data_5ARF # _model_server_result.job_id Sy90kjhgeOffpR1hTCejfQ _model_server_result.datetime_utc '2024-11-20 17:27:16' _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 5arf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1002}' # _entry.id 5ARF # _exptl.entry_id 5ARF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 3 _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 5ARF _cell.length_a 130.493 _cell.length_b 51.759 _cell.length_c 69.568 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ARF _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 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,F,G _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 C _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 disulf ? disulf1 A SG CYS 68 A CYS 68 1_555 A SG CYS 90 A CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? disulf ? disulf2 A SG CYS 209 A CYS 209 1_555 A SG CYS 267 A CYS 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc1 A SG CYS 52 A CYS 52 1_555 E ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc2 A SG CYS 55 A CYS 55 1_555 E ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc3 A SG CYS 65 A CYS 65 1_555 F ZN ZN . A ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc4 A SG CYS 74 A CYS 74 1_555 E ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc5 A SG CYS 78 A CYS 78 1_555 E ZN ZN . A ZN 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc6 A NE2 HIS 86 A HIS 86 1_555 F ZN ZN . A ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc7 A SG CYS 90 A CYS 90 1_555 F ZN ZN . A ZN 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc8 A SG CYS 209 A CYS 209 1_555 D ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc9 A SG CYS 262 A CYS 262 1_555 D ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc10 A SG CYS 264 A CYS 264 1_555 D ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc11 A SG CYS 267 A CYS 267 1_555 D ZN ZN . A ZN 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? # _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 334 n n N HN1 SAM sing 335 n n N HN2 SAM sing 336 n n CA C SAM sing 337 n n CA CB SAM sing 338 n n CA HA SAM sing 339 n n C O SAM doub 340 n n C OXT SAM sing 341 n n CB CG SAM sing 342 n n CB HB1 SAM sing 343 n n CB HB2 SAM sing 344 n n CG SD SAM sing 345 n n CG HG1 SAM sing 346 n n CG HG2 SAM sing 347 n n SD CE SAM sing 348 n n SD C5' SAM sing 349 n n CE HE1 SAM sing 350 n n CE HE2 SAM sing 351 n n CE HE3 SAM sing 352 n n C5' C4' SAM sing 353 n n C5' "H5'1" SAM sing 354 n n C5' "H5'2" SAM sing 355 n n C4' O4' SAM sing 356 n n C4' C3' SAM sing 357 n n C4' H4' SAM sing 358 n n O4' C1' SAM sing 359 n n C3' O3' SAM sing 360 n n C3' C2' SAM sing 361 n n C3' H3' SAM sing 362 n n O3' HO3' SAM sing 363 n n C2' O2' SAM sing 364 n n C2' C1' SAM sing 365 n n C2' H2' SAM sing 366 n n O2' HO2' SAM sing 367 n n C1' N9 SAM sing 368 n n C1' H1' SAM sing 369 n n N9 C8 SAM sing 370 n y N9 C4 SAM sing 371 n y C8 N7 SAM doub 372 n y C8 H8 SAM sing 373 n n N7 C5 SAM sing 374 n y C5 C6 SAM sing 375 n y C5 C4 SAM doub 376 n y C6 N6 SAM sing 377 n n C6 N1 SAM doub 378 n y N6 HN61 SAM sing 379 n n N6 HN62 SAM sing 380 n n N1 C2 SAM sing 381 n y C2 N3 SAM doub 382 n y C2 H2 SAM sing 383 n n N3 C4 SAM sing 384 n y # _atom_sites.entry_id 5ARF _atom_sites.fract_transf_matrix[1][1] 0.007663 _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] 0.01932 _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] 0.014374 _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 I9H A 1 1001 1001 I9H I9H . C 3 SAM A 1 1002 1002 SAM SAM . D 4 ZN A 1 1003 1003 ZN ZN . E 4 ZN A 1 1004 1004 ZN ZN . F 4 ZN A 1 1005 1005 ZN ZN . G 5 HOH A 1 2001 2001 HOH HOH . G 5 HOH A 2 2002 2002 HOH HOH . G 5 HOH A 3 2003 2003 HOH HOH . G 5 HOH A 4 2004 2004 HOH HOH . G 5 HOH A 5 2005 2005 HOH HOH . G 5 HOH A 6 2006 2006 HOH HOH . G 5 HOH A 7 2007 2007 HOH HOH . G 5 HOH A 8 2008 2008 HOH HOH . G 5 HOH A 9 2009 2009 HOH HOH . G 5 HOH A 10 2010 2010 HOH HOH . G 5 HOH A 11 2011 2011 HOH HOH . G 5 HOH A 12 2012 2012 HOH HOH . G 5 HOH A 13 2013 2013 HOH HOH . G 5 HOH A 14 2014 2014 HOH HOH . G 5 HOH A 15 2015 2015 HOH HOH . G 5 HOH A 16 2016 2016 HOH HOH . G 5 HOH A 17 2017 2017 HOH HOH . G 5 HOH A 18 2018 2018 HOH HOH . G 5 HOH A 19 2019 2019 HOH HOH . G 5 HOH A 20 2020 2020 HOH HOH . G 5 HOH A 21 2021 2021 HOH HOH . G 5 HOH A 22 2022 2022 HOH HOH . G 5 HOH A 23 2023 2023 HOH HOH . G 5 HOH A 24 2024 2024 HOH HOH . G 5 HOH A 25 2025 2025 HOH HOH . G 5 HOH A 26 2026 2026 HOH HOH . G 5 HOH A 27 2027 2027 HOH HOH . G 5 HOH A 28 2028 2028 HOH HOH . G 5 HOH A 29 2029 2029 HOH HOH . G 5 HOH A 30 2030 2030 HOH HOH . G 5 HOH A 31 2031 2031 HOH HOH . G 5 HOH A 32 2032 2032 HOH HOH . G 5 HOH A 33 2033 2033 HOH HOH . G 5 HOH A 34 2034 2034 HOH HOH . G 5 HOH A 35 2035 2035 HOH HOH . G 5 HOH A 36 2036 2036 HOH HOH . G 5 HOH A 37 2037 2037 HOH HOH . G 5 HOH A 38 2038 2038 HOH HOH . G 5 HOH A 39 2039 2039 HOH HOH . G 5 HOH A 40 2040 2040 HOH HOH . G 5 HOH A 41 2041 2041 HOH HOH . G 5 HOH A 42 2042 2042 HOH HOH . G 5 HOH A 43 2043 2043 HOH HOH . G 5 HOH A 44 2044 2044 HOH HOH . G 5 HOH A 45 2045 2045 HOH HOH . G 5 HOH A 46 2046 2046 HOH HOH . G 5 HOH A 47 2047 2047 HOH HOH . G 5 HOH A 48 2048 2048 HOH HOH . G 5 HOH A 49 2049 2049 HOH HOH . G 5 HOH A 50 2050 2050 HOH HOH . G 5 HOH A 51 2051 2051 HOH HOH . G 5 HOH A 52 2052 2052 HOH HOH . G 5 HOH A 53 2053 2053 HOH HOH . G 5 HOH A 54 2054 2054 HOH HOH . G 5 HOH A 55 2055 2055 HOH HOH . G 5 HOH A 56 2056 2056 HOH HOH . G 5 HOH A 57 2057 2057 HOH HOH . G 5 HOH A 58 2058 2058 HOH HOH . G 5 HOH A 59 2059 2059 HOH HOH . G 5 HOH A 60 2060 2060 HOH HOH . G 5 HOH A 61 2061 2061 HOH HOH . G 5 HOH A 62 2062 2062 HOH HOH . G 5 HOH A 63 2063 2063 HOH HOH . G 5 HOH A 64 2064 2064 HOH HOH . G 5 HOH A 65 2065 2065 HOH HOH . G 5 HOH A 66 2066 2066 HOH HOH . G 5 HOH A 67 2067 2067 HOH HOH . G 5 HOH A 68 2068 2068 HOH HOH . G 5 HOH A 69 2069 2069 HOH HOH . G 5 HOH A 70 2070 2070 HOH HOH . G 5 HOH A 71 2071 2071 HOH HOH . G 5 HOH A 72 2072 2072 HOH HOH . G 5 HOH A 73 2073 2073 HOH HOH . G 5 HOH A 74 2074 2074 HOH HOH . G 5 HOH A 75 2075 2075 HOH HOH . G 5 HOH A 76 2076 2076 HOH HOH . G 5 HOH A 77 2077 2077 HOH HOH . G 5 HOH A 78 2078 2078 HOH HOH . G 5 HOH A 79 2079 2079 HOH HOH . G 5 HOH A 80 2080 2080 HOH HOH . G 5 HOH A 81 2081 2081 HOH HOH . G 5 HOH A 82 2082 2082 HOH HOH . G 5 HOH A 83 2083 2083 HOH HOH . G 5 HOH A 84 2084 2084 HOH HOH . G 5 HOH A 85 2085 2085 HOH HOH . G 5 HOH A 86 2086 2086 HOH HOH . G 5 HOH A 87 2087 2087 HOH HOH . G 5 HOH A 88 2088 2088 HOH HOH . G 5 HOH A 89 2089 2089 HOH HOH . G 5 HOH A 90 2090 2090 HOH HOH . G 5 HOH A 91 2091 2091 HOH HOH . G 5 HOH A 92 2092 2092 HOH HOH . G 5 HOH A 93 2093 2093 HOH HOH . G 5 HOH A 94 2094 2094 HOH HOH . G 5 HOH A 95 2095 2095 HOH HOH . G 5 HOH A 96 2096 2096 HOH HOH . G 5 HOH A 97 2097 2097 HOH HOH . G 5 HOH A 98 2098 2098 HOH HOH . G 5 HOH A 99 2099 2099 HOH HOH . G 5 HOH A 100 2100 2100 HOH HOH . G 5 HOH A 101 2101 2101 HOH HOH . G 5 HOH A 102 2102 2102 HOH HOH . G 5 HOH A 103 2103 2103 HOH HOH . G 5 HOH A 104 2104 2104 HOH HOH . G 5 HOH A 105 2105 2105 HOH HOH . G 5 HOH A 106 2106 2106 HOH HOH . G 5 HOH A 107 2107 2107 HOH HOH . G 5 HOH A 108 2108 2108 HOH HOH . G 5 HOH A 109 2109 2109 HOH HOH . G 5 HOH A 110 2110 2110 HOH HOH . G 5 HOH A 111 2111 2111 HOH HOH . G 5 HOH A 112 2112 2112 HOH HOH . G 5 HOH A 113 2113 2113 HOH HOH . G 5 HOH A 114 2114 2114 HOH HOH . G 5 HOH A 115 2115 2115 HOH HOH . G 5 HOH A 116 2116 2116 HOH HOH . G 5 HOH A 117 2117 2117 HOH HOH . G 5 HOH A 118 2118 2118 HOH HOH . G 5 HOH A 119 2119 2119 HOH HOH . G 5 HOH A 120 2120 2120 HOH HOH . G 5 HOH A 121 2121 2121 HOH HOH . G 5 HOH A 122 2122 2122 HOH HOH . G 5 HOH A 123 2123 2123 HOH HOH . G 5 HOH A 124 2124 2124 HOH HOH . G 5 HOH A 125 2125 2125 HOH HOH . G 5 HOH A 126 2126 2126 HOH HOH . G 5 HOH A 127 2127 2127 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 . . . C 3 12.224 -26.976 -10.943 1 32.01 ? N SAM 1002 A 1 HETATM 2 C CA SAM . . . C 3 12.89 -25.774 -11.447 1 34.77 ? CA SAM 1002 A 1 HETATM 3 C C SAM . . . C 3 13.56 -26.094 -12.746 1 53.57 ? C SAM 1002 A 1 HETATM 4 O O SAM . . . C 3 12.972 -26.881 -13.536 1 38.56 ? O SAM 1002 A 1 HETATM 5 O OXT SAM . . . C 3 14.673 -25.575 -12.975 1 38.05 ? OXT SAM 1002 A 1 HETATM 6 C CB SAM . . . C 3 13.903 -25.291 -10.384 1 31.76 ? CB SAM 1002 A 1 HETATM 7 C CG SAM . . . C 3 13.183 -24.152 -9.66 1 26.99 ? CG SAM 1002 A 1 HETATM 8 S SD SAM . . . C 3 13.226 -22.799 -10.613 1 27.02 ? SD SAM 1002 A 1 HETATM 9 C CE SAM . . . C 3 14.061 -21.635 -9.664 1 26.87 ? CE SAM 1002 A 1 HETATM 10 C C5' SAM . . . C 3 11.813 -21.975 -10.768 1 13.67 ? C5' SAM 1002 A 1 HETATM 11 C C4' SAM . . . C 3 10.86 -22.912 -11.648 1 30.29 ? C4' SAM 1002 A 1 HETATM 12 O O4' SAM . . . C 3 10.767 -24.294 -11.168 1 24.91 ? O4' SAM 1002 A 1 HETATM 13 C C3' SAM . . . C 3 9.431 -22.523 -11.852 1 18.03 ? C3' SAM 1002 A 1 HETATM 14 O O3' SAM . . . C 3 9.188 -21.358 -12.771 1 28.24 ? O3' SAM 1002 A 1 HETATM 15 C C2' SAM . . . C 3 8.764 -23.871 -12.272 1 25.01 ? C2' SAM 1002 A 1 HETATM 16 O O2' SAM . . . C 3 9.068 -24.447 -13.67 1 19.58 ? O2' SAM 1002 A 1 HETATM 17 C C1' SAM . . . C 3 9.434 -24.832 -11.304 1 29.22 ? C1' SAM 1002 A 1 HETATM 18 N N9 SAM . . . C 3 8.697 -25.03 -10.014 1 32.17 ? N9 SAM 1002 A 1 HETATM 19 C C8 SAM . . . C 3 9.171 -24.729 -8.757 1 25.14 ? C8 SAM 1002 A 1 HETATM 20 N N7 SAM . . . C 3 8.237 -25.035 -7.781 1 27.27 ? N7 SAM 1002 A 1 HETATM 21 C C5 SAM . . . C 3 7.148 -25.549 -8.444 1 30.54 ? C5 SAM 1002 A 1 HETATM 22 C C6 SAM . . . C 3 5.814 -26.119 -8.079 1 36.47 ? C6 SAM 1002 A 1 HETATM 23 N N6 SAM . . . C 3 5.38 -26.191 -6.769 1 32.21 ? N6 SAM 1002 A 1 HETATM 24 N N1 SAM . . . C 3 5.016 -26.558 -9.111 1 25.97 ? N1 SAM 1002 A 1 HETATM 25 C C2 SAM . . . C 3 5.374 -26.542 -10.411 1 36.69 ? C2 SAM 1002 A 1 HETATM 26 N N3 SAM . . . C 3 6.555 -26.066 -10.797 1 34.44 ? N3 SAM 1002 A 1 HETATM 27 C C4 SAM . . . C 3 7.464 -25.557 -9.896 1 33.81 ? C4 SAM 1002 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 20 _model_server_stats.element_count 27 #