data_3OPE # _model_server_result.job_id d5GHQ9rv3dpfaOq6xeGf5g _model_server_result.datetime_utc '2024-11-21 18:12:43' _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 3ope # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":7}' # _entry.id 3OPE # _exptl.entry_id 3OPE _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 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 120 _cell.entry_id 3OPE _cell.length_a 59.53 _cell.length_b 59.53 _cell.length_c 233.804 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OPE _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,K 1 1 B,G,H,I,J,L 2 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 ? 3 F N N ? 3 J 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 metalc ? metalc1 C ZN ZN . A ZN 1 1_555 A SG CYS 154 A CYS 2220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc2 C ZN ZN . A ZN 1 1_555 A SG CYS 202 A CYS 2268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc3 C ZN ZN . A ZN 1 1_555 A SG CYS 204 A CYS 2270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? metalc ? metalc4 C ZN ZN . A ZN 1 1_555 A SG CYS 209 A CYS 2275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc5 D ZN ZN . A ZN 2 1_555 A SG CYS 51 A CYS 2117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc6 D ZN ZN . A ZN 2 1_555 A SG CYS 56 A CYS 2122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc7 D ZN ZN . A ZN 2 1_555 A SG CYS 62 A CYS 2128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? metalc ? metalc8 E ZN ZN . A ZN 4 1_555 A SG CYS 25 A CYS 2091 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.767 ? metalc ? metalc9 E ZN ZN . A ZN 4 1_555 A SG CYS 27 A CYS 2093 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc10 E ZN ZN . A ZN 4 1_555 A SG CYS 38 A CYS 2104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc11 E ZN ZN . A ZN 4 1_555 A SG CYS 42 A CYS 2108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? metalc ? metalc12 G ZN ZN . B ZN 3 1_555 B SG CYS 154 B CYS 2220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc13 G ZN ZN . B ZN 3 1_555 B SG CYS 202 B CYS 2268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? metalc ? metalc14 H ZN ZN . B ZN 5 1_555 B SG CYS 51 B CYS 2117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc15 H ZN ZN . B ZN 5 1_555 B SG CYS 56 B CYS 2122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc16 H ZN ZN . B ZN 5 1_555 B SG CYS 62 B CYS 2128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc17 I ZN ZN . B ZN 6 1_555 B SG CYS 38 B CYS 2104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? metalc ? metalc18 I ZN ZN . B ZN 6 1_555 B SG CYS 42 B CYS 2108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? # _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 3OPE _atom_sites.fract_transf_matrix[1][1] 0.016798 _atom_sites.fract_transf_matrix[1][2] 0.009698 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019397 _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] 0.004277 _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 ZN A 1 1 1 ZN ZN . D 2 ZN A 1 2 2 ZN ZN . E 2 ZN A 1 4 4 ZN ZN . F 3 SAM A 1 7 7 SAM SAM . G 2 ZN B 1 3 3 ZN ZN . H 2 ZN B 1 5 5 ZN ZN . I 2 ZN B 1 6 6 ZN ZN . J 3 SAM B 1 8 8 SAM SAM . K 4 HOH A 1 3 3 HOH WAT . K 4 HOH A 2 8 8 HOH WAT . K 4 HOH A 3 10 10 HOH WAT . K 4 HOH A 4 11 11 HOH WAT . K 4 HOH A 5 12 12 HOH WAT . K 4 HOH A 6 13 13 HOH WAT . K 4 HOH A 7 14 14 HOH WAT . K 4 HOH A 8 15 15 HOH WAT . K 4 HOH A 9 19 19 HOH WAT . K 4 HOH A 10 22 22 HOH WAT . K 4 HOH A 11 23 23 HOH WAT . K 4 HOH A 12 2289 4 HOH WAT . L 4 HOH B 1 1 1 HOH WAT . L 4 HOH B 2 2 2 HOH WAT . L 4 HOH B 3 7 7 HOH WAT . L 4 HOH B 4 9 9 HOH WAT . L 4 HOH B 5 16 16 HOH WAT . L 4 HOH B 6 17 17 HOH WAT . L 4 HOH B 7 18 18 HOH WAT . L 4 HOH B 8 20 20 HOH WAT . L 4 HOH B 9 21 21 HOH WAT . L 4 HOH B 10 24 24 HOH WAT . L 4 HOH B 11 25 25 HOH WAT . L 4 HOH B 12 26 26 HOH WAT . L 4 HOH B 13 27 27 HOH WAT . L 4 HOH B 14 2289 5 HOH WAT . L 4 HOH B 15 2290 6 HOH WAT . # 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 3 -11.035 10.915 29.592 1 82.05 ? N SAM 7 A 1 HETATM 2 C CA SAM . . . F 3 -10.361 10.336 28.381 1 81.78 ? CA SAM 7 A 1 HETATM 3 C C SAM . . . F 3 -8.85 10.621 28.428 1 82.27 ? C SAM 7 A 1 HETATM 4 O O SAM . . . F 3 -8.105 10.323 27.472 1 82.73 ? O SAM 7 A 1 HETATM 5 O OXT SAM . . . F 3 -8.294 11.163 29.423 1 82.79 ? OXT SAM 7 A 1 HETATM 6 C CB SAM . . . F 3 -11.141 10.74 27.112 1 80.83 ? CB SAM 7 A 1 HETATM 7 C CG SAM . . . F 3 -12.452 9.936 26.849 1 78.59 ? CG SAM 7 A 1 HETATM 8 S SD SAM . . . F 3 -11.874 8.251 26.425 1 75.98 ? SD SAM 7 A 1 HETATM 9 C CE SAM . . . F 3 -12.396 7.999 24.733 1 73.79 ? CE SAM 7 A 1 HETATM 10 C C5' SAM . . . F 3 -12.969 7.141 27.341 1 73.56 ? C5' SAM 7 A 1 HETATM 11 C C4' SAM . . . F 3 -12.441 6.845 28.746 1 73.18 ? C4' SAM 7 A 1 HETATM 12 O O4' SAM . . . F 3 -12.431 7.93 29.628 1 72.25 ? O4' SAM 7 A 1 HETATM 13 C C3' SAM . . . F 3 -13.224 5.794 29.502 1 73.62 ? C3' SAM 7 A 1 HETATM 14 O O3' SAM . . . F 3 -12.786 4.543 28.978 1 73.9 ? O3' SAM 7 A 1 HETATM 15 C C2' SAM . . . F 3 -12.856 6.081 30.946 1 72.64 ? C2' SAM 7 A 1 HETATM 16 O O2' SAM . . . F 3 -11.535 5.51 31.174 1 73.67 ? O2' SAM 7 A 1 HETATM 17 C C1' SAM . . . F 3 -12.846 7.589 30.902 1 72.71 ? C1' SAM 7 A 1 HETATM 18 N N9 SAM . . . F 3 -14.225 8.183 31.031 1 71.24 ? N9 SAM 7 A 1 HETATM 19 C C8 SAM . . . F 3 -14.958 8.847 30.098 1 70.88 ? C8 SAM 7 A 1 HETATM 20 N N7 SAM . . . F 3 -16.155 9.195 30.634 1 70.16 ? N7 SAM 7 A 1 HETATM 21 C C5 SAM . . . F 3 -16.186 8.762 31.937 1 70.44 ? C5 SAM 7 A 1 HETATM 22 C C6 SAM . . . F 3 -17.074 8.795 33.029 1 70.2 ? C6 SAM 7 A 1 HETATM 23 N N6 SAM . . . F 3 -18.285 9.348 33.036 1 69.23 ? N6 SAM 7 A 1 HETATM 24 N N1 SAM . . . F 3 -16.732 8.171 34.216 1 69.79 ? N1 SAM 7 A 1 HETATM 25 C C2 SAM . . . F 3 -15.528 7.59 34.382 1 70.56 ? C2 SAM 7 A 1 HETATM 26 N N3 SAM . . . F 3 -14.645 7.537 33.367 1 69.89 ? N3 SAM 7 A 1 HETATM 27 C C4 SAM . . . F 3 -14.959 8.131 32.166 1 70.25 ? C4 SAM 7 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #