data_6FCB # _model_server_result.job_id vrtPuPIQvQ_WkM7bUw9-og _model_server_result.datetime_utc '2024-11-13 07:41:33' _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 6fcb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 6FCB # _exptl.entry_id 6FCB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 398.437 _entity.id 5 _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 6FCB _cell.length_a 66.33 _cell.length_b 94.87 _cell.length_c 117.37 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6FCB _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 1,2,3,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _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 OD1 ASP 31 A ASP 31 1_555 C MG MG . A MG 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.314 ? metalc ? metalc2 A OD2 ASP 31 A ASP 31 1_555 C MG MG . A MG 402 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.157 ? metalc ? metalc3 A OE2 GLU 57 A GLU 57 1_555 E K K . A K 404 2_555 ? ? ? ? A ? ? ? ? ? ? ? 2.754 ? metalc ? metalc4 A OD1 ASP 258 A ASP 258 1_555 E K K . A K 404 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.036 ? metalc ? metalc5 A OD2 ASP 258 A ASP 258 1_555 E K K . A K 404 1_555 ? ? ? ? A ? ? ? ? ? ? ? 3.349 ? metalc ? metalc6 A O ALA 259 A ALA 259 1_555 E K K . A K 404 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.614 ? metalc ? metalc7 A OD2 ASP 291 A ASP 291 1_555 D MG MG . A MG 403 2_555 ? ? ? ? A ? ? ? ? ? ? ? 2.693 ? metalc ? metalc8 B O2G PPK . A PPK 401 1_555 C MG MG . A MG 402 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.563 ? metalc ? metalc9 B O1B PPK . A PPK 401 1_555 C MG MG . A MG 402 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.485 ? metalc ? metalc10 B O3G PPK . A PPK 401 1_555 D MG MG . A MG 403 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.363 ? metalc ? metalc11 B O4A PPK . A PPK 401 1_555 D MG MG . A MG 403 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.226 ? metalc ? metalc12 B O1B PPK . A PPK 401 1_555 E K K . A K 404 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.821 ? # _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 311 n n N HN1 SAM sing 312 n n N HN2 SAM sing 313 n n CA C SAM sing 314 n n CA CB SAM sing 315 n n CA HA SAM sing 316 n n C O SAM doub 317 n n C OXT SAM sing 318 n n CB CG SAM sing 319 n n CB HB1 SAM sing 320 n n CB HB2 SAM sing 321 n n CG SD SAM sing 322 n n CG HG1 SAM sing 323 n n CG HG2 SAM sing 324 n n SD CE SAM sing 325 n n SD C5' SAM sing 326 n n CE HE1 SAM sing 327 n n CE HE2 SAM sing 328 n n CE HE3 SAM sing 329 n n C5' C4' SAM sing 330 n n C5' "H5'1" SAM sing 331 n n C5' "H5'2" SAM sing 332 n n C4' O4' SAM sing 333 n n C4' C3' SAM sing 334 n n C4' H4' SAM sing 335 n n O4' C1' SAM sing 336 n n C3' O3' SAM sing 337 n n C3' C2' SAM sing 338 n n C3' H3' SAM sing 339 n n O3' HO3' SAM sing 340 n n C2' O2' SAM sing 341 n n C2' C1' SAM sing 342 n n C2' H2' SAM sing 343 n n O2' HO2' SAM sing 344 n n C1' N9 SAM sing 345 n n C1' H1' SAM sing 346 n n N9 C8 SAM sing 347 n y N9 C4 SAM sing 348 n y C8 N7 SAM doub 349 n y C8 H8 SAM sing 350 n n N7 C5 SAM sing 351 n y C5 C6 SAM sing 352 n y C5 C4 SAM doub 353 n y C6 N6 SAM sing 354 n n C6 N1 SAM doub 355 n y N6 HN61 SAM sing 356 n n N6 HN62 SAM sing 357 n n N1 C2 SAM sing 358 n y C2 N3 SAM doub 359 n y C2 H2 SAM sing 360 n n N3 C4 SAM sing 361 n y # _atom_sites.entry_id 6FCB _atom_sites.fract_transf_matrix[1][1] 0.015076 _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] 0.010541 _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] 0.00852 _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 PPK A 1 401 400 PPK PPK . C 3 MG A 1 402 401 MG MG . D 3 MG A 1 403 402 MG MG . E 4 K A 1 404 403 K K . F 5 SAM A 1 405 405 SAM SAM . G 6 PEG A 1 406 412 PEG PEG . H 7 HOH A 1 501 418 HOH HOH . H 7 HOH A 2 502 417 HOH HOH . H 7 HOH A 3 503 419 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 . A . F 5 10.324 -7.642 -15.877 1 66.25 ? N SAM 405 A 1 HETATM 2 C CA SAM . A . F 5 10.677 -9.047 -15.87 1 64.02 ? CA SAM 405 A 1 HETATM 3 C C SAM . A . F 5 11.989 -9.21 -15.206 1 57.69 ? C SAM 405 A 1 HETATM 4 O O SAM . A . F 5 13.029 -9.259 -15.888 1 50.64 ? O SAM 405 A 1 HETATM 5 O OXT SAM . A . F 5 11.955 -9.29 -13.966 1 55.23 ? OXT SAM 405 A 1 HETATM 6 C CB SAM . A . F 5 10.686 -9.501 -17.308 1 68.17 ? CB SAM 405 A 1 HETATM 7 C CG SAM . A . F 5 9.239 -9.732 -17.722 1 71.73 ? CG SAM 405 A 1 HETATM 8 S SD SAM . A . F 5 8.81 -11.328 -17.727 1 75.29 ? SD SAM 405 A 1 HETATM 9 C CE SAM . A . F 5 10.038 -12.201 -18.401 1 75.02 ? CE SAM 405 A 1 HETATM 10 C C5' SAM . A . F 5 7.554 -11.362 -18.785 1 72.46 ? C5' SAM 405 A 1 HETATM 11 C C4' SAM . A . F 5 6.612 -12.539 -18.634 1 66.96 ? C4' SAM 405 A 1 HETATM 12 O O4' SAM . A . F 5 7.235 -13.719 -19.109 1 62.89 ? O4' SAM 405 A 1 HETATM 13 C C3' SAM . A . F 5 6.189 -12.818 -17.208 1 62.55 ? C3' SAM 405 A 1 HETATM 14 O O3' SAM . A . F 5 5.072 -12.05 -16.841 1 59.45 ? O3' SAM 405 A 1 HETATM 15 C C2' SAM . A . F 5 5.876 -14.274 -17.258 1 58.31 ? C2' SAM 405 A 1 HETATM 16 O O2' SAM . A . F 5 4.551 -14.515 -17.667 1 55.45 ? O2' SAM 405 A 1 HETATM 17 C C1' SAM . A . F 5 6.82 -14.807 -18.305 1 57.39 ? C1' SAM 405 A 1 HETATM 18 N N9 SAM . A . F 5 7.932 -15.391 -17.556 1 53.96 ? N9 SAM 405 A 1 HETATM 19 C C8 SAM . A . F 5 8.242 -15.139 -16.28 1 53.78 ? C8 SAM 405 A 1 HETATM 20 N N7 SAM . A . F 5 9.287 -15.868 -15.892 1 52.33 ? N7 SAM 405 A 1 HETATM 21 C C5 SAM . A . F 5 9.663 -16.579 -16.916 1 52.2 ? C5 SAM 405 A 1 HETATM 22 C C6 SAM . A . F 5 10.709 -17.547 -17.148 1 54.02 ? C6 SAM 405 A 1 HETATM 23 N N6 SAM . A . F 5 11.561 -17.858 -16.173 1 56.9 ? N6 SAM 405 A 1 HETATM 24 N N1 SAM . A . F 5 10.794 -18.1 -18.356 1 52.87 ? N1 SAM 405 A 1 HETATM 25 C C2 SAM . A . F 5 9.939 -17.774 -19.326 1 52.74 ? C2 SAM 405 A 1 HETATM 26 N N3 SAM . A . F 5 8.953 -16.887 -19.191 1 53.83 ? N3 SAM 405 A 1 HETATM 27 C C4 SAM . A . F 5 8.777 -16.27 -18.02 1 53.14 ? C4 SAM 405 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #