data_6VO9
#
_model_server_result.job_id            CcFh-Z39oLeaSwu5lsqj4A 
_model_server_result.datetime_utc      '2024-11-18 06:25:47' 
_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          6vo9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":201}' 
#
_entry.id    6VO9 
#
_exptl.entry_id    6VO9 
_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            6VO9 
_cell.length_a            57.861 
_cell.length_b            57.861 
_cell.length_c            184.65 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VO9 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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 57.861 57.861 0 
3 'crystal symmetry operation' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 57.861 57.861 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? 
metalc ? metalc2 B FE1 KM3 . A KM3 201 1_555 C O ACT . A ACT 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? 
metalc ? metalc3 B FE1 KM3 . A KM3 201 1_555 C OXT ACT . A ACT 202 10_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc4 B FE1 KM3 . A KM3 201 1_555 D O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
metalc ? metalc5 B FE1 KM3 . A KM3 201 1_555 D O HOH . A HOH 301 10_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
#
_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 166 n y 
C19 C20 KM3 sing 167 n y 
C17 C18 KM3 sing 168 n n 
C17 N3 KM3 sing 169 n n 
C18 N5 KM3 sing 170 n y 
C20 C21 KM3 doub 171 n y 
C11 N3 KM3 sing 172 n n 
C11 C12 KM3 sing 173 n n 
N3 C23 KM3 sing 174 n n 
N3 FE1 KM3 sing 175 n n 
C12 C13 KM3 doub 176 n y 
C12 N4 KM3 sing 177 n y 
N5 C22 KM3 doub 178 n y 
N5 FE1 KM3 sing 179 n n 
C21 C22 KM3 sing 180 n y 
C13 C14 KM3 sing 181 n y 
C23 C26 KM3 sing 182 n n 
FE1 N4 KM3 sing 183 n n 
N4 C16 KM3 doub 184 n y 
C14 C15 KM3 doub 185 n y 
C26 C25 KM3 sing 186 n n 
C24 C25 KM3 sing 187 n n 
C24 N6 KM3 sing 188 n n 
O1 C01 KM3 doub 189 n n 
C16 C15 KM3 sing 190 n y 
C01 N6 KM3 sing 191 n n 
C01 C2 KM3 sing 192 n n 
C2 C3 KM3 sing 193 n n 
C3 C4 KM3 sing 194 n n 
C4 C5 KM3 sing 195 n n 
C5 C6 KM3 sing 196 n n 
C6 C10 KM3 sing 197 n n 
C6 S1 KM3 sing 198 n n 
N2 C10 KM3 sing 199 n n 
N2 C9 KM3 sing 200 n n 
C10 C8 KM3 sing 201 n n 
S1 C7 KM3 sing 202 n n 
C9 O3 KM3 doub 203 n n 
C9 N1 KM3 sing 204 n n 
C8 C7 KM3 sing 205 n n 
C8 N1 KM3 sing 206 n n 
N1 H1 KM3 sing 207 n n 
N2 H2 KM3 sing 208 n n 
C10 H3 KM3 sing 209 n n 
C8 H4 KM3 sing 210 n n 
C7 H5 KM3 sing 211 n n 
C7 H6 KM3 sing 212 n n 
C6 H7 KM3 sing 213 n n 
C5 H8 KM3 sing 214 n n 
C5 H9 KM3 sing 215 n n 
C4 H10 KM3 sing 216 n n 
C4 H11 KM3 sing 217 n n 
C3 H12 KM3 sing 218 n n 
C3 H13 KM3 sing 219 n n 
C2 H14 KM3 sing 220 n n 
C2 H15 KM3 sing 221 n n 
C25 H16 KM3 sing 222 n n 
C25 H17 KM3 sing 223 n n 
N6 H18 KM3 sing 224 n n 
C26 H19 KM3 sing 225 n n 
C26 H20 KM3 sing 226 n n 
C23 H21 KM3 sing 227 n n 
C23 H22 KM3 sing 228 n n 
C24 H23 KM3 sing 229 n n 
C24 H24 KM3 sing 230 n n 
C11 H25 KM3 sing 231 n n 
C11 H26 KM3 sing 232 n n 
C17 H27 KM3 sing 233 n n 
C17 H28 KM3 sing 234 n n 
C16 H29 KM3 sing 235 n n 
C15 H30 KM3 sing 236 n n 
C14 H31 KM3 sing 237 n n 
C13 H32 KM3 sing 238 n n 
C22 H33 KM3 sing 239 n n 
C21 H34 KM3 sing 240 n n 
C20 H35 KM3 sing 241 n n 
C19 H36 KM3 sing 242 n n 
#
_atom_sites.entry_id                     6VO9 
_atom_sites.fract_transf_matrix[1][1]    0.017283 
_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]    0.017283 
_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]    0.005416 
_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 ACT A 1 202 1 ACT ACT . 
D 4 HOH A 1 301 1 HOH HOH . 
D 4 HOH A 2 302 18 HOH HOH . 
D 4 HOH A 3 303 132 HOH HOH . 
D 4 HOH A 4 304 57 HOH HOH . 
D 4 HOH A 5 305 99 HOH HOH . 
D 4 HOH A 6 306 4 HOH HOH . 
D 4 HOH A 7 307 50 HOH HOH . 
D 4 HOH A 8 308 47 HOH HOH . 
D 4 HOH A 9 309 53 HOH HOH . 
D 4 HOH A 10 310 36 HOH HOH . 
D 4 HOH A 11 311 96 HOH HOH . 
D 4 HOH A 12 312 30 HOH HOH . 
D 4 HOH A 13 313 17 HOH HOH . 
D 4 HOH A 14 314 63 HOH HOH . 
D 4 HOH A 15 315 29 HOH HOH . 
D 4 HOH A 16 316 5 HOH HOH . 
D 4 HOH A 17 317 19 HOH HOH . 
D 4 HOH A 18 318 2 HOH HOH . 
D 4 HOH A 19 319 49 HOH HOH . 
D 4 HOH A 20 320 20 HOH HOH . 
D 4 HOH A 21 321 12 HOH HOH . 
D 4 HOH A 22 322 7 HOH HOH . 
D 4 HOH A 23 323 8 HOH HOH . 
D 4 HOH A 24 324 52 HOH HOH . 
D 4 HOH A 25 325 107 HOH HOH . 
D 4 HOH A 26 326 32 HOH HOH . 
D 4 HOH A 27 327 74 HOH HOH . 
D 4 HOH A 28 328 15 HOH HOH . 
D 4 HOH A 29 329 60 HOH HOH . 
D 4 HOH A 30 330 69 HOH HOH . 
D 4 HOH A 31 331 85 HOH HOH . 
D 4 HOH A 32 332 38 HOH HOH . 
D 4 HOH A 33 333 16 HOH HOH . 
D 4 HOH A 34 334 6 HOH HOH . 
D 4 HOH A 35 335 91 HOH HOH . 
D 4 HOH A 36 336 72 HOH HOH . 
D 4 HOH A 37 337 27 HOH HOH . 
D 4 HOH A 38 338 92 HOH HOH . 
D 4 HOH A 39 339 56 HOH HOH . 
D 4 HOH A 40 340 75 HOH HOH . 
D 4 HOH A 41 341 66 HOH HOH . 
D 4 HOH A 42 342 59 HOH HOH . 
D 4 HOH A 43 343 80 HOH HOH . 
D 4 HOH A 44 344 31 HOH HOH . 
D 4 HOH A 45 345 10 HOH HOH . 
D 4 HOH A 46 346 58 HOH HOH . 
D 4 HOH A 47 347 23 HOH HOH . 
D 4 HOH A 48 348 73 HOH HOH . 
D 4 HOH A 49 349 79 HOH HOH . 
D 4 HOH A 50 350 3 HOH HOH . 
D 4 HOH A 51 351 21 HOH HOH . 
D 4 HOH A 52 352 33 HOH HOH . 
D 4 HOH A 53 353 61 HOH HOH . 
D 4 HOH A 54 354 179 HOH HOH . 
D 4 HOH A 55 355 22 HOH HOH . 
D 4 HOH A 56 356 71 HOH HOH . 
D 4 HOH A 57 357 67 HOH HOH . 
D 4 HOH A 58 358 11 HOH HOH . 
D 4 HOH A 59 359 62 HOH HOH . 
D 4 HOH A 60 360 14 HOH HOH . 
D 4 HOH A 61 361 26 HOH HOH . 
D 4 HOH A 62 362 41 HOH HOH . 
D 4 HOH A 63 363 64 HOH HOH . 
D 4 HOH A 64 364 40 HOH HOH . 
D 4 HOH A 65 365 65 HOH HOH . 
D 4 HOH A 66 366 93 HOH HOH . 
D 4 HOH A 67 367 113 HOH HOH . 
D 4 HOH A 68 368 44 HOH HOH . 
D 4 HOH A 69 369 181 HOH HOH . 
D 4 HOH A 70 370 9 HOH HOH . 
D 4 HOH A 71 371 43 HOH HOH . 
D 4 HOH A 72 372 81 HOH HOH . 
D 4 HOH A 73 373 24 HOH HOH . 
D 4 HOH A 74 374 34 HOH HOH . 
D 4 HOH A 75 375 55 HOH HOH . 
D 4 HOH A 76 376 76 HOH HOH . 
D 4 HOH A 77 377 51 HOH HOH . 
D 4 HOH A 78 378 90 HOH HOH . 
D 4 HOH A 79 379 35 HOH HOH . 
D 4 HOH A 80 380 25 HOH HOH . 
D 4 HOH A 81 381 42 HOH HOH . 
D 4 HOH A 82 382 100 HOH HOH . 
D 4 HOH A 83 383 46 HOH HOH . 
D 4 HOH A 84 384 45 HOH HOH . 
D 4 HOH A 85 385 37 HOH HOH . 
D 4 HOH A 86 386 88 HOH HOH . 
D 4 HOH A 87 387 39 HOH HOH . 
D 4 HOH A 88 388 182 HOH HOH . 
D 4 HOH A 89 389 177 HOH HOH . 
D 4 HOH A 90 390 105 HOH HOH . 
D 4 HOH A 91 391 103 HOH HOH . 
D 4 HOH A 92 392 54 HOH HOH . 
D 4 HOH A 93 393 70 HOH HOH . 
D 4 HOH A 94 394 48 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 14.398 29.536 -8.241 1 9.21 ? O3 KM3 201 A 1 
HETATM 2 C C9 KM3 . . . B 2 15.618 29.476 -8.503 1 9.98 ? C9 KM3 201 A 1 
HETATM 3 N N1 KM3 . . . B 2 16.585 29.633 -7.595 1 10.08 ? N1 KM3 201 A 1 
HETATM 4 N N2 KM3 . . . B 2 16.173 29.264 -9.685 1 9.74 ? N2 KM3 201 A 1 
HETATM 5 C C10 KM3 . . . B 2 17.642 29.253 -9.668 1 9.71 ? C10 KM3 201 A 1 
HETATM 6 C C8 KM3 . . . B 2 17.936 29.53 -8.147 1 8.69 ? C8 KM3 201 A 1 
HETATM 7 C C7 KM3 . . . B 2 18.704 28.292 -7.643 1 9.83 ? C7 KM3 201 A 1 
HETATM 8 S S1 KM3 . . . B 2 18.064 26.883 -8.613 1 10.49 ? S1 KM3 201 A 1 
HETATM 9 C C6 KM3 . . . B 2 18.176 27.874 -10.089 1 9.03 ? C6 KM3 201 A 1 
HETATM 10 C C5 KM3 . . . B 2 17.613 27.291 -11.405 1 9.87 ? C5 KM3 201 A 1 
HETATM 11 C C4 KM3 . . . B 2 18.424 26.084 -11.899 1 9.3 ? C4 KM3 201 A 1 
HETATM 12 C C3 KM3 . . . B 2 17.88 25.571 -13.228 1 10.89 ? C3 KM3 201 A 1 
HETATM 13 C C2 KM3 . . . B 2 18.672 24.401 -13.781 1 11.87 ? C2 KM3 201 A 1 
HETATM 14 C C01 KM3 . . . B 2 19.93 24.92 -14.452 1 11.25 ? C01 KM3 201 A 1 
HETATM 15 C C25 KM3 . . . B 2 23.223 25.285 -14.623 1 22.87 ? C25 KM3 201 A 1 
HETATM 16 N N6 KM3 . . . B 2 21.05 24.126 -14.323 1 12.36 ? N6 KM3 201 A 1 
HETATM 17 C C26 KM3 . . . B 2 24.528 25.217 -15.469 1 29.37 ? C26 KM3 201 A 1 
HETATM 18 O O1 KM3 . . . B 2 19.949 26.035 -15.094 1 12.29 ? O1 KM3 201 A 1 
HETATM 19 C C23 KM3 . . . B 2 24.707 26.523 -16.23 1 30.97 ? C23 KM3 201 A 1 
HETATM 20 C C24 KM3 . . . B 2 22.19 24.343 -15.224 1 18.62 ? C24 KM3 201 A 1 
HETATM 21 N N3 KM3 . . . B 2 25.955 26.755 -17.061 1 28.25 ? N3 KM3 201 A 1 
HETATM 22 C C11 KM3 . . . B 2 26.523 25.488 -17.605 1 28.38 ? C11 KM3 201 A 1 
HETATM 23 C C17 KM3 . . . B 2 25.396 27.5 -18.206 1 29.25 ? C17 KM3 201 A 1 
HETATM 24 FE FE1 KM3 . . . B 2 27.307 27.844 -15.959 1 29.56 ? FE1 KM3 201 A 1 
HETATM 25 N N4 KM3 . . . B 2 27.984 26.058 -15.783 1 30.28 ? N4 KM3 201 A 1 
HETATM 26 C C16 KM3 . . . B 2 28.867 25.684 -14.907 1 35.4 ? C16 KM3 201 A 1 
HETATM 27 C C15 KM3 . . . B 2 29.275 24.435 -14.856 1 32.88 ? C15 KM3 201 A 1 
HETATM 28 C C14 KM3 . . . B 2 28.864 23.561 -15.622 1 35.05 ? C14 KM3 201 A 1 
HETATM 29 C C13 KM3 . . . B 2 28.032 23.822 -16.496 1 30.81 ? C13 KM3 201 A 1 
HETATM 30 C C12 KM3 . . . B 2 27.56 25.018 -16.609 1 28.42 ? C12 KM3 201 A 1 
HETATM 31 N N5 KM3 . . . B 2 26.047 29.235 -16.621 1 36.44 ? N5 KM3 201 A 1 
HETATM 32 C C18 KM3 . . . B 2 25.184 28.931 -17.736 1 33.36 ? C18 KM3 201 A 1 
HETATM 33 C C22 KM3 . . . B 2 25.996 30.499 -16.097 1 40.51 ? C22 KM3 201 A 1 
HETATM 34 C C21 KM3 . . . B 2 25.102 31.471 -16.586 1 37.36 ? C21 KM3 201 A 1 
HETATM 35 C C20 KM3 . . . B 2 24.243 31.17 -17.644 1 40.04 ? C20 KM3 201 A 1 
HETATM 36 C C19 KM3 . . . B 2 24.286 29.892 -18.227 1 40.54 ? C19 KM3 201 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           282 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           36 
#