data_1XDU # _model_server_result.job_id PgK56bI1qiyo-jHMfj3Jpw _model_server_result.datetime_utc '2025-07-05 13:13:34' _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 1xdu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":5635}' # _entry.id 1XDU # _exptl.entry_id 1XDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 381.387 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SINEFUNGIN _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 1XDU _cell.length_a 62.758 _cell.length_b 86.813 _cell.length_c 117.395 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XDU _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 PISA,PQS dimeric 2 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,B,C,D 1 1 A,B,C,D 2 1,2 # 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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 62.758 0 58.6975 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 covale ? covale1 A C PRO 30 A PRO 30 1_555 A N MSE 31 A MSE 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C MSE 31 A MSE 31 1_555 A N ALA 32 A ALA 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A C GLY 95 A GLY 95 1_555 A N MSE 96 A MSE 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale4 A C MSE 96 A MSE 96 1_555 A N LEU 97 A LEU 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 A C LEU 162 A LEU 162 1_555 A N MSE 163 A MSE 163 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale6 A C MSE 163 A MSE 163 1_555 A N SER 164 A SER 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 A C GLY 195 A GLY 195 1_555 A N MSE 196 A MSE 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 A C MSE 196 A MSE 196 1_555 A N LEU 197 A LEU 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 A C ARG 307 A ARG 307 1_555 A N MSE 308 A MSE 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale10 A C MSE 308 A MSE 308 1_555 A N LEU 309 A LEU 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 A C PHE 311 A PHE 311 1_555 A N MSE 312 A MSE 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale12 A C MSE 312 A MSE 312 1_555 A N GLY 313 A GLY 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? # _chem_comp.formula 'C15 H23 N7 O5' _chem_comp.formula_weight 381.387 _chem_comp.id SFG _chem_comp.mon_nstd_flag . _chem_comp.name SINEFUNGIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ADENOSYL-ORNITHINE # 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 SFG sing 315 n n N HN1 SFG sing 316 n n N HN2 SFG sing 317 n n CA C SFG sing 318 n n CA CB SFG sing 319 n n CA HA SFG sing 320 n n C O SFG doub 321 n n C OXT SFG sing 322 n n OXT HXT SFG sing 323 n n CB CG SFG sing 324 n n CB HB1 SFG sing 325 n n CB HB2 SFG sing 326 n n CG CD SFG sing 327 n n CG HG1 SFG sing 328 n n CG HG2 SFG sing 329 n n CD NE SFG sing 330 n n CD C5' SFG sing 331 n n CD HD SFG sing 332 n n NE HNE1 SFG sing 333 n n NE HNE2 SFG sing 334 n n C5' C4' SFG sing 335 n n C5' "H5'1" SFG sing 336 n n C5' "H5'2" SFG sing 337 n n C4' O4' SFG sing 338 n n C4' C3' SFG sing 339 n n C4' H4' SFG sing 340 n n O4' C1' SFG sing 341 n n C3' O3' SFG sing 342 n n C3' C2' SFG sing 343 n n C3' H3' SFG sing 344 n n O3' HO3' SFG sing 345 n n C2' O2' SFG sing 346 n n C2' C1' SFG sing 347 n n C2' H2' SFG sing 348 n n O2' HO2' SFG sing 349 n n C1' N9 SFG sing 350 n n C1' H1' SFG sing 351 n n N9 C8 SFG sing 352 n y N9 C4 SFG sing 353 n y C8 N7 SFG doub 354 n y C8 H8 SFG sing 355 n n N7 C5 SFG sing 356 n y C5 C6 SFG sing 357 n y C5 C4 SFG doub 358 n y C6 N6 SFG sing 359 n n C6 N1 SFG doub 360 n y N6 HN61 SFG sing 361 n n N6 HN62 SFG sing 362 n n N1 C2 SFG sing 363 n y C2 N3 SFG doub 364 n y C2 H2 SFG sing 365 n n N3 C4 SFG sing 366 n y # _atom_sites.entry_id 1XDU _atom_sites.fract_transf_matrix[1][1] 0.015934 _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] 0.011519 _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] 0.008518 _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 ACT A 1 421 421 ACT ACT . C 3 SFG A 1 5635 5635 SFG SFG . D 4 HOH A 1 5636 2 HOH HOH . D 4 HOH A 2 5637 3 HOH HOH . D 4 HOH A 3 5638 4 HOH HOH . D 4 HOH A 4 5639 6 HOH HOH . D 4 HOH A 5 5640 7 HOH HOH . D 4 HOH A 6 5641 9 HOH HOH . D 4 HOH A 7 5642 10 HOH HOH . D 4 HOH A 8 5643 14 HOH HOH . D 4 HOH A 9 5644 15 HOH HOH . D 4 HOH A 10 5645 25 HOH HOH . D 4 HOH A 11 5646 29 HOH HOH . D 4 HOH A 12 5647 30 HOH HOH . D 4 HOH A 13 5648 36 HOH HOH . D 4 HOH A 14 5649 38 HOH HOH . D 4 HOH A 15 5650 46 HOH HOH . D 4 HOH A 16 5651 47 HOH HOH . D 4 HOH A 17 5652 48 HOH HOH . D 4 HOH A 18 5653 56 HOH HOH . D 4 HOH A 19 5654 58 HOH HOH . D 4 HOH A 20 5655 59 HOH HOH . D 4 HOH A 21 5656 61 HOH HOH . D 4 HOH A 22 5657 63 HOH HOH . D 4 HOH A 23 5658 64 HOH HOH . D 4 HOH A 24 5659 67 HOH HOH . D 4 HOH A 25 5660 69 HOH HOH . D 4 HOH A 26 5661 77 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 SFG . . . C 3 6.356 58.326 45.026 1 18.93 ? N SFG 5635 A 1 HETATM 2 C CA SFG . . . C 3 6.822 57.832 43.738 1 19.37 ? CA SFG 5635 A 1 HETATM 3 C C SFG . . . C 3 6.353 56.41 43.569 1 19.34 ? C SFG 5635 A 1 HETATM 4 O O SFG . . . C 3 5.299 56.046 44.073 1 19.4 ? O SFG 5635 A 1 HETATM 5 O OXT SFG . . . C 3 7.082 55.538 42.883 1 19.12 ? OXT SFG 5635 A 1 HETATM 6 C CB SFG . . . C 3 8.354 57.922 43.688 1 19.41 ? CB SFG 5635 A 1 HETATM 7 C CG SFG . . . C 3 8.893 58.269 42.303 1 19.53 ? CG SFG 5635 A 1 HETATM 8 C CD SFG . . . C 3 10.415 58.485 42.291 1 20.97 ? CD SFG 5635 A 1 HETATM 9 N NE SFG . . . C 3 11.074 57.261 42.716 1 20.51 ? NE SFG 5635 A 1 HETATM 10 C C5' SFG . . . C 3 10.904 59.665 43.158 1 22.47 ? C5' SFG 5635 A 1 HETATM 11 C C4' SFG . . . C 3 10.168 60.975 42.861 1 23.29 ? C4' SFG 5635 A 1 HETATM 12 O O4' SFG . . . C 3 10.491 62.094 43.709 1 24.23 ? O4' SFG 5635 A 1 HETATM 13 C C3' SFG . . . C 3 10.39 61.416 41.425 1 23.8 ? C3' SFG 5635 A 1 HETATM 14 O O3' SFG . . . C 3 9.163 61.29 40.722 1 23.68 ? O3' SFG 5635 A 1 HETATM 15 C C2' SFG . . . C 3 10.843 62.861 41.462 1 24.01 ? C2' SFG 5635 A 1 HETATM 16 O O2' SFG . . . C 3 10.083 63.704 40.616 1 25.23 ? O2' SFG 5635 A 1 HETATM 17 C C1' SFG . . . C 3 10.772 63.272 42.93 1 24.25 ? C1' SFG 5635 A 1 HETATM 18 N N9 SFG . . . C 3 11.891 64.159 43.33 1 24.09 ? N9 SFG 5635 A 1 HETATM 19 C C8 SFG . . . C 3 13.209 64.052 43.057 1 24.35 ? C8 SFG 5635 A 1 HETATM 20 N N7 SFG . . . C 3 13.937 65.097 43.561 1 24.16 ? N7 SFG 5635 A 1 HETATM 21 C C5 SFG . . . C 3 13.062 65.912 44.162 1 24.28 ? C5 SFG 5635 A 1 HETATM 22 C C6 SFG . . . C 3 13.055 67.189 44.91 1 24.82 ? C6 SFG 5635 A 1 HETATM 23 N N6 SFG . . . C 3 14.228 67.823 45.115 1 25.4 ? N6 SFG 5635 A 1 HETATM 24 N N1 SFG . . . C 3 11.881 67.687 45.376 1 24.99 ? N1 SFG 5635 A 1 HETATM 25 C C2 SFG . . . C 3 10.692 67.073 45.184 1 25.09 ? C2 SFG 5635 A 1 HETATM 26 N N3 SFG . . . C 3 10.575 65.908 44.515 1 25.04 ? N3 SFG 5635 A 1 HETATM 27 C C4 SFG . . . C 3 11.768 65.298 43.982 1 24.01 ? C4 SFG 5635 A 1 # _model_server_stats.io_time_ms 38 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 256 _model_server_stats.encode_time_ms 42 _model_server_stats.element_count 27 #