data_5ZW3 # _model_server_result.job_id VGguPlOUIiw-vG-KqoERwg _model_server_result.datetime_utc '2024-10-19 07:41:37' _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 5zw3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 5ZW3 # _exptl.entry_id 5ZW3 _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 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 5ZW3 _cell.length_a 76.874 _cell.length_b 116.738 _cell.length_c 43.437 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ZW3 _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 _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 metalc ? metalc1 A OD1 ASP 133 A ASP 133 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc2 A OD2 ASP 159 A ASP 159 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc3 A OD1 ASN 160 A ASN 160 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc4 D MG MG . A MG 302 1_555 G O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc5 D MG MG . A MG 302 1_555 G O HOH . A HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc6 D MG MG . A MG 302 1_555 G O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc7 B OD1 ASP 133 B ASP 133 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc8 B OD2 ASP 159 B ASP 159 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc9 B OD1 ASN 160 B ASN 160 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc10 F MG MG . B MG 302 1_555 H O HOH . B HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? metalc ? metalc11 F MG MG . B MG 302 1_555 H O HOH . B HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc12 F MG MG . B MG 302 1_555 H O HOH . B HOH 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? # _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 264 n n N HN1 SAH sing 265 n n N HN2 SAH sing 266 n n CA CB SAH sing 267 n n CA C SAH sing 268 n n CA HA SAH sing 269 n n CB CG SAH sing 270 n n CB HB1 SAH sing 271 n n CB HB2 SAH sing 272 n n CG SD SAH sing 273 n n CG HG1 SAH sing 274 n n CG HG2 SAH sing 275 n n SD C5' SAH sing 276 n n C O SAH doub 277 n n C OXT SAH sing 278 n n OXT HXT SAH sing 279 n n C5' C4' SAH sing 280 n n C5' "H5'1" SAH sing 281 n n C5' "H5'2" SAH sing 282 n n C4' O4' SAH sing 283 n n C4' C3' SAH sing 284 n n C4' H4' SAH sing 285 n n O4' C1' SAH sing 286 n n C3' O3' SAH sing 287 n n C3' C2' SAH sing 288 n n C3' H3' SAH sing 289 n n O3' HO3' SAH sing 290 n n C2' O2' SAH sing 291 n n C2' C1' SAH sing 292 n n C2' H2' SAH sing 293 n n O2' HO2' SAH sing 294 n n C1' N9 SAH sing 295 n n C1' H1' SAH sing 296 n n N9 C8 SAH sing 297 n y N9 C4 SAH sing 298 n y C8 N7 SAH doub 299 n y C8 H8 SAH sing 300 n n N7 C5 SAH sing 301 n y C5 C6 SAH sing 302 n y C5 C4 SAH doub 303 n y C6 N6 SAH sing 304 n n C6 N1 SAH doub 305 n y N6 HN61 SAH sing 306 n n N6 HN62 SAH sing 307 n n N1 C2 SAH sing 308 n y C2 N3 SAH doub 309 n y C2 H2 SAH sing 310 n n N3 C4 SAH sing 311 n y # _atom_sites.entry_id 5ZW3 _atom_sites.fract_transf_matrix[1][1] 0.013008 _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] 0.008566 _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] 0.023022 _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 SAH A 1 301 1 SAH SAH . D 3 MG A 1 302 2 MG MG . E 2 SAH B 1 301 2 SAH SAH . F 3 MG B 1 302 1 MG MG . G 4 HOH A 1 401 64 HOH HOH . G 4 HOH A 2 402 85 HOH HOH . G 4 HOH A 3 403 55 HOH HOH . G 4 HOH A 4 404 34 HOH HOH . G 4 HOH A 5 405 44 HOH HOH . G 4 HOH A 6 406 5 HOH HOH . G 4 HOH A 7 407 22 HOH HOH . G 4 HOH A 8 408 70 HOH HOH . G 4 HOH A 9 409 16 HOH HOH . G 4 HOH A 10 410 33 HOH HOH . G 4 HOH A 11 411 79 HOH HOH . G 4 HOH A 12 412 62 HOH HOH . G 4 HOH A 13 413 73 HOH HOH . G 4 HOH A 14 414 4 HOH HOH . G 4 HOH A 15 415 53 HOH HOH . G 4 HOH A 16 416 15 HOH HOH . G 4 HOH A 17 417 45 HOH HOH . G 4 HOH A 18 418 30 HOH HOH . G 4 HOH A 19 419 11 HOH HOH . G 4 HOH A 20 420 59 HOH HOH . G 4 HOH A 21 421 12 HOH HOH . G 4 HOH A 22 422 78 HOH HOH . G 4 HOH A 23 423 81 HOH HOH . G 4 HOH A 24 424 52 HOH HOH . G 4 HOH A 25 425 80 HOH HOH . G 4 HOH A 26 426 43 HOH HOH . G 4 HOH A 27 427 9 HOH HOH . G 4 HOH A 28 428 25 HOH HOH . G 4 HOH A 29 429 51 HOH HOH . G 4 HOH A 30 430 23 HOH HOH . G 4 HOH A 31 431 60 HOH HOH . G 4 HOH A 32 432 8 HOH HOH . G 4 HOH A 33 433 50 HOH HOH . G 4 HOH A 34 434 24 HOH HOH . G 4 HOH A 35 435 84 HOH HOH . G 4 HOH A 36 436 38 HOH HOH . G 4 HOH A 37 437 82 HOH HOH . G 4 HOH A 38 438 77 HOH HOH . G 4 HOH A 39 439 28 HOH HOH . G 4 HOH A 40 440 75 HOH HOH . G 4 HOH A 41 441 63 HOH HOH . G 4 HOH A 42 442 76 HOH HOH . G 4 HOH A 43 443 86 HOH HOH . G 4 HOH A 44 444 83 HOH HOH . G 4 HOH A 45 445 41 HOH HOH . G 4 HOH A 46 446 29 HOH HOH . G 4 HOH A 47 447 7 HOH HOH . H 4 HOH B 1 401 46 HOH HOH . H 4 HOH B 2 402 21 HOH HOH . H 4 HOH B 3 403 37 HOH HOH . H 4 HOH B 4 404 2 HOH HOH . H 4 HOH B 5 405 32 HOH HOH . H 4 HOH B 6 406 67 HOH HOH . H 4 HOH B 7 407 87 HOH HOH . H 4 HOH B 8 408 3 HOH HOH . H 4 HOH B 9 409 58 HOH HOH . H 4 HOH B 10 410 68 HOH HOH . H 4 HOH B 11 411 72 HOH HOH . H 4 HOH B 12 412 66 HOH HOH . H 4 HOH B 13 413 6 HOH HOH . H 4 HOH B 14 414 49 HOH HOH . H 4 HOH B 15 415 18 HOH HOH . H 4 HOH B 16 416 17 HOH HOH . H 4 HOH B 17 417 42 HOH HOH . H 4 HOH B 18 418 39 HOH HOH . H 4 HOH B 19 419 61 HOH HOH . H 4 HOH B 20 420 36 HOH HOH . H 4 HOH B 21 421 1 HOH HOH . H 4 HOH B 