data_3OXG # _model_server_result.job_id fr41TdLIcwrM-DVcYdPYzQ _model_server_result.datetime_utc '2025-02-27 01:44:17' _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 3oxg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":432}' # _entry.id 3OXG # _exptl.entry_id 3OXG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _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 120 _cell.entry_id 3OXG _cell.length_a 103.439 _cell.length_b 103.439 _cell.length_c 112.202 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OXG _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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 _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 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 SG CYS 85 A CYS 49 1_555 B ZN ZN . A ZN 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc2 A SG CYS 88 A CYS 52 1_555 B ZN ZN . A ZN 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc3 A SG CYS 98 A CYS 62 1_555 C ZN ZN . A ZN 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc4 A SG CYS 101 A CYS 65 1_555 C ZN ZN . A ZN 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc5 A SG CYS 107 A CYS 71 1_555 B ZN ZN . A ZN 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? metalc ? metalc6 A SG CYS 111 A CYS 75 1_555 B ZN ZN . A ZN 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc7 A NE2 HIS 119 A HIS 83 1_555 C ZN ZN . A ZN 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? metalc ? metalc8 A SG CYS 123 A CYS 87 1_555 C ZN ZN . A ZN 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc9 A SG CYS 244 A CYS 208 1_555 D ZN ZN . A ZN 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc10 A SG CYS 297 A CYS 261 1_555 D ZN ZN . A ZN 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc11 A SG CYS 299 A CYS 263 1_555 D ZN ZN . A ZN 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? metalc ? metalc12 A SG CYS 302 A CYS 266 1_555 D ZN ZN . A ZN 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? # _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 275 n n N HN1 SAH sing 276 n n N HN2 SAH sing 277 n n CA CB SAH sing 278 n n CA C SAH sing 279 n n CA HA SAH sing 280 n n CB CG SAH sing 281 n n CB HB1 SAH sing 282 n n CB HB2 SAH sing 283 n n CG SD SAH sing 284 n n CG HG1 SAH sing 285 n n CG HG2 SAH sing 286 n n SD C5' SAH sing 287 n n C O SAH doub 288 n n C OXT SAH sing 289 n n OXT HXT SAH sing 290 n n C5' C4' SAH sing 291 n n C5' "H5'1" SAH sing 292 n n C5' "H5'2" SAH sing 293 n n C4' O4' SAH sing 294 n n C4' C3' SAH sing 295 n n C4' H4' SAH sing 296 n n O4' C1' SAH sing 297 n n C3' O3' SAH sing 298 n n C3' C2' SAH sing 299 n n C3' H3' SAH sing 300 n n O3' HO3' SAH sing 301 n n C2' O2' SAH sing 302 n n C2' C1' SAH sing 303 n n C2' H2' SAH sing 304 n n O2' HO2' SAH sing 305 n n C1' N9 SAH sing 306 n n C1' H1' SAH sing 307 n n N9 C8 SAH sing 308 n y N9 C4 SAH sing 309 n y C8 N7 SAH doub 310 n y C8 H8 SAH sing 311 n n N7 C5 SAH sing 312 n y C5 C6 SAH sing 313 n y C5 C4 SAH doub 314 n y C6 N6 SAH sing 315 n n C6 N1 SAH doub 316 n y N6 HN61 SAH sing 317 n n N6 HN62 SAH sing 318 n n N1 C2 SAH sing 319 n y C2 N3 SAH doub 320 n y C2 H2 SAH sing 321 n n N3 C4 SAH sing 322 n y # _atom_sites.entry_id 3OXG _atom_sites.fract_transf_matrix[1][1] 0.009668 _atom_sites.fract_transf_matrix[1][2] 0.005582 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011163 _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] 0.008912 _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 ZN A 1 429 1 ZN ZN . C 2 ZN A 1 430 2 ZN ZN . D 2 ZN A 1 431 3 ZN ZN . E 3 SAH A 1 432 100 SAH SAH . # 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 3 39.411 1.717 14.338 0.8 56.67 ? N SAH 432 A 1 HETATM 2 C CA SAH . . . E 3 38.695 2.578 13.327 0.8 56.67 ? CA SAH 432 A 1 HETATM 3 C CB SAH . . . E 3 37.833 1.773 12.33 0.8 56.44 ? CB SAH 432 A 1 HETATM 4 C CG SAH . . . E 3 37.266 2.657 11.197 0.8 56.48 ? CG SAH 432 A 1 HETATM 5 S SD SAH . . . E 3 38.049 4.257 11.044 0.8 57.49 ? SD SAH 432 A 1 HETATM 6 C C SAH . . . E 3 37.884 3.702 13.963 0.8 56.69 ? C SAH 432 A 1 HETATM 7 O O SAH . . . E 3 38.451 4.641 14.55 0.8 56.33 ? O SAH 432 A 1 HETATM 8 O OXT SAH . . . E 3 36.638 3.737 13.86 0.8 56.56 ? OXT SAH 432 A 1 HETATM 9 C C5' SAH . . . E 3 39.753 3.758 10.92 0.8 57.75 ? C5' SAH 432 A 1 HETATM 10 C C4' SAH . . . E 3 40.854 4.793 11.172 0.8 57.8 ? C4' SAH 432 A 1 HETATM 11 O O4' SAH . . . E 3 40.814 5.276 12.528 0.8 57.27 ? O4' SAH 432 A 1 HETATM 12 C C3' SAH . . . E 3 42.253 4.143 11.005 0.8 57.73 ? C3' SAH 432 A 1 HETATM 13 O O3' SAH . . . E 3 43.103 4.942 10.153 0.8 57.25 ? O3' SAH 432 A 1 HETATM 14 C C2' SAH . . . E 3 42.825 4.054 12.417 0.8 56.07 ? C2' SAH 432 A 1 HETATM 15 O O2' SAH . . . E 3 44.252 4.143 12.501 0.8 54.21 ? O2' SAH 432 A 1 HETATM 16 C C1' SAH . . . E 3 42.192 5.324 12.946 0.8 55.62 ? C1' SAH 432 A 1 HETATM 17 N N9 SAH . . . E 3 42.391 5.471 14.387 0.8 53.32 ? N9 SAH 432 A 1 HETATM 18 C C8 SAH . . . E 3 42.179 4.538 15.325 0.8 53.08 ? C8 SAH 432 A 1 HETATM 19 N N7 SAH . . . E 3 42.472 5.04 16.557 0.8 52.32 ? N7 SAH 432 A 1 HETATM 20 C C5 SAH . . . E 3 42.881 6.309 16.39 0.8 51.51 ? C5 SAH 432 A 1 HETATM 21 C C6 SAH . . . E 3 43.339 7.397 17.281 0.8 50.77 ? C6 SAH 432 A 1 HETATM 22 N N6 SAH . . . E 3 43.399 7.16 18.615 0.8 49.92 ? N6 SAH 432 A 1 HETATM 23 N N1 SAH . . . E 3 43.679 8.592 16.719 0.8 50 ? N1 SAH 432 A 1 HETATM 24 C C2 SAH . . . E 3 43.603 8.781 15.378 0.8 50.89 ? C2 SAH 432 A 1 HETATM 25 N N3 SAH . . . E 3 43.195 7.829 14.498 0.8 51.69 ? N3 SAH 432 A 1 HETATM 26 C C4 SAH . . . E 3 42.827 6.595 14.948 0.8 52.24 ? C4 SAH 432 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #