data_3U4X # _model_server_result.job_id OP5yeq1jOS8UX_i_XDFuWw _model_server_result.datetime_utc '2024-12-05 03:24:34' _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 3u4x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":239}' # _entry.id 3U4X # _exptl.entry_id 3U4X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 408.629 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description '5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside' _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 3U4X _cell.length_a 65.94 _cell.length_b 66.78 _cell.length_c 107.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3U4X _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 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,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' 2_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -66.78 0 3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 4 'crystal symmetry operation' 4_545 x,-y-1,-z 1 0 0 0 -1 0 0 0 -1 0 -66.78 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 OE2 GLU 8 A GLU 8 1_555 C MN MN . A MN 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc2 A OD1 ASP 10 A ASP 10 1_555 B CA CA . A CA 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc3 A OD2 ASP 10 A ASP 10 1_555 B CA CA . A CA 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? metalc ? metalc4 A OD1 ASP 10 A ASP 10 1_555 C MN MN . A MN 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc5 A O TYR 12 A TYR 12 1_555 B CA CA . A CA 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc6 A OD1 ASN 14 A ASN 14 1_555 B CA CA . A CA 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc7 A OD2 ASP 19 A ASP 19 1_555 B CA CA . A CA 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc8 A OD1 ASP 19 A ASP 19 1_555 C MN MN . A MN 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc9 A NE2 HIS 24 A HIS 24 1_555 C MN MN . A MN 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc10 B CA CA . A CA 237 1_555 E O HOH . A HOH 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc11 B CA CA . A CA 237 1_555 E O HOH . A HOH 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc12 C MN MN . A MN 238 1_555 E O HOH . A HOH 249 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? # _chem_comp.formula 'C14 H15 Br Cl N O6' _chem_comp.formula_weight 408.629 _chem_comp.id XMM _chem_comp.mon_nstd_flag n _chem_comp.name '5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms '(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL;(5-BROMO-4-CHLORO-3-INDOLYL)-Alpha-D-MANNOSE;5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannoside;5-bromo-4-chloro-1H-indol-3-yl D-mannoside;5-bromo-4-chloro-1H-indol-3-yl mannoside' # 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 O2 C2 XMM sing 344 n n O2 HO2 XMM sing 345 n n C2 C3 XMM sing 346 n n C2 C1 XMM sing 347 n n C2 H2 XMM sing 348 n n C3 O3 XMM sing 349 n n C3 C4 XMM sing 350 n n C3 H3 XMM sing 351 n n O3 HO3 XMM sing 352 n n C4 O4 XMM sing 353 n n C4 C5 XMM sing 354 n n C4 H4 XMM sing 355 n n O4 HO4 XMM sing 356 n n C5 O5 XMM sing 357 n n C5 C6 XMM sing 358 n n C5 H5 XMM sing 359 n n O5 C1 XMM sing 360 n n C6 O6 XMM sing 361 n n C6 H61 XMM sing 362 n n C6 H62 XMM sing 363 n n O6 HO6 XMM sing 364 n n C1 O1 XMM sing 365 n n C1 H1 XMM sing 366 n n O1 C7 XMM sing 367 n n C7 C8 XMM sing 368 n y C7 C11 XMM doub 369 n y C8 C9 XMM doub 370 n y C8 C10 XMM sing 371 n y C9 N1 XMM sing 372 n y C9 C12 XMM sing 373 n y N1 C11 XMM sing 374 n y N1 HN1 XMM sing 375 n n C11 H11 XMM sing 376 n n C10 CL XMM sing 377 n n C10 C13 XMM doub 378 n y C13 BR XMM sing 379 n n C13 C14 XMM sing 380 n y C14 C12 XMM doub 381 n y C14 H14 XMM sing 382 n n C12 H12 XMM sing 383 n n # _atom_sites.entry_id 3U4X _atom_sites.fract_transf_matrix[1][1] 0.015165 _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] 0.014975 _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] 0.009285 _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 CA A 1 237 237 CA CA . C 3 MN A 1 238 238 MN MN . D 4 XMM A 1 239 1 XMM XMM . E 5 HOH A 1 240 1 HOH HOH . E 5 HOH A 2 241 2 HOH HOH . E 5 HOH A 3 242 3 HOH HOH . E 5 HOH A 4 243 4 HOH HOH . E 5 HOH A 5 244 5 HOH HOH . E 5 HOH A 6 245 6 HOH HOH . E 5 HOH A 7 246 7 HOH HOH . E 5 HOH A 8 247 8 HOH HOH . E 5 HOH A 9 248 9 HOH HOH . E 5 HOH A 10 249 10 HOH HOH . E 5 HOH A 11 250 11 HOH HOH . E 5 HOH A 12 251 12 HOH HOH . E 5 HOH A 13 252 13 HOH HOH . E 5 HOH A 14 253 14 HOH HOH . E 5 HOH A 15 254 15 HOH HOH . E 5 HOH A 16 255 16 HOH HOH . E 5 HOH A 17 256 17 HOH HOH . E 5 HOH A 18 257 18 HOH HOH . E 5 HOH A 19 258 19 HOH HOH . E 5 HOH A 20 259 20 HOH HOH . E 5 HOH A 21 260 21 HOH HOH . E 5 HOH A 22 261 22 HOH HOH . E 5 HOH A 23 262 23 HOH HOH . E 5 HOH A 24 263 24 HOH HOH . E 5 HOH A 25 264 25 HOH HOH . E 5 HOH A 26 265 26 HOH HOH . E 5 HOH A 27 266 27 HOH HOH . E 5 HOH A 28 267 28 HOH HOH . E 5 HOH A 29 268 29 HOH HOH . E 5 HOH A 30 269 30 HOH HOH . E 5 HOH A 31 270 31 HOH HOH . E 5 HOH A 32 271 32 HOH HOH . E 5 HOH A 33 272 33 HOH HOH . E 5 HOH A 34 273 34 HOH HOH . E 5 HOH A 35 274 35 HOH HOH . E 5 HOH A 36 275 36 HOH HOH . E 5 HOH A 37 276 37 HOH HOH . E 5 HOH A 38 277 38 HOH HOH . E 5 HOH A 39 278 39 HOH HOH . E 5 HOH A 40 279 40 HOH HOH . E 5 HOH A 41 280 41 HOH HOH . E 5 HOH A 42 281 42 HOH HOH . E 5 HOH A 43 282 43 HOH HOH . E 5 HOH A 44 283 44 HOH HOH . E 5 HOH A 45 284 45 HOH HOH . E 5 HOH A 46 285 46 HOH HOH . E 5 HOH A 47 286 47 HOH HOH . E 5 HOH A 48 287 48 HOH HOH . E 5 HOH A 49 288 49 HOH HOH . E 5 HOH A 50 289 50 HOH HOH . E 5 HOH A 51 290 51 HOH HOH . E 5 HOH A 52 291 52 HOH HOH . E 5 HOH A 53 292 53 HOH HOH . E 5 HOH A 54 293 54 HOH HOH . E 5 HOH A 55 294 55 HOH HOH . E 5 HOH A 56 295 56 HOH HOH . E 5 HOH A 57 296 57 HOH HOH . E 5 HOH A 58 297 58 HOH HOH . E 5 HOH A 59 298 59 HOH HOH . E 5 HOH A 60 299 60 HOH HOH . E 5 HOH A 61 300 61 HOH HOH . E 5 HOH A 62 301 62 HOH HOH . E 5 HOH A 63 302 63 HOH HOH . E 5 HOH A 64 303 64 HOH HOH . E 5 HOH A 65 304 65 HOH HOH . E 5 HOH A 66 305 66 HOH HOH . E 5 HOH A 67 306 67 HOH HOH . E 5 HOH A 68 307 68 HOH HOH . E 5 HOH A 69 308 69 HOH HOH . E 5 HOH A 70 309 70 HOH HOH . E 5 HOH A 71 310 71 HOH HOH . E 5 HOH A 72 311 72 HOH HOH . E 5 HOH A 73 312 73 HOH HOH . E 5 HOH A 74 313 74 HOH HOH . E 5 HOH A 75 314 75 HOH HOH . E 5 HOH A 76 315 76 HOH HOH . E 5 HOH A 77 316 77 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 O2 XMM . . . D 4 -25.844 -10.216 22.199 1 15.99 ? O2 XMM 239 A 1 HETATM 2 C C2 XMM . . . D 4 -25.405 -9.958 23.542 1 15.68 ? C2 XMM 239 A 1 HETATM 3 C C3 XMM . . . D 4 -24.168 -10.812 23.825 1 14.89 ? C3 XMM 239 A 1 HETATM 4 O O3 XMM . . . D 4 -24.453 -12.159 23.475 1 11.4 ? O3 XMM 239 A 1 HETATM 5 C C4 XMM . . . D 4 -22.96 -10.328 23.032 1 14.09 ? C4 XMM 239 A 1 HETATM 6 O O4 XMM . . . D 4 -21.876 -11.121 23.501 1 15.14 ? O4 XMM 239 A 1 HETATM 7 C C5 XMM . . . D 4 -22.7 -8.83 23.265 1 14.03 ? C5 XMM 239 A 1 HETATM 8 O O5 XMM . . . D 4 -23.901 -8.132 22.977 1 15.71 ? O5 XMM 239 A 1 HETATM 9 C C6 XMM . . . D 4 -21.584 -8.284 22.397 1 12.81 ? C6 XMM 239 A 1 HETATM 10 O O6 XMM . . . D 4 -21.989 -8.339 21.033 1 15.35 ? O6 XMM 239 A 1 HETATM 11 C C1 XMM . . . D 4 -25.069 -8.489 23.725 1 15.49 ? C1 XMM 239 A 1 HETATM 12 O O1 XMM . . . D 4 -24.815 -8.171 25.093 1 18.42 ? O1 XMM 239 A 1 HETATM 13 C C7 XMM . . . D 4 -24.676 -6.839 25.46 1 18.54 ? C7 XMM 239 A 1 HETATM 14 C C8 XMM . . . D 4 -25.729 -6.011 25.844 1 18.55 ? C8 XMM 239 A 1 HETATM 15 C C9 XMM . . . D 4 -25.098 -4.786 26.133 1 16.89 ? C9 XMM 239 A 1 HETATM 16 N N1 XMM . . . D 4 -23.754 -4.951 25.917 1 17.82 ? N1 XMM 239 A 1 HETATM 17 C C11 XMM . . . D 4 -23.457 -6.206 25.508 1 14.74 ? C11 XMM 239 A 1 HETATM 18 C C10 XMM . . . D 4 -27.089 -6.157 25.978 1 19.59 ? C10 XMM 239 A 1 HETATM 19 CL CL XMM . . . D 4 -27.938 -7.718 25.656 1 21.62 ? CL XMM 239 A 1 HETATM 20 C C13 XMM . . . D 4 -27.845 -5.065 26.409 1 20.72 ? C13 XMM 239 A 1 HETATM 21 BR BR XMM . . . D 4 -29.713 -5.327 26.548 1 24.54 ? BR XMM 239 A 1 HETATM 22 C C14 XMM . . . D 4 -27.239 -3.835 26.691 1 20.59 ? C14 XMM 239 A 1 HETATM 23 C C12 XMM . . . D 4 -25.848 -3.693 26.545 1 16.48 ? C12 XMM 239 A 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 23 #