data_5V21 # _model_server_result.job_id WHZRk0AOLJI-kj2xpYi7UA _model_server_result.datetime_utc '2024-10-12 12:20:34' _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 5v21 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1804}' # _entry.id 5V21 # _exptl.entry_id 5V21 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYLMETHIONINE _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 5V21 _cell.length_a 58.493 _cell.length_b 76.316 _cell.length_c 77.179 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5V21 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc2 A SG CYS 87 A CYS 1501 1_555 D ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc3 A SG CYS 102 A CYS 1516 1_555 C ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc4 A SG CYS 102 A CYS 1516 1_555 D ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc5 A SG CYS 106 A CYS 1520 1_555 D ZN ZN . A ZN 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc6 A SG CYS 115 A CYS 1529 1_555 C ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc7 A SG CYS 119 A CYS 1533 1_555 C ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc8 A SG CYS 125 A CYS 1539 1_555 C ZN ZN . A ZN 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc9 A SG CYS 217 A CYS 1631 1_555 E ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc10 A SG CYS 264 A CYS 1678 1_555 E ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc11 A SG CYS 266 A CYS 1680 1_555 E ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc12 A SG CYS 271 A CYS 1685 1_555 E ZN ZN . A ZN 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? # _chem_comp.formula 'C15 H22 N6 O5 S' _chem_comp.formula_weight 398.437 _chem_comp.id SAM _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYLMETHIONINE _chem_comp.type non-polymer _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 SAM sing 277 n n N HN1 SAM sing 278 n n N HN2 SAM sing 279 n n CA C SAM sing 280 n n CA CB SAM sing 281 n n CA HA SAM sing 282 n n C O SAM doub 283 n n C OXT SAM sing 284 n n CB CG SAM sing 285 n n CB HB1 SAM sing 286 n n CB HB2 SAM sing 287 n n CG SD SAM sing 288 n n CG HG1 SAM sing 289 n n CG HG2 SAM sing 290 n n SD CE SAM sing 291 n n SD C5' SAM sing 292 n n CE HE1 SAM sing 293 n n CE HE2 SAM sing 294 n n CE HE3 SAM sing 295 n n C5' C4' SAM sing 296 n n C5' "H5'1" SAM sing 297 n n C5' "H5'2" SAM sing 298 n n C4' O4' SAM sing 299 n n C4' C3' SAM sing 300 n n C4' H4' SAM sing 301 n n O4' C1' SAM sing 302 n n C3' O3' SAM sing 303 n n C3' C2' SAM sing 304 n n C3' H3' SAM sing 305 n n O3' HO3' SAM sing 306 n n C2' O2' SAM sing 307 n n C2' C1' SAM sing 308 n n C2' H2' SAM sing 309 n n O2' HO2' SAM sing 310 n n C1' N9 SAM sing 311 n n C1' H1' SAM sing 312 n n N9 C8 SAM sing 313 n y N9 C4 SAM sing 314 n y C8 N7 SAM doub 315 n y C8 H8 SAM sing 316 n n N7 C5 SAM sing 317 n y C5 C6 SAM sing 318 n y C5 C4 SAM doub 319 n y C6 N6 SAM sing 320 n n C6 N1 SAM doub 321 n y N6 HN61 SAM sing 322 n n N6 HN62 SAM sing 323 n n N1 C2 SAM sing 324 n y C2 N3 SAM doub 325 n y C2 H2 SAM sing 326 n n N3 C4 SAM sing 327 n y # _atom_sites.entry_id 5V21 _atom_sites.fract_transf_matrix[1][1] 0.017096 _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] 0.013103 _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] 0.012957 _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 SAM A 1 1804 1804 SAM SAM . G 5 HOH A 1 1901 39 HOH HOH . G 5 HOH A 2 1902 14 HOH HOH . G 5 HOH A 3 1903 7 HOH HOH . G 5 HOH A 4 1904 6 HOH HOH . G 5 HOH A 5 1905 21 HOH HOH . G 5 HOH A 6 1906 16 HOH HOH . G 5 HOH A 7 1907 37 HOH HOH . G 5 HOH A 8 1908 2 HOH HOH . G 5 HOH A 9 1909 3 HOH HOH . G 5 HOH A 10 1910 8 HOH HOH . G 5 HOH A 11 1911 17 HOH HOH . G 5 HOH A 12 1912 36 HOH HOH . G 5 HOH A 13 1913 15 HOH HOH . G 5 HOH A 14 1914 30 HOH HOH . G 5 HOH A 15 1915 1 HOH HOH . G 5 HOH A 16 1916 27 HOH HOH . G 5 HOH A 17 1917 20 HOH HOH . G 5 HOH A 18 1918 11 HOH HOH . G 5 HOH A 19 1919 9 HOH HOH . G 5 HOH A 20 1920 13 HOH HOH . G 5 HOH A 21 1921 5 HOH HOH . G 5 HOH A 22 1922 34 HOH HOH . G 5 HOH A 23 1923 31 HOH HOH . G 5 HOH A 24 1924 4 HOH HOH . G 5 HOH A 25 1925 35 HOH HOH . G 5 HOH A 26 1926 38 HOH HOH . G 5 HOH A 27 1927 25 HOH HOH . G 5 HOH A 28 1928 22 HOH HOH . G 5 HOH A 29 1929 26 HOH HOH . G 5 HOH A 30 1930 23 HOH HOH . G 5 HOH A 31 1931 33 HOH HOH . G 5 HOH A 32 1932 24 HOH HOH . H 5 HOH B 1 101 10 HOH HOH . H 5 HOH B 2 102 12 HOH HOH . H 5 HOH B 3 103 29 HOH HOH . H 5 HOH B 4 104 32 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 SAM . . . F 4 -17.967 -0.012 -7.976 1 24.36 ? N SAM 1804 A 1 HETATM 2 C CA SAM . . . F 4 -18.7 -1.001 -7.221 1 26.57 ? CA SAM 1804 A 1 HETATM 3 C C SAM . . . F 4 -20.019 -0.459 -6.833 1 27.62 ? C SAM 1804 A 1 HETATM 4 O O SAM . . . F 4 -20.423 0.664 -7.256 1 27.34 ? O SAM 1804 A 1 HETATM 5 O OXT SAM . . . F 4 -20.743 -1.172 -6.084 1 28.42 ? OXT SAM 1804 A 1 HETATM 6 C CB SAM . . . F 4 -17.975 -1.42 -5.986 1 23.29 ? CB SAM 1804 A 1 HETATM 7 C CG SAM . . . F 4 -16.77 -2.259 -6.353 1 22.83 ? CG SAM 1804 A 1 HETATM 8 S SD SAM . . . F 4 -17.14 -4.012 -6.565 1 24.61 ? SD SAM 1804 A 1 HETATM 9 C CE SAM . . . F 4 -16.226 -4.911 -5.348 1 23.21 ? CE SAM 1804 A 1 HETATM 10 C C5' SAM . . . F 4 -16.595 -4.634 -8.166 1 23.55 ? C5' SAM 1804 A 1 HETATM 11 C C4' SAM . . . F 4 -17.465 -4.139 -9.3 1 24.01 ? C4' SAM 1804 A 1 HETATM 12 O O4' SAM . . . F 4 -17.203 -2.798 -9.604 1 19.13 ? O4' SAM 1804 A 1 HETATM 13 C C3' SAM . . . F 4 -17.241 -4.936 -10.543 1 28.86 ? C3' SAM 1804 A 1 HETATM 14 O O3' SAM . . . F 4 -18.069 -6.047 -10.55 1 29.18 ? O3' SAM 1804 A 1 HETATM 15 C C2' SAM . . . F 4 -17.509 -3.943 -11.623 1 25.82 ? C2' SAM 1804 A 1 HETATM 16 O O2' SAM . . . F 4 -18.852 -3.818 -11.913 1 24.55 ? O2' SAM 1804 A 1 HETATM 17 C C1' SAM . . . F 4 -17.095 -2.665 -10.992 1 25.08 ? C1' SAM 1804 A 1 HETATM 18 N N9 SAM . . . F 4 -15.737 -2.295 -11.3 1 26.62 ? N9 SAM 1804 A 1 HETATM 19 C C8 SAM . . . F 4 -14.754 -2.278 -10.354 1 25.52 ? C8 SAM 1804 A 1 HETATM 20 N N7 SAM . . . F 4 -13.601 -1.911 -10.934 1 28.19 ? N7 SAM 1804 A 1 HETATM 21 C C5 SAM . . . F 4 -13.821 -1.659 -12.304 1 27.06 ? C5 SAM 1804 A 1 HETATM 22 C C6 SAM . . . F 4 -12.982 -1.232 -13.388 1 27.14 ? C6 SAM 1804 A 1 HETATM 23 N N6 SAM . . . F 4 -11.598 -0.974 -13.178 1 24.97 ? N6 SAM 1804 A 1 HETATM 24 N N1 SAM . . . F 4 -13.54 -1.072 -14.61 1 27.11 ? N1 SAM 1804 A 1 HETATM 25 C C2 SAM . . . F 4 -14.85 -1.324 -14.777 1 26.04 ? C2 SAM 1804 A 1 HETATM 26 N N3 SAM . . . F 4 -15.684 -1.735 -13.811 1 28.36 ? N3 SAM 1804 A 1 HETATM 27 C C4 SAM . . . F 4 -15.238 -1.909 -12.558 1 27.64 ? C4 SAM 1804 A 1 # _model_server_stats.io_time_ms 102 _model_server_stats.parse_time_ms 148 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 368 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #