data_6VOB
#
_model_server_result.job_id            QWeDYpQnJINMSj2LqGgDhA 
_model_server_result.datetime_utc      '2025-06-24 12:59:35' 
_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          6vob 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    6VOB 
#
_exptl.entry_id    6VOB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              552.513 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            {N-(4-{bis[(pyridin-2-yl-kappaN)methyl]amino-kappaN}butyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide}iron(3+) 
_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            6VOB 
_cell.length_a            57.66 
_cell.length_b            57.66 
_cell.length_c            183.78 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VOB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        98 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41 2 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_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    1,2,3,4 
#
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' 8_665 -y+1,-x+1,-z 0 -1 0 -1 0 0 0 0 -1 57.66 57.66 0 
3 'crystal symmetry operation' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 57.66 57.66 0 
4 'crystal symmetry operation' 15_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 OH TYR 124 A TYR 124 1_555 B FE1 KM3 . A KM3 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.807 ? 
metalc ? metalc2 B FE1 KM3 . A KM3 201 1_555 C N1 AZI . A AZI 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc3 B FE1 KM3 . A KM3 201 1_555 C N3 AZI . A AZI 202 10_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc4 B FE1 KM3 . A KM3 201 1_555 E O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc5 B FE1 KM3 . A KM3 201 1_555 E O HOH . A HOH 302 10_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
#
_chem_comp.formula           'C26 H36 Fe N6 O2 S 3' 
_chem_comp.formula_weight    552.513 
_chem_comp.id                KM3 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              {N-(4-{bis[(pyridin-2-yl-kappaN)methyl]amino-kappaN}butyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide}iron(3+) 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
C19 C18 KM3 doub 168 n y 
C19 C20 KM3 sing 169 n y 
C17 C18 KM3 sing 170 n n 
C17 N3 KM3 sing 171 n n 
C18 N5 KM3 sing 172 n y 
C20 C21 KM3 doub 173 n y 
C11 N3 KM3 sing 174 n n 
C11 C12 KM3 sing 175 n n 
N3 C23 KM3 sing 176 n n 
N3 FE1 KM3 sing 177 n n 
C12 C13 KM3 doub 178 n y 
C12 N4 KM3 sing 179 n y 
N5 C22 KM3 doub 180 n y 
N5 FE1 KM3 sing 181 n n 
C21 C22 KM3 sing 182 n y 
C13 C14 KM3 sing 183 n y 
C23 C26 KM3 sing 184 n n 
FE1 N4 KM3 sing 185 n n 
N4 C16 KM3 doub 186 n y 
C14 C15 KM3 doub 187 n y 
C26 C25 KM3 sing 188 n n 
C24 C25 KM3 sing 189 n n 
C24 N6 KM3 sing 190 n n 
O1 C01 KM3 doub 191 n n 
C16 C15 KM3 sing 192 n y 
C01 N6 KM3 sing 193 n n 
C01 C2 KM3 sing 194 n n 
C2 C3 KM3 sing 195 n n 
C3 C4 KM3 sing 196 n n 
C4 C5 KM3 sing 197 n n 
C5 C6 KM3 sing 198 n n 
C6 C10 KM3 sing 199 n n 
C6 S1 KM3 sing 200 n n 
N2 C10 KM3 sing 201 n n 
N2 C9 KM3 sing 202 n n 
C10 C8 KM3 sing 203 n n 
S1 C7 KM3 sing 204 n n 
C9 O3 KM3 doub 205 n n 
C9 N1 KM3 sing 206 n n 
C8 C7 KM3 sing 207 n n 
C8 N1 KM3 sing 208 n n 
N1 H1 KM3 sing 209 n n 
N2 H2 KM3 sing 210 n n 
C10 H3 KM3 sing 211 n n 
C8 H4 KM3 sing 212 n n 
C7 H5 KM3 sing 213 n n 
C7 H6 KM3 sing 214 n n 
C6 H7 KM3 sing 215 n n 
C5 H8 KM3 sing 216 n n 
C5 H9 KM3 sing 217 n n 
C4 H10 KM3 sing 218 n n 
C4 H11 KM3 sing 219 n n 
C3 H12 KM3 sing 220 n n 
C3 H13 KM3 sing 221 n n 
C2 H14 KM3 sing 222 n n 
C2 H15 KM3 sing 223 n n 
C25 H16 KM3 sing 224 n n 
C25 H17 KM3 sing 225 n n 
N6 H18 KM3 sing 226 n n 
C26 H19 KM3 sing 227 n n 
C26 H20 KM3 sing 228 n n 
C23 H21 KM3 sing 229 n n 
C23 H22 KM3 sing 230 n n 
C24 H23 KM3 sing 231 n n 
C24 H24 KM3 sing 232 n n 
C11 H25 KM3 sing 233 n n 
C11 H26 KM3 sing 234 n n 
C17 H27 KM3 sing 235 n n 
C17 H28 KM3 sing 236 n n 
C16 H29 KM3 sing 237 n n 
C15 H30 KM3 sing 238 n n 
C14 H31 KM3 sing 239 n n 
C13 H32 KM3 sing 240 n n 
C22 H33 KM3 sing 241 n n 
C21 H34 KM3 sing 242 n n 
C20 H35 KM3 sing 243 n n 
C19 H36 KM3 sing 244 n n 
#
_atom_sites.entry_id                     6VOB 
_atom_sites.fract_transf_matrix[1][1]    0.017343 
_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]    0.017343 
_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]    0.005441 
_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 KM3 A 1 201 1 KM3 KM3 . 
C 3 AZI A 1 202 1 AZI AZI . 
D 4 ACT A 1 203 1 ACT ACT . 
E 5 HOH A 1 301 34 HOH HOH . 
E 5 HOH A 2 302 1 HOH HOH . 
E 5 HOH A 3 303 94 HOH HOH . 
E 5 HOH A 4 304 157 HOH HOH . 
E 5 HOH A 5 305 40 HOH HOH . 
E 5 HOH A 6 306 68 HOH HOH . 
E 5 HOH A 7 307 17 HOH HOH . 
E 5 HOH A 8 308 55 HOH HOH . 
E 5 HOH A 9 309 43 HOH HOH . 
E 5 HOH A 10 310 29 HOH HOH . 
E 5 HOH A 11 311 5 HOH HOH . 
E 5 HOH A 12 312 85 HOH HOH . 
E 5 HOH A 13 313 10 HOH HOH . 
E 5 HOH A 14 314 31 HOH HOH . 
E 5 HOH A 15 315 37 HOH HOH . 
E 5 HOH A 16 316 98 HOH HOH . 
E 5 HOH A 17 317 22 HOH HOH . 
E 5 HOH A 18 318 3 HOH HOH . 
E 5 HOH A 19 319 25 HOH HOH . 
E 5 HOH A 20 320 9 HOH HOH . 
E 5 HOH A 21 321 7 HOH HOH . 
E 5 HOH A 22 322 27 HOH HOH . 
E 5 HOH A 23 323 45 HOH HOH . 
E 5 HOH A 24 324 155 HOH HOH . 
E 5 HOH A 25 325 93 HOH HOH . 
E 5 HOH A 26 326 38 HOH HOH . 
E 5 HOH A 27 327 60 HOH HOH . 
E 5 HOH A 28 328 57 HOH HOH . 
E 5 HOH A 29 329 51 HOH HOH . 
E 5 HOH A 30 330 16 HOH HOH . 
E 5 HOH A 31 331 39 HOH HOH . 
E 5 HOH A 32 332 92 HOH HOH . 
E 5 HOH A 33 333 154 HOH HOH . 
E 5 HOH A 34 334 24 HOH HOH . 
E 5 HOH A 35 335 33 HOH HOH . 
E 5 HOH A 36 336 2 HOH HOH . 
E 5 HOH A 37 337 23 HOH HOH . 
E 5 HOH A 38 338 56 HOH HOH . 
E 5 HOH A 39 339 46 HOH HOH . 
E 5 HOH A 40 340 67 HOH HOH . 
E 5 HOH A 41 341 58 HOH HOH . 
E 5 HOH A 42 342 76 HOH HOH . 
E 5 HOH A 43 343 13 HOH HOH . 
E 5 HOH A 44 344 20 HOH HOH . 
E 5 HOH A 45 345 8 HOH HOH . 
E 5 HOH A 46 346 42 HOH HOH . 
E 5 HOH A 47 347 66 HOH HOH . 
E 5 HOH A 48 348 32 HOH HOH . 
E 5 HOH A 49 349 12 HOH HOH . 
E 5 HOH A 50 350 26 HOH HOH . 
E 5 HOH A 51 351 11 HOH HOH . 
E 5 HOH A 52 352 48 HOH HOH . 
E 5 HOH A 53 353 50 HOH HOH . 
E 5 HOH A 54 354 15 HOH HOH . 
E 5 HOH A 55 355 129 HOH HOH . 
E 5 HOH A 56 356 65 HOH HOH . 
E 5 HOH A 57 357 44 HOH HOH . 
E 5 HOH A 58 358 84 HOH HOH . 
E 5 HOH A 59 359 35 HOH HOH . 
E 5 HOH A 60 360 73 HOH HOH . 
E 5 HOH A 61 361 4 HOH HOH . 
E 5 HOH A 62 362 18 HOH HOH . 
E 5 HOH A 63 363 53 HOH HOH . 
E 5 HOH A 64 364 19 HOH HOH . 
E 5 HOH A 65 365 6 HOH HOH . 
E 5 HOH A 66 366 78 HOH HOH . 
E 5 HOH A 67 367 28 HOH HOH . 
E 5 HOH A 68 368 82 HOH HOH . 
E 5 HOH A 69 369 49 HOH HOH . 
E 5 HOH A 70 370 119 HOH HOH . 
E 5 HOH A 71 371 47 HOH HOH . 
E 5 HOH A 72 372 143 HOH HOH . 
E 5 HOH A 73 373 69 HOH HOH . 
E 5 HOH A 74 374 61 HOH HOH . 
E 5 HOH A 75 375 156 HOH HOH . 
E 5 HOH A 76 376 36 HOH HOH . 
E 5 HOH A 77 377 138 HOH HOH . 
E 5 HOH A 78 378 89 HOH HOH . 
E 5 HOH A 79 379 126 HOH HOH . 
E 5 HOH A 80 380 41 HOH HOH . 
E 5 HOH A 81 381 62 HOH HOH . 
E 5 HOH A 82 382 70 HOH HOH . 
E 5 HOH A 83 383 139 HOH HOH . 
E 5 HOH A 84 384 140 HOH HOH . 
E 5 HOH A 85 385 71 HOH HOH . 
E 5 HOH A 86 386 72 HOH HOH . 
E 5 HOH A 87 387 77 HOH HOH . 
E 5 HOH A 88 388 91 HOH HOH . 
E 5 HOH A 89 389 63 HOH HOH . 
E 5 HOH A 90 390 110 HOH HOH . 
E 5 HOH A 91 391 75 HOH HOH . 
E 5 HOH A 92 392 103 HOH HOH . 
E 5 HOH A 93 393 86 HOH HOH . 
E 5 HOH A 94 394 54 HOH HOH . 
E 5 HOH A 95 395 142 HOH HOH . 
E 5 HOH A 96 396 99 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 O O3 KM3 . . . B 2 14.268 29.442 -8.207 1 11.43 ? O3 KM3 201 A 1 
HETATM 2 C C9 KM3 . . . B 2 15.49 29.387 -8.448 1 10.74 ? C9 KM3 201 A 1 
HETATM 3 N N1 KM3 . . . B 2 16.45 29.553 -7.523 1 11.2 ? N1 KM3 201 A 1 
HETATM 4 N N2 KM3 . . . B 2 16.005 29.21 -9.691 1 10.17 ? N2 KM3 201 A 1 
HETATM 5 C C10 KM3 . . . B 2 17.465 29.229 -9.641 1 10.01 ? C10 KM3 201 A 1 
HETATM 6 C C8 KM3 . . . B 2 17.802 29.494 -8.095 1 9.78 ? C8 KM3 201 A 1 
HETATM 7 C C7 KM3 . . . B 2 18.564 28.236 -7.614 1 10.2 ? C7 KM3 201 A 1 
HETATM 8 S S1 KM3 . . . B 2 17.969 26.822 -8.583 1 11.36 ? S1 KM3 201 A 1 
HETATM 9 C C6 KM3 . . . B 2 18.103 27.906 -10.045 1 10.68 ? C6 KM3 201 A 1 
HETATM 10 C C5 KM3 . . . B 2 17.522 27.236 -11.291 1 10.93 ? C5 KM3 201 A 1 
HETATM 11 C C4 KM3 . . . B 2 18.42 26.13 -11.922 1 10.87 ? C4 KM3 201 A 1 
HETATM 12 C C3 KM3 . . . B 2 17.721 25.48 -13.143 1 12.07 ? C3 KM3 201 A 1 
HETATM 13 C C2 KM3 . . . B 2 18.609 24.347 -13.731 1 11.85 ? C2 KM3 201 A 1 
HETATM 14 C C01 KM3 . . . B 2 19.862 24.89 -14.401 1 13.03 ? C01 KM3 201 A 1 
HETATM 15 C C25 KM3 . . . B 2 23.19 25.309 -14.441 1 20.09 ? C25 KM3 201 A 1 
HETATM 16 N N6 KM3 . . . B 2 21.008 24.135 -14.229 1 14.34 ? N6 KM3 201 A 1 
HETATM 17 C C26 KM3 . . . B 2 24.482 25.303 -15.284 1 25.41 ? C26 KM3 201 A 1 
HETATM 18 O O1 KM3 . . . B 2 19.904 26.012 -15.037 1 12.99 ? O1 KM3 201 A 1 
HETATM 19 C C23 KM3 . . . B 2 24.504 26.5 -16.232 1 26.62 ? C23 KM3 201 A 1 
HETATM 20 C C24 KM3 . . . B 2 22.186 24.366 -15.103 1 17.57 ? C24 KM3 201 A 1 
HETATM 21 N N3 KM3 . . . B 2 25.782 26.795 -16.995 1 26.41 ? N3 KM3 201 A 1 
HETATM 22 C C11 KM3 . . . B 2 26.348 25.521 -17.547 1 27.47 ? C11 KM3 201 A 1 
HETATM 23 C C17 KM3 . . . B 2 25.277 27.572 -18.15 1 27.37 ? C17 KM3 201 A 1 
HETATM 24 FE FE1 KM3 . . . B 2 27.192 27.847 -15.856 1 30.42 ? FE1 KM3 201 A 1 
HETATM 25 N N4 KM3 . . . B 2 27.818 25.983 -15.723 1 27.18 ? N4 KM3 201 A 1 
HETATM 26 C C16 KM3 . . . B 2 28.683 25.519 -14.843 1 33.04 ? C16 KM3 201 A 1 
HETATM 27 C C15 KM3 . . . B 2 29.073 24.262 -14.837 1 31.95 ? C15 KM3 201 A 1 
HETATM 28 C C14 KM3 . . . B 2 28.626 23.422 -15.646 1 36.98 ? C14 KM3 201 A 1 
HETATM 29 C C13 KM3 . . . B 2 27.792 23.725 -16.497 1 30.65 ? C13 KM3 201 A 1 
HETATM 30 C C12 KM3 . . . B 2 27.38 24.967 -16.577 1 30.38 ? C12 KM3 201 A 1 
HETATM 31 N N5 KM3 . . . B 2 25.921 29.253 -16.567 1 33.27 ? N5 KM3 201 A 1 
HETATM 32 C C18 KM3 . . . B 2 25.039 29.003 -17.685 1 31.21 ? C18 KM3 201 A 1 
HETATM 33 C C22 KM3 . . . B 2 25.842 30.529 -16.031 1 35.6 ? C22 KM3 201 A 1 
HETATM 34 C C21 KM3 . . . B 2 24.958 31.539 -16.508 1 32.16 ? C21 KM3 201 A 1 
HETATM 35 C C20 KM3 . . . B 2 24.103 31.268 -17.586 1 35.83 ? C20 KM3 201 A 1 
HETATM 36 C C19 KM3 . . . B 2 24.135 29.988 -18.163 1 34.25 ? C19 KM3 201 A 1 
#
_model_server_stats.io_time_ms              73 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           482 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           36 
#