22 422 13 HOH HOH . H 4 HOH B 23 423 14 HOH HOH . H 4 HOH B 24 424 19 HOH HOH . H 4 HOH B 25 425 74 HOH HOH . H 4 HOH B 26 426 31 HOH HOH . H 4 HOH B 27 427 48 HOH HOH . H 4 HOH B 28 428 47 HOH HOH . H 4 HOH B 29 429 57 HOH HOH . H 4 HOH B 30 430 10 HOH HOH . H 4 HOH B 31 431 65 HOH HOH . H 4 HOH B 32 432 56 HOH HOH . H 4 HOH B 33 433 40 HOH HOH . H 4 HOH B 34 434 54 HOH HOH . H 4 HOH B 35 435 71 HOH HOH . H 4 HOH B 36 436 27 HOH HOH . H 4 HOH B 37 437 20 HOH HOH . H 4 HOH B 38 438 26 HOH HOH . H 4 HOH B 39 439 35 HOH HOH . H 4 HOH B 40 440 88 HOH HOH . H 4 HOH B 41 441 69 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 . . . E 2 21.177 10.081 9.003 1 39 ? N SAH 301 B 1 HETATM 2 C CA SAH . . . E 2 22.181 9.384 8.148 1 38.21 ? CA SAH 301 B 1 HETATM 3 C CB SAH . . . E 2 21.569 9.009 6.802 1 36.51 ? CB SAH 301 B 1 HETATM 4 C CG SAH . . . E 2 20.395 8.053 6.968 1 34.13 ? CG SAH 301 B 1 HETATM 5 S SD SAH . . . E 2 19.99 7.343 5.407 1 33.69 ? SD SAH 301 B 1 HETATM 6 C C SAH . . . E 2 23.361 10.282 7.924 1 41.04 ? C SAH 301 B 1 HETATM 7 O O SAH . . . E 2 23.211 11.426 7.491 1 38.57 ? O SAH 301 B 1 HETATM 8 O OXT SAH . . . E 2 24.509 9.869 8.083 1 42.7 ? OXT SAH 301 B 1 HETATM 9 C C5' SAH . . . E 2 18.413 6.639 5.762 1 32.77 ? C5' SAH 301 B 1 HETATM 10 C C4' SAH . . . E 2 18.579 5.355 6.569 1 31.4 ? C4' SAH 301 B 1 HETATM 11 O O4' SAH . . . E 2 17.421 5.122 7.375 1 30.24 ? O4' SAH 301 B 1 HETATM 12 C C3' SAH . . . E 2 18.758 4.134 5.675 1 32.6 ? C3' SAH 301 B 1 HETATM 13 O O3' SAH . . . E 2 20.029 3.525 5.936 1 33.52 ? O3' SAH 301 B 1 HETATM 14 C C2' SAH . . . E 2 17.625 3.189 6.035 1 31.04 ? C2' SAH 301 B 1 HETATM 15 O O2' SAH . . . E 2 18.101 1.849 6.201 1 32.42 ? O2' SAH 301 B 1 HETATM 16 C C1' SAH . . . E 2 17.066 3.737 7.339 1 31.67 ? C1' SAH 301 B 1 HETATM 17 N N9 SAH . . . E 2 15.595 3.564 7.429 1 32.78 ? N9 SAH 301 B 1 HETATM 18 C C8 SAH . . . E 2 14.703 3.879 6.474 1 33.54 ? C8 SAH 301 B 1 HETATM 19 N N7 SAH . . . E 2 13.447 3.599 6.903 1 34.14 ? N7 SAH 301 B 1 HETATM 20 C C5 SAH . . . E 2 13.498 3.416 8.235 1 33.49 ? C5 SAH 301 B 1 HETATM 21 C C6 SAH . . . E 2 12.56 2.837 9.228 1 33.45 ? C6 SAH 301 B 1 HETATM 22 N N6 SAH . . . E 2 11.222 2.9 9.027 1 37.04 ? N6 SAH 301 B 1 HETATM 23 N N1 SAH . . . E 2 13.054 2.479 10.434 1 33.53 ? N1 SAH 301 B 1 HETATM 24 C C2 SAH . . . E 2 14.365 2.577 10.705 1 32.99 ? C2 SAH 301 B 1 HETATM 25 N N3 SAH . . . E 2 15.282 2.76 9.741 1 35.69 ? N3 SAH 301 B 1 HETATM 26 C C4 SAH . . . E 2 14.933 3.339 8.567 1 33.31 ? C4 SAH 301 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 358 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 26 #