data_3OE5
#
_model_server_result.job_id            jX_JKql5bc1CUZ9wXiHmew 
_model_server_result.datetime_utc      '2024-11-22 18:04:38' 
_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          3oe5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":223}' 
#
_entry.id    3OE5 
#
_exptl.entry_id    3OE5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              449.434 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-[(E)-3-[(2R,3S,4R,5S)-3,4-dihydroxy-5-pyridin-4-ylsulfanyl-oxolan-2-yl]prop-2-enyl]-2,3-dihydroxy-5-nitro-benzamide 
_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         120 
_cell.entry_id            3OE5 
_cell.length_a            50.687 
_cell.length_b            50.687 
_cell.length_c            167.765 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3OE5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 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
? monomeric 1 author_defined_assembly 1 
PISA dimeric 2 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,B,C,D 1 1 
A,B,C,D 2 1,2 
#
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' 4_645 y+1,x-1,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 76.0305 -43.89623 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 OD1 ASP 141 A ASP 141 1_555 B MG MG . A MG 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
metalc ? metalc2 A OD2 ASP 169 A ASP 169 1_555 B MG MG . A MG 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc3 A OD1 ASN 170 A ASN 170 1_555 B MG MG . A MG 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc4 B MG MG . A MG 222 1_555 C O22 611 . A 611 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc5 B MG MG . A MG 222 1_555 C O23 611 . A 611 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? 
metalc ? metalc6 B MG MG . A MG 222 1_555 D O HOH . A HOH 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
#
_chem_comp.formula           'C19 H19 N3 O8 S' 
_chem_comp.formula_weight    449.434 
_chem_comp.id                611 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-[(E)-3-[(2R,3S,4R,5S)-3,4-dihydroxy-5-pyridin-4-ylsulfanyl-oxolan-2-yl]prop-2-enyl]-2,3-dihydroxy-5-nitro-benzamide 
_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
C1 C2 611 sing 1 n n 
C1 C5 611 sing 2 n n 
C1 O8 611 sing 3 n n 
C2 C3 611 sing 4 n n 
C2 O9 611 sing 5 n n 
C3 O4 611 sing 6 n n 
C3 S7 611 sing 7 n n 
O4 C5 611 sing 8 n n 
C5 C6 611 sing 9 n n 
C6 C10 611 doub 10 n n 
S7 C11 611 sing 11 n n 
C10 C12 611 sing 12 n n 
C11 C27 611 doub 13 n y 
C11 C31 611 sing 14 e y 
C12 N13 611 sing 15 n n 
N13 C14 611 sing 16 n n 
C14 C15 611 sing 17 n n 
C14 O24 611 doub 18 n n 
C15 C16 611 doub 19 n y 
C15 C20 611 sing 20 n y 
C16 C17 611 sing 21 n y 
C16 O22 611 sing 22 n n 
C17 C18 611 doub 23 n y 
C17 O23 611 sing 24 n n 
C18 C19 611 sing 25 n y 
C19 C20 611 doub 26 n y 
C19 N21 611 sing 27 n n 
N21 O25 611 doub 28 n n 
N21 O26 611 sing 29 n n 
C27 C28 611 sing 30 n y 
C28 N29 611 doub 31 n y 
N29 C30 611 sing 32 n y 
C30 C31 611 doub 33 n y 
C1 H1 611 sing 34 n n 
C2 H2 611 sing 35 n n 
C3 H3 611 sing 36 n n 
C5 H5 611 sing 37 n n 
C6 H6 611 sing 38 n n 
O8 HO8 611 sing 39 n n 
O9 HO9 611 sing 40 n n 
C10 H10 611 sing 41 n n 
C12 H12 611 sing 42 n n 
C12 H12A 611 sing 43 n n 
N13 HN13 611 sing 44 n n 
C18 H18 611 sing 45 n n 
C20 H20 611 sing 46 n n 
O22 HO22 611 sing 47 n n 
O23 HO23 611 sing 48 n n 
C27 H27 611 sing 49 n n 
C28 H28 611 sing 50 n n 
C30 H30 611 sing 51 n n 
C31 H31 611 sing 52 n n 
#
_atom_sites.entry_id                     3OE5 
_atom_sites.fract_transf_matrix[1][1]    0.019729 
_atom_sites.fract_transf_matrix[1][2]    0.011391 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022781 
_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]    0.005961 
_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 MG A 1 222 1 MG MG . 
C 3 611 A 1 223 1 611 UNL . 
D 4 HOH A 1 224 1 HOH HOH . 
D 4 HOH A 2 225 2 HOH HOH . 
D 4 HOH A 3 226 3 HOH HOH . 
D 4 HOH A 4 227 4 HOH HOH . 
D 4 HOH A 5 228 5 HOH HOH . 
D 4 HOH A 6 229 6 HOH HOH . 
D 4 HOH A 7 230 7 HOH HOH . 
D 4 HOH A 8 231 8 HOH HOH . 
D 4 HOH A 9 232 9 HOH HOH . 
D 4 HOH A 10 233 10 HOH HOH . 
D 4 HOH A 11 234 11 HOH HOH . 
D 4 HOH A 12 235 12 HOH HOH . 
D 4 HOH A 13 236 13 HOH HOH . 
D 4 HOH A 14 237 14 HOH HOH . 
D 4 HOH A 15 238 15 HOH HOH . 
D 4 HOH A 16 239 16 HOH HOH . 
D 4 HOH A 17 240 17 HOH HOH . 
D 4 HOH A 18 241 18 HOH HOH . 
D 4 HOH A 19 242 19 HOH HOH . 
D 4 HOH A 20 243 20 HOH HOH . 
D 4 HOH A 21 244 21 HOH HOH . 
D 4 HOH A 22 245 22 HOH HOH . 
D 4 HOH A 23 246 23 HOH HOH . 
D 4 HOH A 24 247 24 HOH HOH . 
D 4 HOH A 25 248 25 HOH HOH . 
D 4 HOH A 26 249 26 HOH HOH . 
D 4 HOH A 27 250 27 HOH HOH . 
D 4 HOH A 28 251 28 HOH HOH . 
D 4 HOH A 29 252 29 HOH HOH . 
D 4 HOH A 30 253 30 HOH HOH . 
D 4 HOH A 31 254 31 HOH HOH . 
D 4 HOH A 32 255 32 HOH HOH . 
D 4 HOH A 33 256 33 HOH HOH . 
D 4 HOH A 34 257 34 HOH HOH . 
D 4 HOH A 35 258 35 HOH HOH . 
D 4 HOH A 36 259 36 HOH HOH . 
D 4 HOH A 37 260 37 HOH HOH . 
D 4 HOH A 38 261 38 HOH HOH . 
D 4 HOH A 39 262 39 HOH HOH . 
D 4 HOH A 40 263 40 HOH HOH . 
D 4 HOH A 41 264 41 HOH HOH . 
D 4 HOH A 42 265 42 HOH HOH . 
D 4 HOH A 43 266 43 HOH HOH . 
D 4 HOH A 44 267 44 HOH HOH . 
D 4 HOH A 45 268 45 HOH HOH . 
D 4 HOH A 46 269 46 HOH HOH . 
D 4 HOH A 47 270 47 HOH HOH . 
D 4 HOH A 48 271 48 HOH HOH . 
D 4 HOH A 49 272 49 HOH HOH . 
D 4 HOH A 50 273 50 HOH HOH . 
D 4 HOH A 51 274 51 HOH HOH . 
D 4 HOH A 52 275 52 HOH HOH . 
D 4 HOH A 53 276 53 HOH HOH . 
D 4 HOH A 54 277 54 HOH HOH . 
D 4 HOH A 55 278 55 HOH HOH . 
D 4 HOH A 56 279 56 HOH HOH . 
D 4 HOH A 57 280 57 HOH HOH . 
D 4 HOH A 58 281 58 HOH HOH . 
D 4 HOH A 59 282 59 HOH HOH . 
D 4 HOH A 60 283 60 HOH HOH . 
D 4 HOH A 61 284 61 HOH HOH . 
D 4 HOH A 62 285 62 HOH HOH . 
D 4 HOH A 63 286 63 HOH HOH . 
D 4 HOH A 64 287 64 HOH HOH . 
D 4 HOH A 65 288 65 HOH HOH . 
D 4 HOH A 66 289 66 HOH HOH . 
D 4 HOH A 67 290 67 HOH HOH . 
D 4 HOH A 68 291 68 HOH HOH . 
D 4 HOH A 69 292 69 HOH HOH . 
D 4 HOH A 70 293 70 HOH HOH . 
D 4 HOH A 71 294 71 HOH HOH . 
D 4 HOH A 72 295 72 HOH HOH . 
D 4 HOH A 73 296 73 HOH HOH . 
D 4 HOH A 74 297 74 HOH HOH . 
D 4 HOH A 75 298 75 HOH HOH . 
D 4 HOH A 76 299 77 HOH HOH . 
D 4 HOH A 77 300 78 HOH HOH . 
D 4 HOH A 78 301 79 HOH HOH . 
D 4 HOH A 79 302 80 HOH HOH . 
D 4 HOH A 80 303 81 HOH HOH . 
D 4 HOH A 81 304 82 HOH HOH . 
D 4 HOH A 82 305 83 HOH HOH . 
D 4 HOH A 83 306 84 HOH HOH . 
D 4 HOH A 84 307 85 HOH HOH . 
D 4 HOH A 85 308 86 HOH HOH . 
D 4 HOH A 86 309 87 HOH HOH . 
D 4 HOH A 87 310 88 HOH HOH . 
D 4 HOH A 88 311 89 HOH HOH . 
D 4 HOH A 89 312 90 HOH HOH . 
D 4 HOH A 90 313 91 HOH HOH . 
D 4 HOH A 91 314 92 HOH HOH . 
D 4 HOH A 92 315 93 HOH HOH . 
D 4 HOH A 93 316 94 HOH HOH . 
D 4 HOH A 94 317 95 HOH HOH . 
D 4 HOH A 95 318 96 HOH HOH . 
D 4 HOH A 96 319 97 HOH HOH . 
D 4 HOH A 97 320 98 HOH HOH . 
D 4 HOH A 98 321 99 HOH HOH . 
D 4 HOH A 99 322 100 HOH HOH . 
D 4 HOH A 100 323 101 HOH HOH . 
D 4 HOH A 101 324 102 HOH HOH . 
D 4 HOH A 102 325 103 HOH HOH . 
D 4 HOH A 103 326 104 HOH HOH . 
D 4 HOH A 104 327 105 HOH HOH . 
D 4 HOH A 105 328 106 HOH HOH . 
D 4 HOH A 106 329 107 HOH HOH . 
D 4 HOH A 107 330 108 HOH HOH . 
D 4 HOH A 108 331 109 HOH HOH . 
D 4 HOH A 109 332 110 HOH HOH . 
D 4 HOH A 110 333 111 HOH HOH . 
D 4 HOH A 111 334 112 HOH HOH . 
D 4 HOH A 112 335 113 HOH HOH . 
D 4 HOH A 113 336 114 HOH HOH . 
D 4 HOH A 114 337 115 HOH HOH . 
D 4 HOH A 115 338 116 HOH HOH . 
D 4 HOH A 116 339 117 HOH HOH . 
D 4 HOH A 117 340 118 HOH HOH . 
D 4 HOH A 118 341 119 HOH HOH . 
D 4 HOH A 119 342 120 HOH HOH . 
D 4 HOH A 120 343 121 HOH HOH . 
D 4 HOH A 121 344 122 HOH HOH . 
D 4 HOH A 122 345 123 HOH HOH . 
D 4 HOH A 123 346 124 HOH HOH . 
D 4 HOH A 124 347 125 HOH HOH . 
D 4 HOH A 125 348 126 HOH HOH . 
D 4 HOH A 126 349 127 HOH HOH . 
D 4 HOH A 127 350 128 HOH HOH . 
D 4 HOH A 128 351 129 HOH HOH . 
D 4 HOH A 129 352 130 HOH HOH . 
D 4 HOH A 130 353 131 HOH HOH . 
D 4 HOH A 131 354 132 HOH HOH . 
D 4 HOH A 132 355 133 HOH HOH . 
D 4 HOH A 133 356 134 HOH HOH . 
D 4 HOH A 134 357 135 HOH HOH . 
D 4 HOH A 135 358 136 HOH HOH . 
D 4 HOH A 136 359 137 HOH HOH . 
D 4 HOH A 137 360 138 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 C C1 611 . . . C 3 20.464 -30.329 13.322 1 25.5 ? C1 611 223 A 1 
HETATM 2 C C2 611 . . . C 3 19.387 -31.433 13.33 1 24.97 ? C2 611 223 A 1 
HETATM 3 C C3 611 . . . C 3 18.068 -30.667 13.201 1 23.11 ? C3 611 223 A 1 
HETATM 4 O O4 611 . . . C 3 18.423 -29.406 12.616 1 23.78 ? O4 611 223 A 1 
HETATM 5 C C5 611 . . . C 3 19.784 -29.416 12.256 1 23.34 ? C5 611 223 A 1 
HETATM 6 C C6 611 . . . C 3 19.918 -30.003 10.916 1 27.18 ? C6 611 223 A 1 
HETATM 7 S S7 611 . . . C 3 16.95 -31.614 12.158 1 23.77 ? S7 611 223 A 1 
HETATM 8 O O8 611 . . . C 3 20.477 -29.62 14.559 1 26.87 ? O8 611 223 A 1 
HETATM 9 O O9 611 . . . C 3 19.38 -32.212 14.533 1 26.07 ? O9 611 223 A 1 
HETATM 10 C C10 611 . . . C 3 20.68 -29.442 10.019 1 25.88 ? C10 611 223 A 1 
HETATM 11 C C11 611 . . . C 3 15.409 -31.14 12.597 1 18.43 ? C11 611 223 A 1 
HETATM 12 C C12 611 . . . C 3 20.846 -29.974 8.634 1 23.72 ? C12 611 223 A 1 
HETATM 13 N N13 611 . . . C 3 21.798 -29.219 7.86 1 20.3 ? N13 611 223 A 1 
HETATM 14 C C14 611 . . . C 3 22.614 -29.7 6.904 1 23.44 ? C14 611 223 A 1 
HETATM 15 C C15 611 . . . C 3 23.668 -28.849 6.296 1 23.01 ? C15 611 223 A 1 
HETATM 16 C C16 611 . . . C 3 23.693 -27.44 6.5 1 21.2 ? C16 611 223 A 1 
HETATM 17 C C17 611 . . . C 3 24.767 -26.726 5.902 1 20.47 ? C17 611 223 A 1 
HETATM 18 C C18 611 . . . C 3 25.743 -27.29 5.13 1 22.59 ? C18 611 223 A 1 
HETATM 19 C C19 611 . . . C 3 25.693 -28.692 4.965 1 24.36 ? C19 611 223 A 1 
HETATM 20 C C20 611 . . . C 3 24.662 -29.466 5.541 1 22.98 ? C20 611 223 A 1 
HETATM 21 N N21 611 . . . C 3 26.693 -29.36 4.162 1 30.39 ? N21 611 223 A 1 
HETATM 22 O O22 611 . . . C 3 22.782 -26.746 7.191 1 20.56 ? O22 611 223 A 1 
HETATM 23 O O23 611 . . . C 3 24.812 -25.357 6.088 1 22.18 ? O23 611 223 A 1 
HETATM 24 O O24 611 . . . C 3 22.504 -30.901 6.519 1 22.8 ? O24 611 223 A 1 
HETATM 25 O O25 611 . . . C 3 27.496 -28.742 3.514 1 33.35 ? O25 611 223 A 1 
HETATM 26 O O26 611 . . . C 3 26.658 -30.582 4.153 1 37.09 ? O26 611 223 A 1 
HETATM 27 C C27 611 . . . C 3 14.235 -31.884 12.159 1 21.15 ? C27 611 223 A 1 
HETATM 28 C C28 611 . . . C 3 12.955 -31.486 12.564 1 22.56 ? C28 611 223 A 1 
HETATM 29 N N29 611 . . . C 3 12.699 -30.395 13.361 1 25.19 ? N29 611 223 A 1 
HETATM 30 C C30 611 . . . C 3 13.814 -29.677 13.773 1 20.21 ? C30 611 223 A 1 
HETATM 31 C C31 611 . . . C 3 15.119 -30.017 13.429 1 22.53 ? C31 611 223 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           262 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           31 
#