data_3SW9 # _model_server_result.job_id S5_CsZCBkyXg4iEBSZ8gkw _model_server_result.datetime_utc '2024-11-04 23:45:31' _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 3sw9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":101}' # _entry.id 3SW9 # _exptl.entry_id 3SW9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 381.387 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SINEFUNGIN _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 3SW9 _cell.length_a 80.14 _cell.length_b 91.14 _cell.length_c 95.07 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SW9 _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA tetrameric 4 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,O 1 1 C,D,J,K,L,M,N,P,Q 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q 3 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 ? 4 I N N ? 4 N 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 E ZN ZN . A ZN 1 1_555 A SG CYS 81 A CYS 1031 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc2 E ZN ZN . A ZN 1 1_555 A SG CYS 94 A CYS 1044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc3 E ZN ZN . A ZN 1 1_555 A SG CYS 124 A CYS 1074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc4 E ZN ZN . A ZN 1 1_555 A SG CYS 128 A CYS 1078 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc5 F ZN ZN . A ZN 2 1_555 A SG CYS 87 A CYS 1037 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc6 F ZN ZN . A ZN 2 1_555 A SG CYS 124 A CYS 1074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc7 F ZN ZN . A ZN 2 1_555 A SG CYS 130 A CYS 1080 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc8 F ZN ZN . A ZN 2 1_555 A SG CYS 134 A CYS 1084 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc9 G ZN ZN . A ZN 3 1_555 A SG CYS 81 A CYS 1031 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc10 G ZN ZN . A ZN 3 1_555 A SG CYS 83 A CYS 1033 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc11 G ZN ZN . A ZN 3 1_555 A SG CYS 87 A CYS 1037 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc12 G ZN ZN . A ZN 3 1_555 A SG CYS 92 A CYS 1042 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc13 H ZN ZN . A ZN 4 1_555 A SG CYS 222 A CYS 1172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc14 H ZN ZN . A ZN 4 1_555 A SG CYS 275 A CYS 1225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc15 H ZN ZN . A ZN 4 1_555 A SG CYS 277 A CYS 1227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc16 H ZN ZN . A ZN 4 1_555 A SG CYS 282 A CYS 1232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.611 ? metalc ? metalc17 J ZN ZN . B ZN 5 1_555 C SG CYS 81 B CYS 1031 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc18 J ZN ZN . B ZN 5 1_555 C SG CYS 94 B CYS 1044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc19 J ZN ZN . B ZN 5 1_555 C SG CYS 124 B CYS 1074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc20 J ZN ZN . B ZN 5 1_555 C SG CYS 128 B CYS 1078 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? metalc ? metalc21 K ZN ZN . B ZN 6 1_555 C SG CYS 87 B CYS 1037 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc22 K ZN ZN . B ZN 6 1_555 C SG CYS 124 B CYS 1074 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc23 K ZN ZN . B ZN 6 1_555 C SG CYS 130 B CYS 1080 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc24 K ZN ZN . B ZN 6 1_555 C SG CYS 134 B CYS 1084 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc25 L ZN ZN . B ZN 7 1_555 C SG CYS 81 B CYS 1031 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc26 L ZN ZN . B ZN 7 1_555 C SG CYS 83 B CYS 1033 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc27 L ZN ZN . B ZN 7 1_555 C SG CYS 87 B CYS 1037 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc28 L ZN ZN . B ZN 7 1_555 C SG CYS 92 B CYS 1042 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc29 M ZN ZN . B ZN 8 1_555 C SG CYS 222 B CYS 1172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? metalc ? metalc30 M ZN ZN . B ZN 8 1_555 C SG CYS 275 B CYS 1225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc31 M ZN ZN . B ZN 8 1_555 C SG CYS 277 B CYS 1227 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc32 M ZN ZN . B ZN 8 1_555 C SG CYS 282 B CYS 1232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? # _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 290 n n N HN1 SFG sing 291 n n N HN2 SFG sing 292 n n CA C SFG sing 293 n n CA CB SFG sing 294 n n CA HA SFG sing 295 n n C O SFG doub 296 n n C OXT SFG sing 297 n n OXT HXT SFG sing 298 n n CB CG SFG sing 299 n n CB HB1 SFG sing 300 n n CB HB2 SFG sing 301 n n CG CD SFG sing 302 n n CG HG1 SFG sing 303 n n CG HG2 SFG sing 304 n n CD NE SFG sing 305 n n CD C5' SFG sing 306 n n CD HD SFG sing 307 n n NE HNE1 SFG sing 308 n n NE HNE2 SFG sing 309 n n C5' C4' SFG sing 310 n n C5' "H5'1" SFG sing 311 n n C5' "H5'2" SFG sing 312 n n C4' O4' SFG sing 313 n n C4' C3' SFG sing 314 n n C4' H4' SFG sing 315 n n O4' C1' SFG sing 316 n n C3' O3' SFG sing 317 n n C3' C2' SFG sing 318 n n C3' H3' SFG sing 319 n n O3' HO3' SFG sing 320 n n C2' O2' SFG sing 321 n n C2' C1' SFG sing 322 n n C2' H2' SFG sing 323 n n O2' HO2' SFG sing 324 n n C1' N9 SFG sing 325 n n C1' H1' SFG sing 326 n n N9 C8 SFG sing 327 n y N9 C4 SFG sing 328 n y C8 N7 SFG doub 329 n y C8 H8 SFG sing 330 n n N7 C5 SFG sing 331 n y C5 C6 SFG sing 332 n y C5 C4 SFG doub 333 n y C6 N6 SFG sing 334 n n C6 N1 SFG doub 335 n y N6 HN61 SFG sing 336 n n N6 HN62 SFG sing 337 n n N1 C2 SFG sing 338 n y C2 N3 SFG doub 339 n y C2 H2 SFG sing 340 n n N3 C4 SFG sing 341 n y # _atom_sites.entry_id 3SW9 _atom_sites.fract_transf_matrix[1][1] 0.012478 _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] 0.010972 _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] 0.010519 _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 E 3 ZN A 1 1 1 ZN ZN . F 3 ZN A 1 2 2 ZN ZN . G 3 ZN A 1 3 3 ZN ZN . H 3 ZN A 1 4 4 ZN ZN . I 4 SFG A 1 101 101 SFG SFG . J 3 ZN B 1 5 5 ZN ZN . K 3 ZN B 1 6 6 ZN ZN . L 3 ZN B 1 7 7 ZN ZN . M 3 ZN B 1 8 8 ZN ZN . N 4 SFG B 1 102 102 SFG SFG . O 5 HOH A 1 206 206 HOH HOH . O 5 HOH A 2 210 210 HOH HOH . O 5 HOH A 3 211 211 HOH HOH . O 5 HOH A 4 212 212 HOH HOH . O 5 HOH A 5 219 219 HOH HOH . O 5 HOH A 6 220 220 HOH HOH . O 5 HOH A 7 221 221 HOH HOH . O 5 HOH A 8 222 222 HOH HOH . P 5 HOH B 1 201 201 HOH HOH . P 5 HOH B 2 202 202 HOH HOH . P 5 HOH B 3 203 203 HOH HOH . P 5 HOH B 4 204 204 HOH HOH . P 5 HOH B 5 205 205 HOH HOH . P 5 HOH B 6 207 207 HOH HOH . P 5 HOH B 7 208 208 HOH HOH . P 5 HOH B 8 209 209 HOH HOH . P 5 HOH B 9 213 213 HOH HOH . P 5 HOH B 10 214 214 HOH HOH . P 5 HOH B 11 215 215 HOH HOH . P 5 HOH B 12 217 217 HOH HOH . P 5 HOH B 13 218 218 HOH HOH . P 5 HOH B 14 223 223 HOH HOH . Q 5 HOH Q 1 216 216 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 . . . I 4 23.931 -33.698 10.25 1 50.12 ? N SFG 101 A 1 HETATM 2 C CA SFG . . . I 4 24.004 -32.258 10.537 1 50.14 ? CA SFG 101 A 1 HETATM 3 C C SFG . . . I 4 23.13 -31.804 11.719 1 49.54 ? C SFG 101 A 1 HETATM 4 O O SFG . . . I 4 22.469 -32.681 12.333 1 46.88 ? O SFG 101 A 1 HETATM 5 O OXT SFG . . . I 4 23.166 -30.593 12.054 1 42.8 ? OXT SFG 101 A 1 HETATM 6 C CB SFG . . . I 4 23.87 -31.364 9.255 1 41.99 ? CB SFG 101 A 1 HETATM 7 C CG SFG . . . I 4 25.197 -31.545 8.444 1 40.85 ? CG SFG 101 A 1 HETATM 8 C CD SFG . . . I 4 26.368 -30.664 8.948 1 38.88 ? CD SFG 101 A 1 HETATM 9 N NE SFG . . . I 4 26.593 -29.453 8.09 1 44.04 ? NE SFG 101 A 1 HETATM 10 C C5' SFG . . . I 4 27.646 -31.5 8.77 1 45.84 ? C5' SFG 101 A 1 HETATM 11 C C4' SFG . . . I 4 27.812 -32.538 9.921 1 50.68 ? C4' SFG 101 A 1 HETATM 12 O O4' SFG . . . I 4 26.924 -33.648 9.733 1 54.68 ? O4' SFG 101 A 1 HETATM 13 C C3' SFG . . . I 4 29.208 -33.163 10.113 1 51.88 ? C3' SFG 101 A 1 HETATM 14 O O3' SFG . . . I 4 29.973 -32.387 11.019 1 43.8 ? O3' SFG 101 A 1 HETATM 15 C C2' SFG . . . I 4 28.868 -34.585 10.557 1 43.96 ? C2' SFG 101 A 1 HETATM 16 O O2' SFG . . . I 4 28.626 -34.68 11.976 1 45.13 ? O2' SFG 101 A 1 HETATM 17 C C1' SFG . . . I 4 27.568 -34.926 9.813 1 47.46 ? C1' SFG 101 A 1 HETATM 18 N N9 SFG . . . I 4 27.61 -35.522 8.451 1 46.2 ? N9 SFG 101 A 1 HETATM 19 C C8 SFG . . . I 4 27.408 -35.017 7.195 1 45.08 ? C8 SFG 101 A 1 HETATM 20 N N7 SFG . . . I 4 27.473 -35.887 6.178 1 43.83 ? N7 SFG 101 A 1 HETATM 21 C C5 SFG . . . I 4 27.77 -37.087 6.81 1 47.17 ? C5 SFG 101 A 1 HETATM 22 C C6 SFG . . . I 4 27.997 -38.423 6.421 1 45.88 ? C6 SFG 101 A 1 HETATM 23 N N6 SFG . . . I 4 27.931 -38.745 5.104 1 43.32 ? N6 SFG 101 A 1 HETATM 24 N N1 SFG . . . I 4 28.296 -39.41 7.355 1 47.12 ? N1 SFG 101 A 1 HETATM 25 C C2 SFG . . . I 4 28.365 -39.131 8.699 1 46.33 ? C2 SFG 101 A 1 HETATM 26 N N3 SFG . . . I 4 28.137 -37.855 9.149 1 47.15 ? N3 SFG 101 A 1 HETATM 27 C C4 SFG . . . I 4 27.857 -36.866 8.219 1 47.98 ? C4 SFG 101 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #