data_4PYL # _model_server_result.job_id 4TBpJdHrDWLOWVhLRhwvbw _model_server_result.datetime_utc '2024-11-22 16:33:10' _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 4pyl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 4PYL # _exptl.entry_id 4PYL _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 120 _cell.entry_id 4PYL _cell.length_a 49.813 _cell.length_b 49.813 _cell.length_c 167.467 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PYL _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _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 metalc ? metalc1 A OD1 ASP 141 A ASP 184 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc2 A OD2 ASP 169 A ASP 212 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc3 A OD1 ASN 170 A ASN 213 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc4 B MG MG . A MG 301 1_555 D O7 TCW . A TCW 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc5 B MG MG . A MG 301 1_555 D O8 TCW . A TCW 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc6 B MG MG . A MG 301 1_555 E O HOH . A HOH 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? # _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 4PYL _atom_sites.fract_transf_matrix[1][1] 0.020075 _atom_sites.fract_transf_matrix[1][2] 0.01159 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023181 _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] 0.005971 _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 MG A 1 301 550 MG MG . C 3 SFG A 1 302 301 SFG SFG . D 4 TCW A 1 303 302 TCW TCW . E 5 HOH A 1 401 1 HOH HOH . E 5 HOH A 2 402 2 HOH HOH . E 5 HOH A 3 403 3 HOH HOH . E 5 HOH A 4 404 4 HOH HOH . E 5 HOH A 5 405 5 HOH HOH . E 5 HOH A 6 406 6 HOH HOH . E 5 HOH A 7 407 7 HOH HOH . E 5 HOH A 8 408 8 HOH HOH . E 5 HOH A 9 409 9 HOH HOH . E 5 HOH A 10 410 10 HOH HOH . E 5 HOH A 11 411 11 HOH HOH . E 5 HOH A 12 412 12 HOH HOH . E 5 HOH A 13 413 13 HOH HOH . E 5 HOH A 14 414 14 HOH HOH . E 5 HOH A 15 415 15 HOH HOH . E 5 HOH A 16 416 16 HOH HOH . E 5 HOH A 17 417 17 HOH HOH . E 5 HOH A 18 418 18 HOH HOH . E 5 HOH A 19 419 19 HOH HOH . E 5 HOH A 20 420 20 HOH HOH . E 5 HOH A 21 421 21 HOH HOH . E 5 HOH A 22 422 22 HOH HOH . E 5 HOH A 23 423 23 HOH HOH . E 5 HOH A 24 424 24 HOH HOH . E 5 HOH A 25 425 25 HOH HOH . E 5 HOH A 26 426 26 HOH HOH . E 5 HOH A 27 427 27 HOH HOH . E 5 HOH A 28 428 28 HOH HOH . E 5 HOH A 29 429 29 HOH HOH . E 5 HOH A 30 430 30 HOH HOH . E 5 HOH A 31 431 31 HOH HOH . E 5 HOH A 32 432 32 HOH HOH . E 5 HOH A 33 433 33 HOH HOH . E 5 HOH A 34 434 34 HOH HOH . E 5 HOH A 35 435 35 HOH HOH . E 5 HOH A 36 436 36 HOH HOH . E 5 HOH A 37 437 37 HOH HOH . E 5 HOH A 38 438 38 HOH HOH . E 5 HOH A 39 439 39 HOH HOH . E 5 HOH A 40 440 40 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 -20.446 22.783 12.237 1 34.24 ? N SFG 302 A 1 HETATM 2 C CA SFG . . . C 3 -21.633 23.455 12.87 1 39.83 ? CA SFG 302 A 1 HETATM 3 C C SFG . . . C 3 -22.79 22.494 12.88 1 44.86 ? C SFG 302 A 1 HETATM 4 O O SFG . . . C 3 -23.333 22.218 13.999 1 52.11 ? O SFG 302 A 1 HETATM 5 O OXT SFG . . . C 3 -23.184 22 11.778 1 44.02 ? OXT SFG 302 A 1 HETATM 6 C CB SFG . . . C 3 -22.018 24.763 12.137 1 40.98 ? CB SFG 302 A 1 HETATM 7 C CG SFG . . . C 3 -20.806 25.734 11.999 1 39.35 ? CG SFG 302 A 1 HETATM 8 C CD SFG . . . C 3 -21.26 27.045 11.301 1 28.67 ? CD SFG 302 A 1 HETATM 9 N NE SFG . . . C 3 -21.784 26.759 9.914 1 26.26 ? NE SFG 302 A 1 HETATM 10 C C5' SFG . . . C 3 -20.102 28.047 11.149 1 31.49 ? C5' SFG 302 A 1 HETATM 11 C C4' SFG . . . C 3 -19.54 28.424 12.53 1 38.02 ? C4' SFG 302 A 1 HETATM 12 O O4' SFG . . . C 3 -18.136 28.629 12.396 1 33.28 ? O4' SFG 302 A 1 HETATM 13 C C3' SFG . . . C 3 -20.12 29.723 13.128 1 46.26 ? C3' SFG 302 A 1 HETATM 14 O O3' SFG . . . C 3 -20.707 29.43 14.42 1 48.07 ? O3' SFG 302 A 1 HETATM 15 C C2' SFG . . . C 3 -18.878 30.644 13.201 1 44.77 ? C2' SFG 302 A 1 HETATM 16 O O2' SFG . . . C 3 -18.912 31.603 14.26 1 43.4 ? O2' SFG 302 A 1 HETATM 17 C C1' SFG . . . C 3 -17.711 29.65 13.303 1 31.54 ? C1' SFG 302 A 1 HETATM 18 N N9 SFG . . . C 3 -16.504 30.165 12.636 1 35.89 ? N9 SFG 302 A 1 HETATM 19 C C8 SFG . . . C 3 -16.448 30.864 11.4 1 33.97 ? C8 SFG 302 A 1 HETATM 20 N N7 SFG . . . C 3 -15.226 31.151 11.034 1 31.58 ? N7 SFG 302 A 1 HETATM 21 C C5 SFG . . . C 3 -14.428 30.616 12.021 1 20.81 ? C5 SFG 302 A 1 HETATM 22 C C6 SFG . . . C 3 -13.029 30.608 12.183 1 33.15 ? C6 SFG 302 A 1 HETATM 23 N N6 SFG . . . C 3 -12.182 31.214 11.258 1 42.53 ? N6 SFG 302 A 1 HETATM 24 N N1 SFG . . . C 3 -12.496 30.015 13.252 1 41.7 ? N1 SFG 302 A 1 HETATM 25 C C2 SFG . . . C 3 -13.321 29.431 14.162 1 37.54 ? C2 SFG 302 A 1 HETATM 26 N N3 SFG . . . C 3 -14.641 29.41 14.085 1 31.94 ? N3 SFG 302 A 1 HETATM 27 C C4 SFG . . . C 3 -15.162 30.008 13.008 1 29.5 ? C4 SFG 302 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #