data_7KBY # _model_server_result.job_id FlufYT7KhUXrvAFqUq7MVA _model_server_result.datetime_utc '2024-11-13 19:10:08' _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 7kby # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 7KBY # _exptl.entry_id 7KBY _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 7KBY _cell.length_a 57.56 _cell.length_b 57.56 _cell.length_c 183.45 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KBY _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 57.56 57.56 0 3 'crystal symmetry operation' 10_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 57.56 57.56 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.827 ? metalc ? metalc2 B FE1 KM3 . A KM3 201 1_555 C N CYN . A CYN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc3 B FE1 KM3 . A KM3 201 1_555 E O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc4 B FE1 KM3 . A KM3 201 1_555 E O HOH . A HOH 301 10_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? # _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 167 n y C19 C20 KM3 sing 168 n y C17 C18 KM3 sing 169 n n C17 N3 KM3 sing 170 n n C18 N5 KM3 sing 171 n y C20 C21 KM3 doub 172 n y C11 N3 KM3 sing 173 n n C11 C12 KM3 sing 174 n n N3 C23 KM3 sing 175 n n N3 FE1 KM3 sing 176 n n C12 C13 KM3 doub 177 n y C12 N4 KM3 sing 178 n y N5 C22 KM3 doub 179 n y N5 FE1 KM3 sing 180 n n C21 C22 KM3 sing 181 n y C13 C14 KM3 sing 182 n y C23 C26 KM3 sing 183 n n FE1 N4 KM3 sing 184 n n N4 C16 KM3 doub 185 n y C14 C15 KM3 doub 186 n y C26 C25 KM3 sing 187 n n C24 C25 KM3 sing 188 n n C24 N6 KM3 sing 189 n n O1 C01 KM3 doub 190 n n C16 C15 KM3 sing 191 n y C01 N6 KM3 sing 192 n n C01 C2 KM3 sing 193 n n C2 C3 KM3 sing 194 n n C3 C4 KM3 sing 195 n n C4 C5 KM3 sing 196 n n C5 C6 KM3 sing 197 n n C6 C10 KM3 sing 198 n n C6 S1 KM3 sing 199 n n N2 C10 KM3 sing 200 n n N2 C9 KM3 sing 201 n n C10 C8 KM3 sing 202 n n S1 C7 KM3 sing 203 n n C9 O3 KM3 doub 204 n n C9 N1 KM3 sing 205 n n C8 C7 KM3 sing 206 n n C8 N1 KM3 sing 207 n n N1 H1 KM3 sing 208 n n N2 H2 KM3 sing 209 n n C10 H3 KM3 sing 210 n n C8 H4 KM3 sing 211 n n C7 H5 KM3 sing 212 n n C7 H6 KM3 sing 213 n n C6 H7 KM3 sing 214 n n C5 H8 KM3 sing 215 n n C5 H9 KM3 sing 216 n n C4 H10 KM3 sing 217 n n C4 H11 KM3 sing 218 n n C3 H12 KM3 sing 219 n n C3 H13 KM3 sing 220 n n C2 H14 KM3 sing 221 n n C2 H15 KM3 sing 222 n n C25 H16 KM3 sing 223 n n C25 H17 KM3 sing 224 n n N6 H18 KM3 sing 225 n n C26 H19 KM3 sing 226 n n C26 H20 KM3 sing 227 n n C23 H21 KM3 sing 228 n n C23 H22 KM3 sing 229 n n C24 H23 KM3 sing 230 n n C24 H24 KM3 sing 231 n n C11 H25 KM3 sing 232 n n C11 H26 KM3 sing 233 n n C17 H27 KM3 sing 234 n n C17 H28 KM3 sing 235 n n C16 H29 KM3 sing 236 n n C15 H30 KM3 sing 237 n n C14 H31 KM3 sing 238 n n C13 H32 KM3 sing 239 n n C22 H33 KM3 sing 240 n n C21 H34 KM3 sing 241 n n C20 H35 KM3 sing 242 n n C19 H36 KM3 sing 243 n n # _atom_sites.entry_id 7KBY _atom_sites.fract_transf_matrix[1][1] 0.017373 _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] 0.017373 _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] 0.005451 _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 CYN A 1 202 1 CYN CYN . D 4 ACT A 1 203 1 ACT ACT . E 5 HOH A 1 301 1 HOH HOH . E 5 HOH A 2 302 128 HOH HOH . E 5 HOH A 3 303 73 HOH HOH . E 5 HOH A 4 304 33 HOH HOH . E 5 HOH A 5 305 3 HOH HOH . E 5 HOH A 6 306 7 HOH HOH . E 5 HOH A 7 307 32 HOH HOH . E 5 HOH A 8 308 43 HOH HOH . E 5 HOH A 9 309 24 HOH HOH . E 5 HOH A 10 310 8 HOH HOH . E 5 HOH A 11 311 20 HOH HOH . E 5 HOH A 12 312 11 HOH HOH . E 5 HOH A 13 313 5 HOH HOH . E 5 HOH A 14 314 16 HOH HOH . E 5 HOH A 15 315 2 HOH HOH . E 5 HOH A 16 316 12 HOH HOH . E 5 HOH A 17 317 29 HOH HOH . E 5 HOH A 18 318 6 HOH HOH . E 5 HOH A 19 319 121 HOH HOH . E 5 HOH A 20 320 10 HOH HOH . E 5 HOH A 21 321 109 HOH HOH . E 5 HOH A 22 322 18 HOH HOH . E 5 HOH A 23 323 42 HOH HOH . E 5 HOH A 24 324 31 HOH HOH . E 5 HOH A 25 325 76 HOH HOH . E 5 HOH A 26 326 129 HOH HOH . E 5 HOH A 27 327 37 HOH HOH . E 5 HOH A 28 328 130 HOH HOH . E 5 HOH A 29 329 15 HOH HOH . E 5 HOH A 30 330 58 HOH HOH . E 5 HOH A 31 331 21 HOH HOH . E 5 HOH A 32 332 36 HOH HOH . E 5 HOH A 33 333 17 HOH HOH . E 5 HOH A 34 334 55 HOH HOH . E 5 HOH A 35 335 25 HOH HOH . E 5 HOH A 36 336 113 HOH HOH . E 5 HOH A 37 337 50 HOH HOH . E 5 HOH A 38 338 46 HOH HOH . E 5 HOH A 39 339 62 HOH HOH . E 5 HOH A 40 340 45 HOH HOH . E 5 HOH A 41 341 13 HOH HOH . E 5 HOH A 42 342 41 HOH HOH . E 5 HOH A 43 343 80 HOH HOH . E 5 HOH A 44 344 26 HOH HOH . E 5 HOH A 45 345 79 HOH HOH . E 5 HOH A 46 346 64 HOH HOH . E 5 HOH A 47 347 30 HOH HOH . E 5 HOH A 48 348 4 HOH HOH . E 5 HOH A 49 349 19 HOH HOH . E 5 HOH A 50 350 35 HOH HOH . E 5 HOH A 51 351 40 HOH HOH . E 5 HOH A 52 352 34 HOH HOH . E 5 HOH A 53 353 68 HOH HOH . E 5 HOH A 54 354 39 HOH HOH . E 5 HOH A 55 355 23 HOH HOH . E 5 HOH A 56 356 22 HOH HOH . E 5 HOH A 57 357 44 HOH HOH . E 5 HOH A 58 358 47 HOH HOH . E 5 HOH A 59 359 48 HOH HOH . E 5 HOH A 60 360 38 HOH HOH . E 5 HOH A 61 361 9 HOH HOH . E 5 HOH A 62 362 53 HOH HOH . E 5 HOH A 63 363 120 HOH HOH . E 5 HOH A 64 364 61 HOH HOH . E 5 HOH A 65 365 104 HOH HOH . E 5 HOH A 66 366 69 HOH HOH . E 5 HOH A 67 367 57 HOH HOH . E 5 HOH A 68 368 72 HOH HOH . E 5 HOH A 69 369 97 HOH HOH . E 5 HOH A 70 370 127 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 14.2 29.422 -8.179 1 13.15 ? O3 KM3 201 A 1 HETATM 2 C C9 KM3 . . . B 2 15.425 29.382 -8.496 1 12.79 ? C9 KM3 201 A 1 HETATM 3 N N1 KM3 . . . B 2 16.406 29.459 -7.561 1 12.95 ? N1 KM3 201 A 1 HETATM 4 N N2 KM3 . . . B 2 15.93 29.194 -9.73 1 11.95 ? N2 KM3 201 A 1 HETATM 5 C C10 KM3 . . . B 2 17.427 29.23 -9.692 1 12.51 ? C10 KM3 201 A 1 HETATM 6 C C8 KM3 . . . B 2 17.757 29.436 -8.132 1 12.02 ? C8 KM3 201 A 1 HETATM 7 C C7 KM3 . . . B 2 18.466 28.172 -7.621 1 13.84 ? C7 KM3 201 A 1 HETATM 8 S S1 KM3 . . . B 2 17.911 26.775 -8.578 1 15.09 ? S1 KM3 201 A 1 HETATM 9 C C6 KM3 . . . B 2 18.045 27.834 -10.018 1 13.88 ? C6 KM3 201 A 1 HETATM 10 C C5 KM3 . . . B 2 17.488 27.149 -11.266 1 14.15 ? C5 KM3 201 A 1 HETATM 11 C C4 KM3 . . . B 2 18.315 26.018 -11.867 1 15.19 ? C4 KM3 201 A 1 HETATM 12 C C3 KM3 . . . B 2 17.709 25.566 -13.214 1 16.87 ? C3 KM3 201 A 1 HETATM 13 C C2 KM3 . . . B 2 18.452 24.367 -13.77 1 16.17 ? C2 KM3 201 A 1 HETATM 14 C C01 KM3 . . . B 2 19.767 24.854 -14.321 1 16.77 ? C01 KM3 201 A 1 HETATM 15 C C25 KM3 . . . B 2 23.132 25.168 -14.523 1 30.98 ? C25 KM3 201 A 1 HETATM 16 N N6 KM3 . . . B 2 20.888 24.018 -14.258 1 18.03 ? N6 KM3 201 A 1 HETATM 17 C C26 KM3 . . . B 2 24.418 25.117 -15.37 1 37.18 ? C26 KM3 201 A 1 HETATM 18 O O1 KM3 . . . B 2 19.818 25.867 -15.035 1 16.92 ? O1 KM3 201 A 1 HETATM 19 C C23 KM3 . . . B 2 24.574 26.416 -16.156 1 42.2 ? C23 KM3 201 A 1 HETATM 20 C C24 KM3 . . . B 2 22.075 24.217 -15.098 1 23.67 ? C24 KM3 201 A 1 HETATM 21 N N3 KM3 . . . B 2 25.818 26.697 -16.973 1 48.83 ? N3 KM3 201 A 1 HETATM 22 C C11 KM3 . . . B 2 26.421 25.467 -17.557 1 44 ? C11 KM3 201 A 1 HETATM 23 C C17 KM3 . . . B 2 25.285 27.423 -18.15 1 44.74 ? C17 KM3 201 A 1 HETATM 24 FE FE1 KM3 . . . B 2 27.187 27.811 -15.878 1 45.99 ? FE1 KM3 201 A 1 HETATM 25 N N4 KM3 . . . B 2 27.801 25.98 -15.671 1 51.24 ? N4 KM3 201 A 1 HETATM 26 C C16 KM3 . . . B 2 28.619 25.604 -14.736 1 54.22 ? C16 KM3 201 A 1 HETATM 27 C C15 KM3 . . . B 2 28.987 24.36 -14.67 1 54.51 ? C15 KM3 201 A 1 HETATM 28 C C14 KM3 . . . B 2 28.603 23.499 -15.456 1 53.92 ? C14 KM3 201 A 1 HETATM 29 C C13 KM3 . . . B 2 27.822 23.743 -16.353 1 52.77 ? C13 KM3 201 A 1 HETATM 30 C C12 KM3 . . . B 2 27.393 24.953 -16.514 1 51.6 ? C12 KM3 201 A 1 HETATM 31 N N5 KM3 . . . B 2 25.909 29.176 -16.618 1 56.75 ? N5 KM3 201 A 1 HETATM 32 C C18 KM3 . . . B 2 25.036 28.859 -17.727 1 52.69 ? C18 KM3 201 A 1 HETATM 33 C C22 KM3 . . . B 2 25.833 30.442 -16.111 1 56.52 ? C22 KM3 201 A 1 HETATM 34 C C21 KM3 . . . B 2 24.928 31.4 -16.62 1 57.57 ? C21 KM3 201 A 1 HETATM 35 C C20 KM3 . . . B 2 24.069 31.092 -17.686 1 57.5 ? C20 KM3 201 A 1 HETATM 36 C C19 KM3 . . . B 2 24.129 29.806 -18.243 1 57.14 ? C19 KM3 201 A 1 # _model_server_stats.io_time_ms 63 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #