data_3Q87 # _model_server_result.job_id MgBu1axGMUTmB39E7WU9Rg _model_server_result.datetime_utc '2025-03-06 03:22:35' _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 3q87 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":300}' # _entry.id 3Q87 # _exptl.entry_id 3Q87 _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 3Q87 _cell.length_a 42.115 _cell.length_b 74.316 _cell.length_c 96.754 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3Q87 _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 _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 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 SG CYS 11 A CYS 11 1_555 C ZN ZN . A ZN 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc2 A SG CYS 14 A CYS 14 1_555 C ZN ZN . A ZN 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc3 A SG CYS 102 A CYS 102 1_555 C ZN ZN . A ZN 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc4 A SG CYS 105 A CYS 105 1_555 C ZN ZN . A ZN 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? # _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 3Q87 _atom_sites.fract_transf_matrix[1][1] 0.023745 _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] 0.013456 _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] 0.010335 _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 1 126 1 ZN ZN . D 4 SAM B 1 300 300 SAM SAM . E 5 HOH A 1 127 127 HOH HOH . E 5 HOH A 2 128 6 HOH HOH . E 5 HOH A 3 129 129 HOH HOH . E 5 HOH A 4 130 11 HOH HOH . E 5 HOH A 5 131 13 HOH HOH . E 5 HOH A 6 132 132 HOH HOH . E 5 HOH A 7 133 14 HOH HOH . E 5 HOH A 8 134 15 HOH HOH . E 5 HOH A 9 135 16 HOH HOH . E 5 HOH A 10 136 17 HOH HOH . E 5 HOH A 11 137 18 HOH HOH . E 5 HOH A 12 138 26 HOH HOH . E 5 HOH A 13 139 29 HOH HOH . E 5 HOH A 14 140 41 HOH HOH . E 5 HOH A 15 141 43 HOH HOH . E 5 HOH A 16 142 44 HOH HOH . E 5 HOH A 17 143 47 HOH HOH . E 5 HOH A 18 144 49 HOH HOH . E 5 HOH A 19 145 53 HOH HOH . E 5 HOH A 20 146 54 HOH HOH . E 5 HOH A 21 147 59 HOH HOH . E 5 HOH A 22 148 62 HOH HOH . E 5 HOH A 23 149 63 HOH HOH . E 5 HOH A 24 150 65 HOH HOH . E 5 HOH A 25 151 67 HOH HOH . E 5 HOH A 26 152 68 HOH HOH . E 5 HOH A 27 153 69 HOH HOH . E 5 HOH A 28 154 72 HOH HOH . E 5 HOH A 29 155 80 HOH HOH . E 5 HOH A 30 156 87 HOH HOH . E 5 HOH A 31 157 89 HOH HOH . E 5 HOH A 32 158 90 HOH HOH . E 5 HOH A 33 159 92 HOH HOH . E 5 HOH A 34 160 94 HOH HOH . E 5 HOH A 35 161 95 HOH HOH . E 5 HOH A 36 162 96 HOH HOH . E 5 HOH A 37 163 101 HOH HOH . E 5 HOH A 38 164 104 HOH HOH . E 5 HOH A 39 165 105 HOH HOH . E 5 HOH A 40 166 106 HOH HOH . E 5 HOH A 41 167 111 HOH HOH . E 5 HOH A 42 168 114 HOH HOH . E 5 HOH A 43 169 117 HOH HOH . E 5 HOH A 44 170 118 HOH HOH . E 5 HOH A 45 171 122 HOH HOH . E 5 HOH A 46 172 123 HOH HOH . E 5 HOH A 47 251 126 HOH HOH . F 5 HOH B 1 171 1 HOH HOH . F 5 HOH B 2 172 2 HOH HOH . F 5 HOH B 3 173 3 HOH HOH . F 5 HOH B 4 174 4 HOH HOH . F 5 HOH B 5 175 5 HOH HOH . F 5 HOH B 6 176 7 HOH HOH . F 5 HOH B 7 177 8 HOH HOH . F 5 HOH B 8 178 9 HOH HOH . F 5 HOH B 9 179 10 HOH HOH . F 5 HOH B 10 180 12 HOH HOH . F 5 HOH B 11 181 19 HOH HOH . F 5 HOH B 12 182 20 HOH HOH . F 5 HOH B 13 183 21 HOH HOH . F 5 HOH B 14 184 22 HOH HOH . F 5 HOH B 15 185 23 HOH HOH . F 5 HOH B 16 186 24 HOH HOH . F 5 HOH B 17 187 25 HOH HOH . F 5 HOH B 18 188 27 HOH HOH . F 5 HOH B 19 189 28 HOH HOH . F 5 HOH B 20 190 30 HOH HOH . F 5 HOH B 21 191 31 HOH HOH . F 5 HOH B 22 192 32 HOH HOH . F 5 HOH B 23 193 33 HOH HOH . F 5 HOH B 24 194 34 HOH HOH . F 5 HOH B 25 195 35 HOH HOH . F 5 HOH B 26 196 36 HOH HOH . F 5 HOH B 27 197 37 HOH HOH . F 5 HOH B 28 198 38 HOH HOH . F 5 HOH B 29 199 39 HOH HOH . F 5 HOH B 30 200 40 HOH HOH . F 5 HOH B 31 201 42 HOH HOH . F 5 HOH B 32 202 45 HOH HOH . F 5 HOH B 33 203 46 HOH HOH . F 5 HOH B 34 204 48 HOH HOH . F 5 HOH B 35 205 50 HOH HOH . F 5 HOH B 36 206 51 HOH HOH . F 5 HOH B 37 207 52 HOH HOH . F 5 HOH B 38 208 55 HOH HOH . F 5 HOH B 39 209 56 HOH HOH . F 5 HOH B 40 210 57 HOH HOH . F 5 HOH B 41 211 58 HOH HOH . F 5 HOH B 42 212 60 HOH HOH . F 5 HOH B 43 213 61 HOH HOH . F 5 HOH B 44 214 64 HOH HOH . F 5 HOH B 45 215 66 HOH HOH . F 5 HOH B 46 216 70 HOH HOH . F 5 HOH B 47 217 71 HOH HOH . F 5 HOH B 48 218 73 HOH HOH . F 5 HOH B 49 219 74 HOH HOH . F 5 HOH B 50 220 75 HOH HOH . F 5 HOH B 51 221 76 HOH HOH . F 5 HOH B 52 222 77 HOH HOH . F 5 HOH B 53 223 78 HOH HOH . F 5 HOH B 54 224 79 HOH HOH . F 5 HOH B 55 225 81 HOH HOH . F 5 HOH B 56 226 82 HOH HOH . F 5 HOH B 57 227 83 HOH HOH . F 5 HOH B 58 228 84 HOH HOH . F 5 HOH B 59 229 85 HOH HOH . F 5 HOH B 60 230 86 HOH HOH . F 5 HOH B 61 231 88 HOH HOH . F 5 HOH B 62 232 91 HOH HOH . F 5 HOH B 63 233 93 HOH HOH . F 5 HOH B 64 234 97 HOH HOH . F 5 HOH B 65 235 98 HOH HOH . F 5 HOH B 66 236 99 HOH HOH . F 5 HOH B 67 237 102 HOH HOH . F 5 HOH B 68 238 103 HOH HOH . F 5 HOH B 69 239 107 HOH HOH . F 5 HOH B 70 240 109 HOH HOH . F 5 HOH B 71 241 110 HOH HOH . F 5 HOH B 72 242 112 HOH HOH . F 5 HOH B 73 243 113 HOH HOH . F 5 HOH B 74 244 115 HOH HOH . F 5 HOH B 75 245 116 HOH HOH . F 5 HOH B 76 246 119 HOH HOH . F 5 HOH B 77 247 120 HOH HOH . F 5 HOH B 78 248 121 HOH HOH . F 5 HOH B 79 249 124 HOH HOH . F 5 HOH B 80 250 125 HOH HOH . F 5 HOH B 81 252 128 HOH HOH . F 5 HOH B 82 253 130 HOH HOH . F 5 HOH B 83 254 131 HOH HOH . F 5 HOH B 84 255 134 HOH HOH . F 5 HOH B 85 256 135 HOH HOH . F 5 HOH B 86 257 136 HOH HOH . F 5 HOH B 87 258 137 HOH HOH . F 5 HOH B 88 259 138 HOH HOH . F 5 HOH B 89 260 139 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 . . . D 4 33.923 18.18 14.799 1 24.16 ? N SAM 300 B 1 HETATM 2 C CA SAM . . . D 4 35.064 18.77 14.086 1 24.35 ? CA SAM 300 B 1 HETATM 3 C C SAM . . . D 4 34.561 19.916 13.196 1 31.3 ? C SAM 300 B 1 HETATM 4 O O SAM . . . D 4 35.305 20.823 12.821 1 28.36 ? O SAM 300 B 1 HETATM 5 O OXT SAM . . . D 4 33.389 19.965 12.829 1 27.94 ? OXT SAM 300 B 1 HETATM 6 C CB SAM . . . D 4 35.943 17.749 13.312 1 18.18 ? CB SAM 300 B 1 HETATM 7 C CG SAM . . . D 4 35.424 17.024 12.045 1 28.11 ? CG SAM 300 B 1 HETATM 8 S SD SAM . . . D 4 36.629 16.025 11.064 1 40.34 ? SD SAM 300 B 1 HETATM 9 C CE SAM . . . D 4 35.998 16.182 9.38 1 25.44 ? CE SAM 300 B 1 HETATM 10 C C5' SAM . . . D 4 36.163 14.315 11.434 1 23.67 ? C5' SAM 300 B 1 HETATM 11 C C4' SAM . . . D 4 36.642 13.962 12.833 1 20.12 ? C4' SAM 300 B 1 HETATM 12 O O4' SAM . . . D 4 36.328 12.608 13.115 1 19.48 ? O4' SAM 300 B 1 HETATM 13 C C3' SAM . . . D 4 38.146 14.119 13.002 1 19.64 ? C3' SAM 300 B 1 HETATM 14 O O3' SAM . . . D 4 38.385 14.837 14.192 1 19.58 ? O3' SAM 300 B 1 HETATM 15 C C2' SAM . . . D 4 38.665 12.702 13.142 1 19.77 ? C2' SAM 300 B 1 HETATM 16 O O2' SAM . . . D 4 39.775 12.579 14.001 1 18.97 ? O2' SAM 300 B 1 HETATM 17 C C1' SAM . . . D 4 37.455 12.005 13.72 1 15.29 ? C1' SAM 300 B 1 HETATM 18 N N9 SAM . . . D 4 37.387 10.588 13.396 1 16.38 ? N9 SAM 300 B 1 HETATM 19 C C8 SAM . . . D 4 37.855 9.923 12.286 1 17.5 ? C8 SAM 300 B 1 HETATM 20 N N7 SAM . . . D 4 37.542 8.616 12.431 1 16.5 ? N7 SAM 300 B 1 HETATM 21 C C5 SAM . . . D 4 36.875 8.461 13.614 1 22.65 ? C5 SAM 300 B 1 HETATM 22 C C6 SAM . . . D 4 36.318 7.372 14.26 1 14.73 ? C6 SAM 300 B 1 HETATM 23 N N6 SAM . . . D 4 36.388 6.168 13.701 1 17.87 ? N6 SAM 300 B 1 HETATM 24 N N1 SAM . . . D 4 35.688 7.539 15.482 1 17.06 ? N1 SAM 300 B 1 HETATM 25 C C2 SAM . . . D 4 35.599 8.787 16.076 1 16.13 ? C2 SAM 300 B 1 HETATM 26 N N3 SAM . . . D 4 36.154 9.871 15.424 1 16.97 ? N3 SAM 300 B 1 HETATM 27 C C4 SAM . . . D 4 36.776 9.701 14.228 1 16.45 ? C4 SAM 300 B 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #