data_3KQM # _model_server_result.job_id P6IZECKGuAP3IQ_GV5-Q9g _model_server_result.datetime_utc '2024-11-06 15:35:21' _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 3kqm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":2001}' # _entry.id 3KQM # _exptl.entry_id 3KQM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _entity.pdbx_number_of_molecules 2 _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 3KQM _cell.length_a 93.78 _cell.length_b 93.78 _cell.length_c 188.661 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KQM _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 48 A CYS 48 1_555 B SG CYS 139 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 139 A CYS 139 1_555 B SG CYS 48 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? # _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 286 n n N HN1 SAH sing 287 n n N HN2 SAH sing 288 n n CA CB SAH sing 289 n n CA C SAH sing 290 n n CA HA SAH sing 291 n n CB CG SAH sing 292 n n CB HB1 SAH sing 293 n n CB HB2 SAH sing 294 n n CG SD SAH sing 295 n n CG HG1 SAH sing 296 n n CG HG2 SAH sing 297 n n SD C5' SAH sing 298 n n C O SAH doub 299 n n C OXT SAH sing 300 n n OXT HXT SAH sing 301 n n C5' C4' SAH sing 302 n n C5' "H5'1" SAH sing 303 n n C5' "H5'2" SAH sing 304 n n C4' O4' SAH sing 305 n n C4' C3' SAH sing 306 n n C4' H4' SAH sing 307 n n O4' C1' SAH sing 308 n n C3' O3' SAH sing 309 n n C3' C2' SAH sing 310 n n C3' H3' SAH sing 311 n n O3' HO3' SAH sing 312 n n C2' O2' SAH sing 313 n n C2' C1' SAH sing 314 n n C2' H2' SAH sing 315 n n O2' HO2' SAH sing 316 n n C1' N9 SAH sing 317 n n C1' H1' SAH sing 318 n n N9 C8 SAH sing 319 n y N9 C4 SAH sing 320 n y C8 N7 SAH doub 321 n y C8 H8 SAH sing 322 n n N7 C5 SAH sing 323 n y C5 C6 SAH sing 324 n y C5 C4 SAH doub 325 n y C6 N6 SAH sing 326 n n C6 N1 SAH doub 327 n y N6 HN61 SAH sing 328 n n N6 HN62 SAH sing 329 n n N1 C2 SAH sing 330 n y C2 N3 SAH doub 331 n y C2 H2 SAH sing 332 n n N3 C4 SAH sing 333 n y # _atom_sites.entry_id 3KQM _atom_sites.fract_transf_matrix[1][1] 0.010663 _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] 0.010663 _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] 0.005301 _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 2 SAH A 1 2001 2001 SAH SAH . D 3 ES3 A 1 290 1 ES3 ES3 . E 2 SAH B 1 2002 2002 SAH SAH . F 3 ES3 B 1 290 2 ES3 ES3 . G 4 HOH A 1 2004 2004 HOH HOH . G 4 HOH A 2 2005 2005 HOH HOH . G 4 HOH A 3 2008 2008 HOH HOH . G 4 HOH A 4 2016 2016 HOH HOH . G 4 HOH A 5 2021 2021 HOH HOH . G 4 HOH A 6 2025 2025 HOH HOH . G 4 HOH A 7 2027 2027 HOH HOH . G 4 HOH A 8 2034 2034 HOH HOH . G 4 HOH A 9 2040 2040 HOH HOH . G 4 HOH A 10 2044 2044 HOH HOH . G 4 HOH A 11 2045 2045 HOH HOH . G 4 HOH A 12 2048 2048 HOH HOH . G 4 HOH A 13 2052 2052 HOH HOH . G 4 HOH A 14 2057 2057 HOH HOH . G 4 HOH A 15 2058 2058 HOH HOH . G 4 HOH A 16 2059 2059 HOH HOH . G 4 HOH A 17 2061 2061 HOH HOH . G 4 HOH A 18 2064 2064 HOH HOH . G 4 HOH A 19 2068 2068 HOH HOH . G 4 HOH A 20 2079 2079 HOH HOH . G 4 HOH A 21 2085 2085 HOH HOH . G 4 HOH A 22 2087 2087 HOH HOH . G 4 HOH A 23 2089 2089 HOH HOH . G 4 HOH A 24 2090 2090 HOH HOH . G 4 HOH A 25 2091 2091 HOH HOH . G 4 HOH A 26 2094 2094 HOH HOH . G 4 HOH A 27 2095 2095 HOH HOH . G 4 HOH A 28 2103 2103 HOH HOH . G 4 HOH A 29 2105 2105 HOH HOH . G 4 HOH A 30 2108 2108 HOH HOH . G 4 HOH A 31 2114 2114 HOH HOH . G 4 HOH A 32 2116 2116 HOH HOH . G 4 HOH A 33 2128 2128 HOH HOH . G 4 HOH A 34 2135 2135 HOH HOH . G 4 HOH A 35 2138 2138 HOH HOH . G 4 HOH A 36 2147 2147 HOH HOH . G 4 HOH A 37 2150 2150 HOH HOH . G 4 HOH A 38 2152 2152 HOH HOH . G 4 HOH A 39 2159 2159 HOH HOH . G 4 HOH A 40 2160 2160 HOH HOH . G 4 HOH A 41 2161 2161 HOH HOH . G 4 HOH A 42 2162 2162 HOH HOH . G 4 HOH A 43 2163 2163 HOH HOH . G 4 HOH A 44 2164 2164 HOH HOH . H 4 HOH B 1 2006 2006 HOH HOH . H 4 HOH B 2 2007 2007 HOH HOH . H 4 HOH B 3 2009 2009 HOH HOH . H 4 HOH B 4 2010 2010 HOH HOH . H 4 HOH B 5 2011 2011 HOH HOH . H 4 HOH B 6 2013 2013 HOH HOH . H 4 HOH B 7 2014 2014 HOH HOH . H 4 HOH B 8 2015 2015 HOH HOH . H 4 HOH B 9 2017 2017 HOH HOH . H 4 HOH B 10 2018 2018 HOH HOH . H 4 HOH B 11 2023 2023 HOH HOH . H 4 HOH B 12 2024 2024 HOH HOH . H 4 HOH B 13 2026 2026 HOH HOH . H 4 HOH B 14 2029 2029 HOH HOH . H 4 HOH B 15 2030 2030 HOH HOH . H 4 HOH B 16 2031 2031 HOH HOH . H 4 HOH B 17 2033 2033 HOH HOH . H 4 HOH B 18 2035 2035 HOH HOH . H 4 HOH B 19 2036 2036 HOH HOH . H 4 HOH B 20 2037 2037 HOH HOH . H 4 HOH B 21 2038 2038 HOH HOH . H 4 HOH B 22 2039 2039 HOH HOH . H 4 HOH B 23 2041 2041 HOH HOH . H 4 HOH B 24 2043 2043 HOH HOH . H 4 HOH B 25 2046 2046 HOH HOH . H 4 HOH B 26 2047 2047 HOH HOH . H 4 HOH B 27 2051 2051 HOH HOH . H 4 HOH B 28 2054 2054 HOH HOH . H 4 HOH B 29 2055 2055 HOH HOH . H 4 HOH B 30 2056 2056 HOH HOH . H 4 HOH B 31 2060 2060 HOH HOH . H 4 HOH B 32 2062 2062 HOH HOH . H 4 HOH B 33 2063 2063 HOH HOH . H 4 HOH B 34 2065 2065 HOH HOH . H 4 HOH B 35 2066 2066 HOH HOH . H 4 HOH B 36 2069 2069 HOH HOH . H 4 HOH B 37 2070 2070 HOH HOH . H 4 HOH B 38 2071 2071 HOH HOH . H 4 HOH B 39 2072 2072 HOH HOH . H 4 HOH B 40 2074 2074 HOH HOH . H 4 HOH B 41 2075 2075 HOH HOH . H 4 HOH B 42 2076 2076 HOH HOH . H 4 HOH B 43 2077 2077 HOH HOH . H 4 HOH B 44 2078 2078 HOH HOH . H 4 HOH B 45 2080 2080 HOH HOH . H 4 HOH B 46 2081 2081 HOH HOH . H 4 HOH B 47 2082 2082 HOH HOH . H 4 HOH B 48 2083 2083 HOH HOH . H 4 HOH B 49 2084 2084 HOH HOH . H 4 HOH B 50 2086 2086 HOH HOH . H 4 HOH B 51 2088 2088 HOH HOH . H 4 HOH B 52 2092 2092 HOH HOH . H 4 HOH B 53 2093 2093 HOH HOH . H 4 HOH B 54 2096 2096 HOH HOH . H 4 HOH B 55 2097 2097 HOH HOH . H 4 HOH B 56 2100 2100 HOH HOH . H 4 HOH B 57 2101 2101 HOH HOH . H 4 HOH B 58 2102 2102 HOH HOH . H 4 HOH B 59 2104 2104 HOH HOH . H 4 HOH B 60 2107 2107 HOH HOH . H 4 HOH B 61 2109 2109 HOH HOH . H 4 HOH B 62 2111 2111 HOH HOH . H 4 HOH B 63 2112 2112 HOH HOH . H 4 HOH B 64 2113 2113 HOH HOH . H 4 HOH B 65 2117 2117 HOH HOH . H 4 HOH B 66 2118 2118 HOH HOH . H 4 HOH B 67 2119 2119 HOH HOH . H 4 HOH B 68 2120 2120 HOH HOH . H 4 HOH B 69 2121 2121 HOH HOH . H 4 HOH B 70 2122 2122 HOH HOH . H 4 HOH B 71 2123 2123 HOH HOH . H 4 HOH B 72 2125 2125 HOH HOH . H 4 HOH B 73 2126 2126 HOH HOH . H 4 HOH B 74 2129 2129 HOH HOH . H 4 HOH B 75 2130 2130 HOH HOH . H 4 HOH B 76 2131 2131 HOH HOH . H 4 HOH B 77 2132 2132 HOH HOH . H 4 HOH B 78 2133 2133 HOH HOH . H 4 HOH B 79 2136 2136 HOH HOH . H 4 HOH B 80 2137 2137 HOH HOH . H 4 HOH B 81 2139 2139 HOH HOH . H 4 HOH B 82 2141 2141 HOH HOH . H 4 HOH B 83 2142 2142 HOH HOH . H 4 HOH B 84 2143 2143 HOH HOH . H 4 HOH B 85 2149 2149 HOH HOH . H 4 HOH B 86 2153 2153 HOH HOH . H 4 HOH B 87 2154 2154 HOH HOH . H 4 HOH B 88 2158 2158 HOH HOH . H 4 HOH B 89 2165 2165 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 . . . C 2 26.683 53.041 17.692 1 45.58 ? N SAH 2001 A 1 HETATM 2 C CA SAH . . . C 2 27.859 52.195 17.502 1 41.77 ? CA SAH 2001 A 1 HETATM 3 C CB SAH . . . C 2 28.166 51.546 18.867 1 47.64 ? CB SAH 2001 A 1 HETATM 4 C CG SAH . . . C 2 29.618 51.807 19.27 1 53.95 ? CG SAH 2001 A 1 HETATM 5 S SD SAH . . . C 2 30.097 50.514 20.462 1 43.37 ? SD SAH 2001 A 1 HETATM 6 C C SAH . . . C 2 27.467 51.085 16.506 1 42.81 ? C SAH 2001 A 1 HETATM 7 O O SAH . . . C 2 26.313 50.834 16.355 1 39.89 ? O SAH 2001 A 1 HETATM 8 O OXT SAH . . . C 2 28.421 50.141 16.104 1 41.96 ? OXT SAH 2001 A 1 HETATM 9 C C5' SAH . . . C 2 29.742 51.096 22.151 1 54.06 ? C5' SAH 2001 A 1 HETATM 10 C C4' SAH . . . C 2 29.912 52.622 22.235 1 54.3 ? C4' SAH 2001 A 1 HETATM 11 O O4' SAH . . . C 2 29.543 53.115 23.562 1 55.51 ? O4' SAH 2001 A 1 HETATM 12 C C3' SAH . . . C 2 31.361 53.077 21.998 1 53.61 ? C3' SAH 2001 A 1 HETATM 13 O O3' SAH . . . C 2 31.378 54.078 21.013 1 45.93 ? O3' SAH 2001 A 1 HETATM 14 C C2' SAH . . . C 2 31.734 53.671 23.332 1 50.97 ? C2' SAH 2001 A 1 HETATM 15 O O2' SAH . . . C 2 32.789 54.6 23.305 1 46.61 ? O2' SAH 2001 A 1 HETATM 16 C C1' SAH . . . C 2 30.416 54.259 23.811 1 50.35 ? C1' SAH 2001 A 1 HETATM 17 N N9 SAH . . . C 2 30.502 54.487 25.242 1 52.29 ? N9 SAH 2001 A 1 HETATM 18 C C8 SAH . . . C 2 31.539 53.929 26.163 1 57.15 ? C8 SAH 2001 A 1 HETATM 19 N N7 SAH . . . C 2 31.216 54.366 27.519 1 56.74 ? N7 SAH 2001 A 1 HETATM 20 C C5 SAH . . . C 2 29.99 55.172 27.444 1 49.03 ? C5 SAH 2001 A 1 HETATM 21 C C6 SAH . . . C 2 29.203 55.875 28.507 1 51.07 ? C6 SAH 2001 A 1 HETATM 22 N N6 SAH . . . C 2 29.649 55.795 29.892 1 53.63 ? N6 SAH 2001 A 1 HETATM 23 N N1 SAH . . . C 2 27.999 56.622 28.139 1 51.37 ? N1 SAH 2001 A 1 HETATM 24 C C2 SAH . . . C 2 27.552 56.688 26.703 1 45.44 ? C2 SAH 2001 A 1 HETATM 25 N N3 SAH . . . C 2 28.348 56.001 25.643 1 43.49 ? N3 SAH 2001 A 1 HETATM 26 C C4 SAH . . . C 2 29.554 55.243 26.027 1 47.8 ? C4 SAH 2001 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 327 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 26 #