data_8X4P # _model_server_result.job_id Wc1jeJoMADTrmtXbaD4b-A _model_server_result.datetime_utc '2024-11-22 07:02:58' _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 8x4p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":301}' # _entry.id 8X4P # _exptl.entry_id 8X4P _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 116.28 _cell.angle_gamma 90 _cell.entry_id 8X4P _cell.length_a 119.06 _cell.length_b 79.96 _cell.length_c 85.41 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8X4P _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,E,F,G,I 1 1 B,H,J 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 ? 3 G N N ? 3 H 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 A OE1 GLU 160 A GLU 160 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc2 A OE1 GLU 188 A GLU 188 1_555 E ZN ZN . A ZN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc3 A NE2 HIS 245 A HIS 245 1_555 F ZN ZN . A ZN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc4 A ND1 HIS 263 A HIS 263 1_555 C ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc5 D ZN ZN . A ZN 302 1_555 B NE2 HIS 245 B HIS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc6 E ZN ZN . A ZN 303 4_546 B NE2 HIS 286 B HIS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc7 F ZN ZN . A ZN 304 1_555 B OE1 GLU 160 B GLU 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? # _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 277 n n N HN1 SFG sing 278 n n N HN2 SFG sing 279 n n CA C SFG sing 280 n n CA CB SFG sing 281 n n CA HA SFG sing 282 n n C O SFG doub 283 n n C OXT SFG sing 284 n n OXT HXT SFG sing 285 n n CB CG SFG sing 286 n n CB HB1 SFG sing 287 n n CB HB2 SFG sing 288 n n CG CD SFG sing 289 n n CG HG1 SFG sing 290 n n CG HG2 SFG sing 291 n n CD NE SFG sing 292 n n CD C5' SFG sing 293 n n CD HD SFG sing 294 n n NE HNE1 SFG sing 295 n n NE HNE2 SFG sing 296 n n C5' C4' SFG sing 297 n n C5' "H5'1" SFG sing 298 n n C5' "H5'2" SFG sing 299 n n C4' O4' SFG sing 300 n n C4' C3' SFG sing 301 n n C4' H4' SFG sing 302 n n O4' C1' SFG sing 303 n n C3' O3' SFG sing 304 n n C3' C2' SFG sing 305 n n C3' H3' SFG sing 306 n n O3' HO3' SFG sing 307 n n C2' O2' SFG sing 308 n n C2' C1' SFG sing 309 n n C2' H2' SFG sing 310 n n O2' HO2' SFG sing 311 n n C1' N9 SFG sing 312 n n C1' H1' SFG sing 313 n n N9 C8 SFG sing 314 n y N9 C4 SFG sing 315 n y C8 N7 SFG doub 316 n y C8 H8 SFG sing 317 n n N7 C5 SFG sing 318 n y C5 C6 SFG sing 319 n y C5 C4 SFG doub 320 n y C6 N6 SFG sing 321 n n C6 N1 SFG doub 322 n y N6 HN61 SFG sing 323 n n N6 HN62 SFG sing 324 n n N1 C2 SFG sing 325 n y C2 N3 SFG doub 326 n y C2 H2 SFG sing 327 n n N3 C4 SFG sing 328 n y # _atom_sites.entry_id 8X4P _atom_sites.fract_transf_matrix[1][1] 0.008399 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004147 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012506 _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] 0.013058 _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 ZN A 1 301 1 ZN ZN . D 2 ZN A 1 302 2 ZN ZN . E 2 ZN A 1 303 3 ZN ZN . F 2 ZN A 1 304 4 ZN ZN . G 3 SFG A 1 305 5 SFG SFG . H 3 SFG B 1 301 6 SFG SFG . I 4 HOH A 1 401 7 HOH HOH . I 4 HOH A 2 402 64 HOH HOH . I 4 HOH A 3 403 17 HOH HOH . I 4 HOH A 4 404 15 HOH HOH . I 4 HOH A 5 405 29 HOH HOH . I 4 HOH A 6 406 3 HOH HOH . I 4 HOH A 7 407 65 HOH HOH . I 4 HOH A 8 408 24 HOH HOH . I 4 HOH A 9 409 31 HOH HOH . I 4 HOH A 10 410 20 HOH HOH . I 4 HOH A 11 411 22 HOH HOH . I 4 HOH A 12 412 35 HOH HOH . I 4 HOH A 13 413 78 HOH HOH . I 4 HOH A 14 414 4 HOH HOH . I 4 HOH A 15 415 76 HOH HOH . I 4 HOH A 16 416 5 HOH HOH . I 4 HOH A 17 417 33 HOH HOH . I 4 HOH A 18 418 34 HOH HOH . I 4 HOH A 19 419 30 HOH HOH . I 4 HOH A 20 420 11 HOH HOH . I 4 HOH A 21 421 6 HOH HOH . I 4 HOH A 22 422 79 HOH HOH . I 4 HOH A 23 423 80 HOH HOH . I 4 HOH A 24 424 8 HOH HOH . I 4 HOH A 25 425 9 HOH HOH . I 4 HOH A 26 426 82 HOH HOH . I 4 HOH A 27 427 67 HOH HOH . I 4 HOH A 28 428 25 HOH HOH . I 4 HOH A 29 429 81 HOH HOH . I 4 HOH A 30 430 27 HOH HOH . I 4 HOH A 31 431 26 HOH HOH . I 4 HOH A 32 432 18 HOH HOH . I 4 HOH A 33 433 1 HOH HOH . I 4 HOH A 34 434 23 HOH HOH . I 4 HOH A 35 435 77 HOH HOH . I 4 HOH A 36 436 2 HOH HOH . I 4 HOH A 37 437 66 HOH HOH . I 4 HOH A 38 438 14 HOH HOH . I 4 HOH A 39 439 21 HOH HOH . I 4 HOH A 40 440 36 HOH HOH . I 4 HOH A 41 441 83 HOH HOH . I 4 HOH A 42 442 72 HOH HOH . I 4 HOH A 43 443 75 HOH HOH . I 4 HOH A 44 444 32 HOH HOH . I 4 HOH A 45 445 73 HOH HOH . I 4 HOH A 46 446 48 HOH HOH . I 4 HOH A 47 447 28 HOH HOH . J 4 HOH B 1 401 85 HOH HOH . J 4 HOH B 2 402 97 HOH HOH . J 4 HOH B 3 403 86 HOH HOH . J 4 HOH B 4 404 40 HOH HOH . J 4 HOH B 5 405 98 HOH HOH . J 4 HOH B 6 406 62 HOH HOH . J 4 HOH B 7 407 55 HOH HOH . J 4 HOH B 8 408 89 HOH HOH . J 4 HOH B 9 409 54 HOH HOH . J 4 HOH B 10 410 37 HOH HOH . J 4 HOH B 11 411 46 HOH HOH . J 4 HOH B 12 412 38 HOH HOH . J 4 HOH B 13 413 51 HOH HOH . J 4 HOH B 14 414 45 HOH HOH . J 4 HOH B 15 415 59 HOH HOH . J 4 HOH B 16 416 100 HOH HOH . J 4 HOH B 17 417 94 HOH HOH . J 4 HOH B 18 418 60 HOH HOH . J 4 HOH B 19 419 90 HOH HOH . J 4 HOH B 20 420 88 HOH HOH . J 4 HOH B 21 421 56 HOH HOH . J 4 HOH B 22 422 53 HOH HOH . J 4 HOH B 23 423 50 HOH HOH . J 4 HOH B 24 424 63 HOH HOH . J 4 HOH B 25 425 70 HOH HOH . J 4 HOH B 26 426 42 HOH HOH . J 4 HOH B 27 427 41 HOH HOH . J 4 HOH B 28 428 74 HOH HOH . J 4 HOH B 29 429 102 HOH HOH . J 4 HOH B 30 430 52 HOH HOH . J 4 HOH B 31 431 92 HOH HOH . J 4 HOH B 32 432 47 HOH HOH . J 4 HOH B 33 433 19 HOH HOH . J 4 HOH B 34 434 12 HOH HOH . J 4 HOH B 35 435 87 HOH HOH . J 4 HOH B 36 436 91 HOH HOH . J 4 HOH B 37 437 39 HOH HOH . J 4 HOH B 38 438 68 HOH HOH . J 4 HOH B 39 439 101 HOH HOH . J 4 HOH B 40 440 43 HOH HOH . J 4 HOH B 41 441 58 HOH HOH . J 4 HOH B 42 442 61 HOH HOH . J 4 HOH B 43 443 71 HOH HOH . J 4 HOH B 44 444 16 HOH HOH . J 4 HOH B 45 445 57 HOH HOH . J 4 HOH B 46 446 44 HOH HOH . J 4 HOH B 47 447 84 HOH HOH . J 4 HOH B 48 448 95 HOH HOH . J 4 HOH B 49 449 93 HOH HOH . J 4 HOH B 50 450 69 HOH HOH . J 4 HOH B 51 451 99 HOH HOH . J 4 HOH B 52 452 13 HOH HOH . J 4 HOH B 53 453 10 HOH HOH . J 4 HOH B 54 454 96 HOH HOH . J 4 HOH B 55 455 49 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 . . . H 3 27.693 -17.308 -4.003 1 45.84 ? N SFG 301 B 1 HETATM 2 C CA SFG . . . H 3 26.916 -16.043 -3.918 1 51.42 ? CA SFG 301 B 1 HETATM 3 C C SFG . . . H 3 27.079 -15.49 -2.5 1 62.08 ? C SFG 301 B 1 HETATM 4 O O SFG . . . H 3 26.243 -14.636 -2.111 1 78.12 ? O SFG 301 B 1 HETATM 5 O OXT SFG . . . H 3 28.045 -15.927 -1.843 1 65.45 ? OXT SFG 301 B 1 HETATM 6 C CB SFG . . . H 3 25.442 -16.236 -4.313 1 46.73 ? CB SFG 301 B 1 HETATM 7 C CG SFG . . . H 3 24.796 -14.974 -4.894 1 45.05 ? CG SFG 301 B 1 HETATM 8 C CD SFG . . . H 3 23.275 -14.967 -5.042 1 44.9 ? CD SFG 301 B 1 HETATM 9 N NE SFG . . . H 3 22.826 -16.23 -5.712 1 44.5 ? NE SFG 301 B 1 HETATM 10 C C5' SFG . . . H 3 22.776 -13.755 -5.848 1 46.43 ? C5' SFG 301 B 1 HETATM 11 C C4' SFG . . . H 3 21.285 -13.422 -5.741 1 46.47 ? C4' SFG 301 B 1 HETATM 12 O O4' SFG . . . H 3 20.826 -14.063 -4.528 1 44.71 ? O4' SFG 301 B 1 HETATM 13 C C3' SFG . . . H 3 20.882 -11.93 -5.633 1 43.96 ? C3' SFG 301 B 1 HETATM 14 O O3' SFG . . . H 3 19.94 -11.456 -6.593 1 42.78 ? O3' SFG 301 B 1 HETATM 15 C C2' SFG . . . H 3 20.06 -11.859 -4.346 1 42.43 ? C2' SFG 301 B 1 HETATM 16 O O2' SFG . . . H 3 18.87 -11.132 -4.525 1 32.31 ? O2' SFG 301 B 1 HETATM 17 C C1' SFG . . . H 3 19.723 -13.325 -4.072 1 44.93 ? C1' SFG 301 B 1 HETATM 18 N N9 SFG . . . H 3 19.536 -13.601 -2.659 1 43.68 ? N9 SFG 301 B 1 HETATM 19 C C8 SFG . . . H 3 20.43 -13.301 -1.664 1 42.61 ? C8 SFG 301 B 1 HETATM 20 N N7 SFG . . . H 3 19.992 -13.639 -0.479 1 50.22 ? N7 SFG 301 B 1 HETATM 21 C C5 SFG . . . H 3 18.733 -14.184 -0.704 1 44.23 ? C5 SFG 301 B 1 HETATM 22 C C6 SFG . . . H 3 17.765 -14.72 0.166 1 48.71 ? C6 SFG 301 B 1 HETATM 23 N N6 SFG . . . H 3 17.917 -14.804 1.493 1 47.98 ? N6 SFG 301 B 1 HETATM 24 N N1 SFG . . . H 3 16.621 -15.183 -0.4 1 53.39 ? N1 SFG 301 B 1 HETATM 25 C C2 SFG . . . H 3 16.481 -15.122 -1.732 1 48.8 ? C2 SFG 301 B 1 HETATM 26 N N3 SFG . . . H 3 17.327 -14.644 -2.64 1 48.96 ? N3 SFG 301 B 1 HETATM 27 C C4 SFG . . . H 3 18.444 -14.176 -2.054 1 44.76 ? C4 SFG 301 B 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #