data_3A4T
#
_model_server_result.job_id            NAQQVyl_mWbJs1N_5H3qKA 
_model_server_result.datetime_utc      '2025-08-31 03:55:23' 
_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          3a4t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    3A4T 
#
_exptl.entry_id    3A4T 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              381.387 
_entity.id                          2 
_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          110.84 
_cell.angle_gamma         90 
_cell.entry_id            3A4T 
_cell.length_a            170.259 
_cell.length_b            40.097 
_cell.length_c            85.951 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3A4T 
_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,E 1 1 
B,D,F 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
? 2 C N N 
? 2 D 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
disulf ? disulf1 A SG CYS 166 A CYS 166 1_555 A SG CYS 212 A CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
disulf ? disulf2 B SG CYS 166 B CYS 166 1_555 B SG CYS 212 B CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
#
_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                     3A4T 
_atom_sites.fract_transf_matrix[1][1]    0.005873 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002236 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.02494 
_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]    0.012449 
_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 SFG A 1 500 500 SFG SFG . 
D 2 SFG B 1 501 501 SFG SFG . 
E 3 HOH A 1 275 2 HOH HOH . 
E 3 HOH A 2 276 3 HOH HOH . 
E 3 HOH A 3 277 5 HOH HOH . 
E 3 HOH A 4 278 7 HOH HOH . 
E 3 HOH A 5 279 8 HOH HOH . 
E 3 HOH A 6 280 9 HOH HOH . 
E 3 HOH A 7 281 11 HOH HOH . 
E 3 HOH A 8 282 12 HOH HOH . 
E 3 HOH A 9 283 15 HOH HOH . 
E 3 HOH A 10 284 17 HOH HOH . 
E 3 HOH A 11 285 18 HOH HOH . 
E 3 HOH A 12 286 21 HOH HOH . 
E 3 HOH A 13 287 26 HOH HOH . 
E 3 HOH A 14 288 32 HOH HOH . 
E 3 HOH A 15 289 33 HOH HOH . 
E 3 HOH A 16 290 36 HOH HOH . 
E 3 HOH A 17 291 37 HOH HOH . 
E 3 HOH A 18 292 39 HOH HOH . 
E 3 HOH A 19 293 40 HOH HOH . 
E 3 HOH A 20 294 44 HOH HOH . 
E 3 HOH A 21 295 45 HOH HOH . 
E 3 HOH A 22 296 47 HOH HOH . 
E 3 HOH A 23 297 51 HOH HOH . 
E 3 HOH A 24 298 52 HOH HOH . 
E 3 HOH A 25 299 53 HOH HOH . 
E 3 HOH A 26 300 56 HOH HOH . 
E 3 HOH A 27 301 58 HOH HOH . 
E 3 HOH A 28 302 63 HOH HOH . 
E 3 HOH A 29 303 66 HOH HOH . 
E 3 HOH A 30 304 70 HOH HOH . 
E 3 HOH A 31 305 72 HOH HOH . 
E 3 HOH A 32 306 74 HOH HOH . 
E 3 HOH A 33 307 76 HOH HOH . 
E 3 HOH A 34 308 78 HOH HOH . 
E 3 HOH A 35 309 79 HOH HOH . 
E 3 HOH A 36 310 80 HOH HOH . 
E 3 HOH A 37 311 81 HOH HOH . 
E 3 HOH A 38 312 95 HOH HOH . 
E 3 HOH A 39 313 96 HOH HOH . 
E 3 HOH A 40 314 101 HOH HOH . 
E 3 HOH A 41 315 104 HOH HOH . 
E 3 HOH A 42 316 105 HOH HOH . 
E 3 HOH A 43 317 109 HOH HOH . 
E 3 HOH A 44 318 110 HOH HOH . 
E 3 HOH A 45 319 112 HOH HOH . 
E 3 HOH A 46 320 113 HOH HOH . 
E 3 HOH A 47 321 114 HOH HOH . 
E 3 HOH A 48 322 115 HOH HOH . 
E 3 HOH A 49 323 117 HOH HOH . 
E 3 HOH A 50 324 120 HOH HOH . 
E 3 HOH A 51 325 123 HOH HOH . 
E 3 HOH A 52 326 128 HOH HOH . 
E 3 HOH A 53 327 129 HOH HOH . 
E 3 HOH A 54 328 131 HOH HOH . 
E 3 HOH A 55 329 132 HOH HOH . 
E 3 HOH A 56 330 135 HOH HOH . 
E 3 HOH A 57 331 136 HOH HOH . 
E 3 HOH A 58 332 139 HOH HOH . 
E 3 HOH A 59 333 140 HOH HOH . 
E 3 HOH A 60 334 141 HOH HOH . 
E 3 HOH A 61 335 145 HOH HOH . 
E 3 HOH A 62 336 146 HOH HOH . 
E 3 HOH A 63 337 147 HOH HOH . 
E 3 HOH A 64 338 148 HOH HOH . 
E 3 HOH A 65 339 151 HOH HOH . 
E 3 HOH A 66 340 153 HOH HOH . 
E 3 HOH A 67 341 154 HOH HOH . 
E 3 HOH A 68 342 155 HOH HOH . 
E 3 HOH A 69 343 164 HOH HOH . 
E 3 HOH A 70 344 165 HOH HOH . 
F 3 HOH B 1 275 1 HOH HOH . 
F 3 HOH B 2 276 4 HOH HOH . 
F 3 HOH B 3 277 6 HOH HOH . 
F 3 HOH B 4 278 10 HOH HOH . 
F 3 HOH B 5 279 13 HOH HOH . 
F 3 HOH B 6 280 14 HOH HOH . 
F 3 HOH B 7 281 16 HOH HOH . 
F 3 HOH B 8 282 19 HOH HOH . 
F 3 HOH B 9 283 20 HOH HOH . 
F 3 HOH B 10 284 22 HOH HOH . 
F 3 HOH B 11 285 23 HOH HOH . 
F 3 HOH B 12 286 24 HOH HOH . 
F 3 HOH B 13 287 25 HOH HOH . 
F 3 HOH B 14 288 27 HOH HOH . 
F 3 HOH B 15 289 28 HOH HOH . 
F 3 HOH B 16 290 29 HOH HOH . 
F 3 HOH B 17 291 30 HOH HOH . 
F 3 HOH B 18 292 31 HOH HOH . 
F 3 HOH B 19 293 34 HOH HOH . 
F 3 HOH B 20 294 35 HOH HOH . 
F 3 HOH B 21 295 38 HOH HOH . 
F 3 HOH B 22 296 41 HOH HOH . 
F 3 HOH B 23 297 42 HOH HOH . 
F 3 HOH B 24 298 43 HOH HOH . 
F 3 HOH B 25 299 46 HOH HOH . 
F 3 HOH B 26 300 48 HOH HOH . 
F 3 HOH B 27 301 49 HOH HOH . 
F 3 HOH B 28 302 50 HOH HOH . 
F 3 HOH B 29 303 54 HOH HOH . 
F 3 HOH B 30 304 55 HOH HOH . 
F 3 HOH B 31 305 57 HOH HOH . 
F 3 HOH B 32 306 59 HOH HOH . 
F 3 HOH B 33 307 60 HOH HOH . 
F 3 HOH B 34 308 61 HOH HOH . 
F 3 HOH B 35 309 62 HOH HOH . 
F 3 HOH B 36 310 64 HOH HOH . 
F 3 HOH B 37 311 65 HOH HOH . 
F 3 HOH B 38 312 67 HOH HOH . 
F 3 HOH B 39 313 68 HOH HOH . 
F 3 HOH B 40 314 69 HOH HOH . 
F 3 HOH B 41 315 71 HOH HOH . 
F 3 HOH B 42 316 73 HOH HOH . 
F 3 HOH B 43 317 75 HOH HOH . 
F 3 HOH B 44 318 77 HOH HOH . 
F 3 HOH B 45 319 82 HOH HOH . 
F 3 HOH B 46 320 83 HOH HOH . 
F 3 HOH B 47 321 84 HOH HOH . 
F 3 HOH B 48 322 85 HOH HOH . 
F 3 HOH B 49 323 86 HOH HOH . 
F 3 HOH B 50 324 87 HOH HOH . 
F 3 HOH B 51 325 88 HOH HOH . 
F 3 HOH B 52 326 89 HOH HOH . 
F 3 HOH B 53 327 90 HOH HOH . 
F 3 HOH B 54 328 91 HOH HOH . 
F 3 HOH B 55 329 92 HOH HOH . 
F 3 HOH B 56 330 93 HOH HOH . 
F 3 HOH B 57 331 94 HOH HOH . 
F 3 HOH B 58 332 97 HOH HOH . 
F 3 HOH B 59 333 98 HOH HOH . 
F 3 HOH B 60 334 99 HOH HOH . 
F 3 HOH B 61 335 100 HOH HOH . 
F 3 HOH B 62 336 102 HOH HOH . 
F 3 HOH B 63 337 103 HOH HOH . 
F 3 HOH B 64 338 106 HOH HOH . 
F 3 HOH B 65 339 107 HOH HOH . 
F 3 HOH B 66 340 108 HOH HOH . 
F 3 HOH B 67 341 111 HOH HOH . 
F 3 HOH B 68 342 116 HOH HOH . 
F 3 HOH B 69 343 118 HOH HOH . 
F 3 HOH B 70 344 119 HOH HOH . 
F 3 HOH B 71 345 121 HOH HOH . 
F 3 HOH B 72 346 122 HOH HOH . 
F 3 HOH B 73 347 124 HOH HOH . 
F 3 HOH B 74 348 125 HOH HOH . 
F 3 HOH B 75 349 126 HOH HOH . 
F 3 HOH B 76 350 127 HOH HOH . 
F 3 HOH B 77 351 130 HOH HOH . 
F 3 HOH B 78 352 133 HOH HOH . 
F 3 HOH B 79 353 134 HOH HOH . 
F 3 HOH B 80 354 137 HOH HOH . 
F 3 HOH B 81 355 138 HOH HOH . 
F 3 HOH B 82 356 142 HOH HOH . 
F 3 HOH B 83 357 143 HOH HOH . 
F 3 HOH B 84 358 144 HOH HOH . 
F 3 HOH B 85 359 149 HOH HOH . 
F 3 HOH B 86 360 150 HOH HOH . 
F 3 HOH B 87 361 152 HOH HOH . 
F 3 HOH B 88 362 156 HOH HOH . 
F 3 HOH B 89 363 157 HOH HOH . 
F 3 HOH B 90 364 158 HOH HOH . 
F 3 HOH B 91 365 159 HOH HOH . 
F 3 HOH B 92 366 160 HOH HOH . 
F 3 HOH B 93 367 161 HOH HOH . 
F 3 HOH B 94 368 162 HOH HOH . 
F 3 HOH B 95 369 163 HOH HOH . 
F 3 HOH B 96 370 166 HOH HOH . 
F 3 HOH B 97 371 167 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 . . . D 2 52.965 -7.746 -19.894 1 30.94 ? N SFG 501 B 1 
HETATM 2 C CA SFG . . . D 2 51.758 -7.274 -19.121 1 31.3 ? CA SFG 501 B 1 
HETATM 3 C C SFG . . . D 2 50.62 -6.951 -20.075 1 30.59 ? C SFG 501 B 1 
HETATM 4 O O SFG . . . D 2 50.822 -6.69 -21.243 1 30.96 ? O SFG 501 B 1 
HETATM 5 O OXT SFG . . . D 2 49.45 -6.944 -19.775 1 29.62 ? OXT SFG 501 B 1 
HETATM 6 C CB SFG . . . D 2 52.174 -6.048 -18.303 1 31.68 ? CB SFG 501 B 1 
HETATM 7 C CG SFG . . . D 2 52.998 -6.377 -17.031 1 34.84 ? CG SFG 501 B 1 
HETATM 8 C CD SFG . . . D 2 53.023 -5.252 -15.973 1 37.75 ? CD SFG 501 B 1 
HETATM 9 N NE SFG . . . D 2 53.214 -3.869 -16.573 1 37.84 ? NE SFG 501 B 1 
HETATM 10 C C5' SFG . . . D 2 54.115 -5.477 -14.898 1 39.37 ? C5' SFG 501 B 1 
HETATM 11 C C4' SFG . . . D 2 54.131 -6.888 -14.312 1 39.77 ? C4' SFG 501 B 1 
HETATM 12 O O4' SFG . . . D 2 55.388 -7.251 -13.768 1 41.73 ? O4' SFG 501 B 1 
HETATM 13 C C3' SFG . . . D 2 53.179 -7.124 -13.15 1 39.64 ? C3' SFG 501 B 1 
HETATM 14 O O3' SFG . . . D 2 52.358 -8.184 -13.636 1 32.44 ? O3' SFG 501 B 1 
HETATM 15 C C2' SFG . . . D 2 54.089 -7.562 -11.998 1 39.23 ? C2' SFG 501 B 1 
HETATM 16 O O2' SFG . . . D 2 53.442 -8.331 -10.966 1 36.96 ? O2' SFG 501 B 1 
HETATM 17 C C1' SFG . . . D 2 55.149 -8.278 -12.798 1 42.79 ? C1' SFG 501 B 1 
HETATM 18 N N9 SFG . . . D 2 56.448 -8.593 -12.155 1 44.3 ? N9 SFG 501 B 1 
HETATM 19 C C8 SFG . . . D 2 57.194 -7.738 -11.426 1 45.2 ? C8 SFG 501 B 1 
HETATM 20 N N7 SFG . . . D 2 58.352 -8.344 -11.043 1 45.38 ? N7 SFG 501 B 1 
HETATM 21 C C5 SFG . . . D 2 58.337 -9.595 -11.547 1 45.96 ? C5 SFG 501 B 1 
HETATM 22 C C6 SFG . . . D 2 59.234 -10.666 -11.436 1 46.07 ? C6 SFG 501 B 1 
HETATM 23 N N6 SFG . . . D 2 60.4 -10.531 -10.737 1 44.01 ? N6 SFG 501 B 1 
HETATM 24 N N1 SFG . . . D 2 58.892 -11.836 -12.059 1 46.01 ? N1 SFG 501 B 1 
HETATM 25 C C2 SFG . . . D 2 57.738 -11.941 -12.775 1 44.33 ? C2 SFG 501 B 1 
HETATM 26 N N3 SFG . . . D 2 56.857 -10.93 -12.851 1 42.4 ? N3 SFG 501 B 1 
HETATM 27 C C4 SFG . . . D 2 57.133 -9.75 -12.258 1 44.45 ? C4 SFG 501 B 1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           322 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#