data_4PL1 # _model_server_result.job_id Bz8USrnaw04zMMIl0Cbi8w _model_server_result.datetime_utc '2024-11-05 00:08:50' _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 4pl1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 4PL1 # _exptl.entry_id 4PL1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 2 _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 90 _cell.entry_id 4PL1 _cell.length_a 55.627 _cell.length_b 55.729 _cell.length_c 254.032 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PL1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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 1 1 B,E,F 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 ? 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 covale ? covale1 A C ALA 338 B ALA 354 1_555 A N SMC 339 B SMC 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C SMC 339 B SMC 355 1_555 A N GLY 340 B GLY 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? metalc ? metalc1 A SG CYS 109 B CYS 125 1_555 D FE3 SF4 . B SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc2 A SG CYS 113 B CYS 129 1_555 D FE1 SF4 . B SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc3 A SG CYS 116 B CYS 132 1_555 D FE2 SF4 . B SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc4 C N SAM . B SAM 401 1_555 D FE4 SF4 . B SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc5 C OXT SAM . B SAM 401 1_555 D FE4 SF4 . B SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc6 B SG CYS 109 A CYS 125 1_555 F FE1 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc7 B SG CYS 113 A CYS 129 1_555 F FE2 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc8 B SG CYS 116 A CYS 132 1_555 F FE3 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc9 E N SAM . A SAM 401 1_555 F FE4 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc10 E OXT SAM . A SAM 401 1_555 F FE4 SF4 . A SF4 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? # _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 275 n n N HN1 SAM sing 276 n n N HN2 SAM sing 277 n n CA C SAM sing 278 n n CA CB SAM sing 279 n n CA HA SAM sing 280 n n C O SAM doub 281 n n C OXT SAM sing 282 n n CB CG SAM sing 283 n n CB HB1 SAM sing 284 n n CB HB2 SAM sing 285 n n CG SD SAM sing 286 n n CG HG1 SAM sing 287 n n CG HG2 SAM sing 288 n n SD CE SAM sing 289 n n SD C5' SAM sing 290 n n CE HE1 SAM sing 291 n n CE HE2 SAM sing 292 n n CE HE3 SAM sing 293 n n C5' C4' SAM sing 294 n n C5' "H5'1" SAM sing 295 n n C5' "H5'2" SAM sing 296 n n C4' O4' SAM sing 297 n n C4' C3' SAM sing 298 n n C4' H4' SAM sing 299 n n O4' C1' SAM sing 300 n n C3' O3' SAM sing 301 n n C3' C2' SAM sing 302 n n C3' H3' SAM sing 303 n n O3' HO3' SAM sing 304 n n C2' O2' SAM sing 305 n n C2' C1' SAM sing 306 n n C2' H2' SAM sing 307 n n O2' HO2' SAM sing 308 n n C1' N9 SAM sing 309 n n C1' H1' SAM sing 310 n n N9 C8 SAM sing 311 n y N9 C4 SAM sing 312 n y C8 N7 SAM doub 313 n y C8 H8 SAM sing 314 n n N7 C5 SAM sing 315 n y C5 C6 SAM sing 316 n y C5 C4 SAM doub 317 n y C6 N6 SAM sing 318 n n C6 N1 SAM doub 319 n y N6 HN61 SAM sing 320 n n N6 HN62 SAM sing 321 n n N1 C2 SAM sing 322 n y C2 N3 SAM doub 323 n y C2 H2 SAM sing 324 n n N3 C4 SAM sing 325 n y # _atom_sites.entry_id 4PL1 _atom_sites.fract_transf_matrix[1][1] 0.017977 _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] 0.017944 _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] 0.003937 _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 SAM B 1 401 406 SAM SAM . D 3 SF4 B 1 402 2 SF4 SF4 . E 2 SAM A 1 401 406 SAM SAM . F 3 SF4 A 1 402 1 SF4 SF4 . # 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 . . . E 2 -22.388 -0.363 17.503 1 58.07 ? N SAM 401 A 1 HETATM 2 C CA SAM . . . E 2 -22.866 -0.293 16.086 1 58.17 ? CA SAM 401 A 1 HETATM 3 C C SAM . . . E 2 -21.949 -1.089 15.158 1 58.28 ? C SAM 401 A 1 HETATM 4 O O SAM . . . E 2 -22.347 -1.433 14.047 1 57.84 ? O SAM 401 A 1 HETATM 5 O OXT SAM . . . E 2 -20.805 -1.405 15.494 1 58.75 ? OXT SAM 401 A 1 HETATM 6 C CB SAM . . . E 2 -23.067 1.137 15.566 1 57.07 ? CB SAM 401 A 1 HETATM 7 C CG SAM . . . E 2 -21.976 2.18 15.802 1 56.52 ? CG SAM 401 A 1 HETATM 8 S SD SAM . . . E 2 -20.385 1.81 15.031 1 56.22 ? SD SAM 401 A 1 HETATM 9 C CE SAM . . . E 2 -19.394 3.237 15.533 1 56.81 ? CE SAM 401 A 1 HETATM 10 C C5' SAM . . . E 2 -20.769 2.224 13.308 1 57.97 ? C5' SAM 401 A 1 HETATM 11 C C4' SAM . . . E 2 -19.739 1.728 12.297 1 58.34 ? C4' SAM 401 A 1 HETATM 12 O O4' SAM . . . E 2 -18.566 2.523 12.36 1 57.72 ? O4' SAM 401 A 1 HETATM 13 C C3' SAM . . . E 2 -19.321 0.275 12.515 1 58.85 ? C3' SAM 401 A 1 HETATM 14 O O3' SAM . . . E 2 -19.503 -0.488 11.343 1 58.05 ? O3' SAM 401 A 1 HETATM 15 C C2' SAM . . . E 2 -17.856 0.378 12.872 1 59.3 ? C2' SAM 401 A 1 HETATM 16 O O2' SAM . . . E 2 -17.107 -0.712 12.4 1 61.13 ? O2' SAM 401 A 1 HETATM 17 C C1' SAM . . . E 2 -17.45 1.675 12.194 1 58.99 ? C1' SAM 401 A 1 HETATM 18 N N9 SAM . . . E 2 -16.209 2.241 12.751 1 59.47 ? N9 SAM 401 A 1 HETATM 19 C C8 SAM . . . E 2 -15.866 2.385 14.072 1 59.6 ? C8 SAM 401 A 1 HETATM 20 N N7 SAM . . . E 2 -14.636 2.944 14.135 1 59.86 ? N7 SAM 401 A 1 HETATM 21 C C5 SAM . . . E 2 -14.194 3.164 12.879 1 58.95 ? C5 SAM 401 A 1 HETATM 22 C C6 SAM . . . E 2 -13.018 3.708 12.38 1 59.1 ? C6 SAM 401 A 1 HETATM 23 N N6 SAM . . . E 2 -12.064 4.135 13.203 1 58.8 ? N6 SAM 401 A 1 HETATM 24 N N1 SAM . . . E 2 -12.848 3.804 11.01 1 60.29 ? N1 SAM 401 A 1 HETATM 25 C C2 SAM . . . E 2 -13.833 3.363 10.143 1 58.37 ? C2 SAM 401 A 1 HETATM 26 N N3 SAM . . . E 2 -14.999 2.822 10.651 1 58.34 ? N3 SAM 401 A 1 HETATM 27 C C4 SAM . . . E 2 -15.174 2.725 11.996 1 59.17 ? C4 SAM 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #