data_5V22 # _model_server_result.job_id mFWipU6tx93tjtLbrc73fQ _model_server_result.datetime_utc '2024-11-19 17:27:07' _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 5v22 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1804}' # _entry.id 5V22 # _exptl.entry_id 5V22 _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 90 _cell.entry_id 5V22 _cell.length_a 60.287 _cell.length_b 77.196 _cell.length_c 76.527 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V22 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id F _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 1499 1_555 D ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc2 A SG CYS 87 A CYS 1501 1_555 D ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc3 A SG CYS 102 A CYS 1516 1_555 C ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc4 A SG CYS 102 A CYS 1516 1_555 D ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc5 A SG CYS 106 A CYS 1520 1_555 D ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc6 A SG CYS 115 A CYS 1529 1_555 C ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc7 A SG CYS 119 A CYS 1533 1_555 C ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc8 A SG CYS 125 A CYS 1539 1_555 C ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc9 A SG CYS 217 A CYS 1631 1_555 E ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc10 A SG CYS 264 A CYS 1678 1_555 E ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc11 A SG CYS 266 A CYS 1680 1_555 E ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc12 A SG CYS 271 A CYS 1685 1_555 E ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? # _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 5V22 _atom_sites.fract_transf_matrix[1][1] 0.016587 _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] 0.012954 _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] 0.013067 _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 3 ZN A 1 1801 1801 ZN ZN . D 3 ZN A 1 1802 1802 ZN ZN . E 3 ZN A 1 1803 1803 ZN ZN . F 4 SAH A 1 1804 1804 SAH SAH . G 5 HOH A 1 1901 13 HOH HOH . G 5 HOH A 2 1902 9 HOH HOH . G 5 HOH A 3 1903 40 HOH HOH . G 5 HOH A 4 1904 85 HOH HOH . G 5 HOH A 5 1905 77 HOH HOH . G 5 HOH A 6 1906 6 HOH HOH . G 5 HOH A 7 1907 68 HOH HOH . G 5 HOH A 8 1908 25 HOH HOH . G 5 HOH A 9 1909 46 HOH HOH . G 5 HOH A 10 1910 19 HOH HOH . G 5 HOH A 11 1911 23 HOH HOH . G 5 HOH A 12 1912 63 HOH HOH . G 5 HOH A 13 1913 15 HOH HOH . G 5 HOH A 14 1914 78 HOH HOH . G 5 HOH A 15 1915 12 HOH HOH . G 5 HOH A 16 1916 5 HOH HOH . G 5 HOH A 17 1917 55 HOH HOH . G 5 HOH A 18 1918 7 HOH HOH . G 5 HOH A 19 1919 36 HOH HOH . G 5 HOH A 20 1920 33 HOH HOH . G 5 HOH A 21 1921 26 HOH HOH . G 5 HOH A 22 1922 10 HOH HOH . G 5 HOH A 23 1923 35 HOH HOH . G 5 HOH A 24 1924 24 HOH HOH . G 5 HOH A 25 1925 14 HOH HOH . G 5 HOH A 26 1926 30 HOH HOH . G 5 HOH A 27 1927 17 HOH HOH . G 5 HOH A 28 1928 41 HOH HOH . G 5 HOH A 29 1929 49 HOH HOH . G 5 HOH A 30 1930 56 HOH HOH . G 5 HOH A 31 1931 50 HOH HOH . G 5 HOH A 32 1932 75 HOH HOH . G 5 HOH A 33 1933 21 HOH HOH . G 5 HOH A 34 1934 57 HOH HOH . G 5 HOH A 35 1935 52 HOH HOH . G 5 HOH A 36 1936 45 HOH HOH . G 5 HOH A 37 1937 3 HOH HOH . G 5 HOH A 38 1938 2 HOH HOH . G 5 HOH A 39 1939 4 HOH HOH . G 5 HOH A 40 1940 32 HOH HOH . G 5 HOH A 41 1941 8 HOH HOH . G 5 HOH A 42 1942 66 HOH HOH . G 5 HOH A 43 1943 31 HOH HOH . G 5 HOH A 44 1944 18 HOH HOH . G 5 HOH A 45 1945 80 HOH HOH . G 5 HOH A 46 1946 61 HOH HOH . G 5 HOH A 47 1947 58 HOH HOH . G 5 HOH A 48 1948 60 HOH HOH . G 5 HOH A 49 1949 67 HOH HOH . G 5 HOH A 50 1950 69 HOH HOH . G 5 HOH A 51 1951 71 HOH HOH . G 5 HOH A 52 1952 59 HOH HOH . G 5 HOH A 53 1953 43 HOH HOH . G 5 HOH A 54 1954 73 HOH HOH . G 5 HOH A 55 1955 48 HOH HOH . G 5 HOH A 56 1956 84 HOH HOH . G 5 HOH A 57 1957 62 HOH HOH . G 5 HOH A 58 1958 29 HOH HOH . G 5 HOH A 59 1959 22 HOH HOH . G 5 HOH A 60 1960 83 HOH HOH . G 5 HOH A 61 1961 39 HOH HOH . G 5 HOH A 62 1962 37 HOH HOH . G 5 HOH A 63 1963 42 HOH HOH . G 5 HOH A 64 1964 20 HOH HOH . G 5 HOH A 65 1965 53 HOH HOH . G 5 HOH A 66 1966 1 HOH HOH . G 5 HOH A 67 1967 70 HOH HOH . G 5 HOH A 68 1968 28 HOH HOH . G 5 HOH A 69 1969 38 HOH HOH . G 5 HOH A 70 1970 65 HOH HOH . G 5 HOH A 71 1971 64 HOH HOH . G 5 HOH A 72 1972 79 HOH HOH . G 5 HOH A 73 1973 47 HOH HOH . G 5 HOH A 74 1974 34 HOH HOH . G 5 HOH A 75 1975 76 HOH HOH . G 5 HOH A 76 1976 74 HOH HOH . G 5 HOH A 77 1977 72 HOH HOH . G 5 HOH A 78 1978 51 HOH HOH . G 5 HOH A 79 1979 11 HOH HOH . G 5 HOH A 80 1980 82 HOH HOH . G 5 HOH A 81 1981 81 HOH HOH . H 5 HOH B 1 101 27 HOH HOH . H 5 HOH B 2 102 44 HOH HOH . H 5 HOH B 3 103 54 HOH HOH . H 5 HOH B 4 104 16 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 . . . F 4 3.459 27.438 -18.914 1 26.55 ? N SAH 1804 A 1 HETATM 2 C CA SAH . . . F 4 4.31 26.631 -18.055 1 33.33 ? CA SAH 1804 A 1 HETATM 3 C CB SAH . . . F 4 3.54 25.399 -17.6 1 34.17 ? CB SAH 1804 A 1 HETATM 4 C CG SAH . . . F 4 2.379 25.722 -16.664 1 31.48 ? CG SAH 1804 A 1 HETATM 5 S SD SAH . . . F 4 2.96 25.788 -14.943 1 42.5 ? SD SAH 1804 A 1 HETATM 6 C C SAH . . . F 4 5.607 26.19 -18.731 1 34.28 ? C SAH 1804 A 1 HETATM 7 O O SAH . . . F 4 6.458 25.581 -18.086 1 37.8 ? O SAH 1804 A 1 HETATM 8 O OXT SAH . . . F 4 5.845 26.418 -19.916 1 35.25 ? OXT SAH 1804 A 1 HETATM 9 C C5' SAH . . . F 4 2.181 27.388 -14.611 1 33.41 ? C5' SAH 1804 A 1 HETATM 10 C C4' SAH . . . F 4 3.054 28.561 -15.028 1 33.31 ? C4' SAH 1804 A 1 HETATM 11 O O4' SAH . . . F 4 2.712 28.963 -16.343 1 32.64 ? O4' SAH 1804 A 1 HETATM 12 C C3' SAH . . . F 4 2.869 29.762 -14.106 1 37.83 ? C3' SAH 1804 A 1 HETATM 13 O O3' SAH . . . F 4 3.896 29.844 -13.14 1 39.2 ? O3' SAH 1804 A 1 HETATM 14 C C2' SAH . . . F 4 2.864 30.944 -15.053 1 38.42 ? C2' SAH 1804 A 1 HETATM 15 O O2' SAH . . . F 4 4.14 31.531 -15.145 1 36.6 ? O2' SAH 1804 A 1 HETATM 16 C C1' SAH . . . F 4 2.535 30.364 -16.413 1 35.94 ? C1' SAH 1804 A 1 HETATM 17 N N9 SAH . . . F 4 1.142 30.664 -16.769 1 34.94 ? N9 SAH 1804 A 1 HETATM 18 C C8 SAH . . . F 4 0.105 29.77 -16.77 1 34.42 ? C8 SAH 1804 A 1 HETATM 19 N N7 SAH . . . F 4 -1.021 30.421 -17.136 1 33.05 ? N7 SAH 1804 A 1 HETATM 20 C C5 SAH . . . F 4 -0.721 31.719 -17.366 1 38.37 ? C5 SAH 1804 A 1 HETATM 21 C C6 SAH . . . F 4 -1.494 32.808 -17.758 1 35.4 ? C6 SAH 1804 A 1 HETATM 22 N N6 SAH . . . F 4 -2.798 32.654 -17.987 1 26.85 ? N6 SAH 1804 A 1 HETATM 23 N N1 SAH . . . F 4 -0.896 34.043 -17.907 1 32.25 ? N1 SAH 1804 A 1 HETATM 24 C C2 SAH . . . F 4 0.452 34.192 -17.664 1 30.96 ? C2 SAH 1804 A 1 HETATM 25 N N3 SAH . . . F 4 1.212 33.11 -17.275 1 33.66 ? N3 SAH 1804 A 1 HETATM 26 C C4 SAH . . . F 4 0.639 31.887 -17.135 1 38.15 ? C4 SAH 1804 A 1 HETATM 27 H H2 SAH . . . F 4 0.919 35.17 -17.779 1 36.99 ? H2 SAH 1804 A 1 HETATM 28 H HN1 SAH . . . F 4 2.705 27.65 -18.56 1 31.7 ? HN1 SAH 1804 A 1 HETATM 29 H HN2 SAH . . . F 4 4.346 27.781 -18.787 1 31.7 ? HN2 SAH 1804 A 1 HETATM 30 H HA SAH . . . F 4 4.548 27.152 -17.26 1 39.83 ? HA SAH 1804 A 1 HETATM 31 H HB1 SAH . . . F 4 4.229 24.724 -17.094 1 40.84 ? HB1 SAH 1804 A 1 HETATM 32 H HB2 SAH . . . F 4 3.157 24.882 -18.479 1 40.84 ? HB2 SAH 1804 A 1 HETATM 33 H HG1 SAH . . . F 4 1.607 24.959 -16.761 1 37.61 ? HG1 SAH 1804 A 1 HETATM 34 H HG2 SAH . . . F 4 1.941 26.682 -16.94 1 37.61 ? HG2 SAH 1804 A 1 HETATM 35 H "H5'1" SAH . . . F 4 1.963 27.466 -13.546 1 39.93 ? "H5'1" SAH 1804 A 1 HETATM 36 H "H5'2" SAH . . . F 4 1.232 27.442 -15.146 1 39.93 ? "H5'2" SAH 1804 A 1 HETATM 37 H H4' SAH . . . F 4 4.098 28.25 -14.994 1 39.81 ? H4' SAH 1804 A 1 HETATM 38 H H3' SAH . . . F 4 1.897 29.692 -13.619 1 45.24 ? H3' SAH 1804 A 1 HETATM 39 H HO3' SAH . . . F 4 4.411 30.666 -13.279 1 46.88 ? HO3' SAH 1804 A 1 HETATM 40 H H2' SAH . . . F 4 2.107 31.669 -14.756 1 45.95 ? H2' SAH 1804 A 1 HETATM 41 H HO2' SAH . . . F 4 4.488 31.417 -16.055 1 43.76 ? HO2' SAH 1804 A 1 HETATM 42 H H1' SAH . . . F 4 3.212 30.791 -17.154 1 42.97 ? H1' SAH 1804 A 1 HETATM 43 H H8 SAH . . . F 4 0.176 28.711 -16.518 1 41.14 ? H8 SAH 1804 A 1 HETATM 44 H HN61 SAH . . . F 4 -3.228 31.741 -17.875 1 32.06 ? HN61 SAH 1804 A 1 HETATM 45 H HN62 SAH . . . F 4 -3.36 33.449 -18.273 1 32.06 ? HN62 SAH 1804 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 45 #