SAH . . . B 2 -6.25 -16.448 -24.126 1 45.93 ? C SAH 301 A 1 HETATM 7 O O SAH . . . B 2 -6.302 -16.159 -25.365 1 40.94 ? O SAH 301 A 1 HETATM 8 O OXT SAH . . . B 2 -7.068 -17.295 -23.612 1 40.81 ? OXT SAH 301 A 1 HETATM 9 C C5' SAH . . . B 2 -0.466 -18.051 -22.221 1 32.97 ? C5' SAH 301 A 1 HETATM 10 C C4' SAH . . . B 2 0.204 -16.779 -21.715 1 31.08 ? C4' SAH 301 A 1 HETATM 11 O O4' SAH . . . B 2 0.698 -16.947 -20.43 1 35.79 ? O4' SAH 301 A 1 HETATM 12 C C3' SAH . . . B 2 1.342 -16.339 -22.599 1 31.59 ? C3' SAH 301 A 1 HETATM 13 O O3' SAH . . . B 2 1.043 -15.104 -23.082 1 37.09 ? O3' SAH 301 A 1 HETATM 14 C C2' SAH . . . B 2 2.58 -16.356 -21.742 1 37.55 ? C2' SAH 301 A 1 HETATM 15 O O2' SAH . . . B 2 3.502 -15.337 -21.946 1 31.73 ? O2' SAH 301 A 1 HETATM 16 C C1' SAH . . . B 2 1.95 -16.315 -20.36 1 42.68 ? C1' SAH 301 A 1 HETATM 17 N N9 SAH . . . B 2 2.818 -16.923 -19.351 1 45.62 ? N9 SAH 301 A 1 HETATM 18 C C8 SAH . . . B 2 3.29 -18.188 -19.353 1 42.2 ? C8 SAH 301 A 1 HETATM 19 N N7 SAH . . . B 2 4.041 -18.395 -18.273 1 39.23 ? N7 SAH 301 A 1 HETATM 20 C C5 SAH . . . B 2 4.082 -17.262 -17.528 1 45.83 ? C5 SAH 301 A 1 HETATM 21 C C6 SAH . . . B 2 4.684 -16.897 -16.334 1 38.82 ? C6 SAH 301 A 1 HETATM 22 N N6 SAH . . . B 2 5.49 -17.822 -15.62 1 37.31 ? N6 SAH 301 A 1 HETATM 23 N N1 SAH . . . B 2 4.511 -15.645 -15.851 1 40.97 ? N1 SAH 301 A 1 HETATM 24 C C2 SAH . . . B 2 3.762 -14.73 -16.498 1 39.71 ? C2 SAH 301 A 1 HETATM 25 N N3 SAH . . . B 2 3.157 -15.053 -17.653 1 41.81 ? N3 SAH 301 A 1 HETATM 26 C C4 SAH . . . B 2 3.3 -16.296 -18.194 1 44.28 ? C4 SAH 301 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 26 #