data_4UD0 # _model_server_result.job_id xGSQslDaLRnGg_6kUGLbnw _model_server_result.datetime_utc '2025-03-06 09:42:51' _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 4ud0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2410}' # _entry.id 4UD0 # _exptl.entry_id 4UD0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 4 _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 4UD0 _cell.length_a 75.61 _cell.length_b 75.61 _cell.length_c 187.95 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4UD0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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' 4_375 y-2,x+2,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 -226.83 130.960362 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 NE2 HIS 168 B HIS 1766 1_555 C ZN ZN . B ZN 2409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.935 ? metalc ? metalc2 A NE2 HIS 200 B HIS 1798 1_555 C ZN ZN . B ZN 2409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc3 A SG CYS 204 B CYS 1802 1_555 C ZN ZN . B ZN 2409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc4 A SG CYS 207 B CYS 1805 1_555 C ZN ZN . B ZN 2409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? # _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 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 4UD0 _atom_sites.fract_transf_matrix[1][1] 0.013226 _atom_sites.fract_transf_matrix[1][2] 0.007636 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015272 _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] 0.005321 _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 SO4 B 1 2408 2408 SO4 SO4 . C 3 ZN B 1 2409 2409 ZN ZN . D 4 SAH B 1 2410 2410 SAH SAH . E 5 HOH B 1 3001 3001 HOH HOH . E 5 HOH B 2 3002 3002 HOH HOH . E 5 HOH B 3 3003 3003 HOH HOH . E 5 HOH B 4 3004 3004 HOH HOH . E 5 HOH B 5 3005 3005 HOH HOH . E 5 HOH B 6 3006 3006 HOH HOH . E 5 HOH B 7 3007 3007 HOH HOH . E 5 HOH B 8 3008 3008 HOH HOH . E 5 HOH B 9 3009 3009 HOH HOH . E 5 HOH B 10 3010 3010 HOH HOH . E 5 HOH B 11 3011 3011 HOH HOH . E 5 HOH B 12 3012 3012 HOH HOH . E 5 HOH B 13 3013 3013 HOH HOH . E 5 HOH B 14 3014 3014 HOH HOH . E 5 HOH B 15 3015 3015 HOH HOH . E 5 HOH B 16 3016 3016 HOH HOH . E 5 HOH B 17 3017 3017 HOH HOH . E 5 HOH B 18 3018 3018 HOH HOH . E 5 HOH B 19 3019 3019 HOH HOH . E 5 HOH B 20 3020 3020 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 . . . D 4 -122.851 21.925 18.609 1 141.43 ? N SAH 2410 B 1 HETATM 2 C CA SAH . . . D 4 -123.578 22.306 17.385 1 140.55 ? CA SAH 2410 B 1 HETATM 3 C CB SAH . . . D 4 -124.56 23.502 17.459 1 139.23 ? CB SAH 2410 B 1 HETATM 4 C CG SAH . . . D 4 -125.845 23.09 18.163 1 138.5 ? CG SAH 2410 B 1 HETATM 5 S SD SAH . . . D 4 -126.833 24.608 18.299 1 138.07 ? SD SAH 2410 B 1 HETATM 6 C C SAH . . . D 4 -122.578 22.521 16.228 1 140.66 ? C SAH 2410 B 1 HETATM 7 O O SAH . . . D 4 -122.895 22.409 15.069 1 140.89 ? O SAH 2410 B 1 HETATM 8 O OXT SAH . . . D 4 -121.377 22.837 16.62 1 140.79 ? OXT SAH 2410 B 1 HETATM 9 C C5' SAH . . . D 4 -128.252 24.111 19.308 1 134.21 ? C5' SAH 2410 B 1 HETATM 10 C C4' SAH . . . D 4 -129.118 23.133 18.54 1 131.87 ? C4' SAH 2410 B 1 HETATM 11 O O4' SAH . . . D 4 -129.879 22.425 19.527 1 129.8 ? O4' SAH 2410 B 1 HETATM 12 C C3' SAH . . . D 4 -130.163 23.756 17.615 1 132.41 ? C3' SAH 2410 B 1 HETATM 13 O O3' SAH . . . D 4 -129.684 23.867 16.274 1 132.6 ? O3' SAH 2410 B 1 HETATM 14 C C2' SAH . . . D 4 -131.377 22.809 17.738 1 131.46 ? C2' SAH 2410 B 1 HETATM 15 O O2' SAH . . . D 4 -131.632 22.097 16.529 1 133.22 ? O2' SAH 2410 B 1 HETATM 16 C C1' SAH . . . D 4 -130.979 21.846 18.869 1 128.16 ? C1' SAH 2410 B 1 HETATM 17 N N9 SAH . . . D 4 -132.013 21.57 19.864 1 124.21 ? N9 SAH 2410 B 1 HETATM 18 C C8 SAH . . . D 4 -132.67 22.473 20.659 1 123.32 ? C8 SAH 2410 B 1 HETATM 19 N N7 SAH . . . D 4 -133.538 21.932 21.48 1 121.87 ? N7 SAH 2410 B 1 HETATM 20 C C5 SAH . . . D 4 -133.444 20.575 21.208 1 121.17 ? C5 SAH 2410 B 1 HETATM 21 C C6 SAH . . . D 4 -134.104 19.45 21.747 1 121.04 ? C6 SAH 2410 B 1 HETATM 22 N N6 SAH . . . D 4 -135.061 19.526 22.675 1 122.56 ? N6 SAH 2410 B 1 HETATM 23 N N1 SAH . . . D 4 -133.755 18.229 21.273 1 119.82 ? N1 SAH 2410 B 1 HETATM 24 C C2 SAH . . . D 4 -132.824 18.151 20.316 1 119.65 ? C2 SAH 2410 B 1 HETATM 25 N N3 SAH . . . D 4 -132.147 19.14 19.724 1 120.11 ? N3 SAH 2410 B 1 HETATM 26 C C4 SAH . . . D 4 -132.503 20.336 20.22 1 121.69 ? C4 SAH 2410 B 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #