data_3I1L # _model_server_result.job_id Tmr9-1Htx6en7riqBgEm7g _model_server_result.datetime_utc '2025-07-14 13:46:09' _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 3i1l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1001}' # _entry.id 3I1L # _exptl.entry_id 3I1L _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 407.37 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.02 _cell.angle_gamma 90 _cell.entry_id 3I1L _cell.length_a 156.03 _cell.length_b 103.69 _cell.length_c 97.07 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3I1L _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_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,D,E,F,G,H,I,J,Z 1 1,2 B,C,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,AA,BA 2 1 # 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_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 K N N ? 2 S N 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 disulf ? disulf1 A SG CYS 27 A CYS 50 1_555 A SG CYS 43 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 74 A CYS 97 1_555 A SG CYS 122 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 94 A CYS 117 1_555 A SG CYS 142 A CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 181 A CYS 204 1_555 A SG CYS 258 A CYS 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 A SG CYS 189 A CYS 212 1_555 A SG CYS 231 A CYS 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 A SG CYS 195 A CYS 218 1_555 A SG CYS 202 A CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 A SG CYS 289 A CYS 312 1_555 A SG CYS 294 A CYS 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf8 A SG CYS 331 A CYS 354 1_555 A SG CYS 356 A CYS 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 B SG CYS 27 B CYS 50 1_555 B SG CYS 43 B CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 B SG CYS 74 B CYS 97 1_555 B SG CYS 122 B CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 B SG CYS 94 B CYS 117 1_555 B SG CYS 142 B CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf12 B SG CYS 181 B CYS 204 1_555 B SG CYS 258 B CYS 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 B SG CYS 189 B CYS 212 1_555 B SG CYS 231 B CYS 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf14 B SG CYS 195 B CYS 218 1_555 B SG CYS 202 B CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf15 B SG CYS 289 B CYS 312 1_555 B SG CYS 294 B CYS 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf16 B SG CYS 331 B CYS 354 1_555 B SG CYS 356 B CYS 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf17 C SG CYS 27 C CYS 50 1_555 C SG CYS 43 C CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf18 C SG CYS 74 C CYS 97 1_555 C SG CYS 122 C CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf19 C SG CYS 94 C CYS 117 1_555 C SG CYS 142 C CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf20 C SG CYS 181 C CYS 204 1_555 C SG CYS 258 C CYS 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf21 C SG CYS 189 C CYS 212 1_555 C SG CYS 231 C CYS 254 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf22 C SG CYS 195 C CYS 218 1_555 C SG CYS 202 C CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf23 C SG CYS 289 C CYS 312 1_555 C SG CYS 294 C CYS 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf24 C SG CYS 331 C CYS 354 1_555 C SG CYS 356 C CYS 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? covale ? covale1 A ND2 ASN 62 A ASN 85 1_555 J C1 NAG . A NAG 5158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 A ND2 ASN 91 A ASN 114 1_555 F C1 NAG . A NAG 5154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 139 A ASN 162 1_555 G C1 NAG . A NAG 5155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale4 A ND2 ASN 221 A ASN 244 1_555 H C1 NAG . A NAG 5156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale5 A ND2 ASN 298 A ASN 321 1_555 I C1 NAG . A NAG 5157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale6 B ND2 ASN 62 B ASN 85 1_555 Q C1 NAG . B NAG 5158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 B ND2 ASN 91 B ASN 114 1_555 M C1 NAG . B NAG 5154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 B ND2 ASN 133 B ASN 156 1_555 R C1 NAG . B NAG 5159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 B ND2 ASN 139 B ASN 162 1_555 N C1 NAG . B NAG 5155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale10 B ND2 ASN 221 B ASN 244 1_555 O C1 NAG . B NAG 5156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 B ND2 ASN 298 B ASN 321 1_555 P C1 NAG . B NAG 5157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale12 C ND2 ASN 62 C ASN 85 1_555 Y C1 NAG . C NAG 5158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale13 C ND2 ASN 91 C ASN 114 1_555 U C1 NAG . C NAG 5154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale14 C ND2 ASN 139 C ASN 162 1_555 V C1 NAG . C NAG 5155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale15 C ND2 ASN 221 C ASN 244 1_555 W C1 NAG . C NAG 5156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale16 C ND2 ASN 298 C ASN 321 1_555 X C1 NAG . C NAG 5157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? # _chem_comp.formula 'C16 H25 N O11' _chem_comp.formula_weight 407.37 _chem_comp.id SIO _chem_comp.mon_nstd_flag n _chem_comp.name 'methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid' _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms 'methyl 4,9-di-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid;methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid;methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosidonic acid;methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosidonic acid' # 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 CA4 OA4 SIO doub 327 n n O4 CA4 SIO sing 328 n n CA4 CM4 SIO sing 329 n n CM4 HM4 SIO sing 330 n n CM4 HM4A SIO sing 331 n n CM4 HM4B SIO sing 332 n n C4 O4 SIO sing 333 n n C5 C4 SIO sing 334 n n C3 C4 SIO sing 335 n n C4 H4 SIO sing 336 n n C6 C5 SIO sing 337 n n C5 N5 SIO sing 338 n n C5 H5 SIO sing 339 n n N5 C10 SIO sing 340 n n N5 HN5 SIO sing 341 n n O10 C10 SIO doub 342 n n C10 C11 SIO sing 343 n n C11 H111 SIO sing 344 n n C11 H113 SIO sing 345 n n C11 H112 SIO sing 346 n n C2 C3 SIO sing 347 n n C3 H32 SIO sing 348 n n C3 H31 SIO sing 349 n n O2 C2 SIO sing 350 n n O6 C2 SIO sing 351 n n C2 C1 SIO sing 352 n n CM2 O2 SIO sing 353 n n CM2 HM2 SIO sing 354 n n CM2 HM2A SIO sing 355 n n CM2 HM2B SIO sing 356 n n O1A C1 SIO doub 357 n n C1 O1B SIO sing 358 n n O1B HO1B SIO sing 359 n n O6 C6 SIO sing 360 n n C7 C6 SIO sing 361 n n C6 H6 SIO sing 362 n n O7 C7 SIO sing 363 n n C8 C7 SIO sing 364 n n C7 H7 SIO sing 365 n n O7 HO7 SIO sing 366 n n C9 C8 SIO sing 367 n n C8 O8 SIO sing 368 n n C8 H8 SIO sing 369 n n O8 HO8 SIO sing 370 n n C9 O9 SIO sing 371 n n C9 H92 SIO sing 372 n n C9 H91 SIO sing 373 n n CA9 O9 SIO sing 374 n n OA9 CA9 SIO doub 375 n n CA9 CM9 SIO sing 376 n n CM9 HM9 SIO sing 377 n n CM9 HM9A SIO sing 378 n n CM9 HM9B SIO sing 379 n n # _atom_sites.entry_id 3I1L _atom_sites.fract_transf_matrix[1][1] 0.006409 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000676 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009644 _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] 0.010359 _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 D 2 SIO A 1 1001 1001 SIO SIO . E 3 ACY A 1 2001 2001 ACY ACY . F 4 NAG A 1 5154 5154 NAG NAG . G 4 NAG A 1 5155 5155 NAG NAG . H 4 NAG A 1 5156 5156 NAG NAG . I 4 NAG A 1 5157 5157 NAG NAG . J 4 NAG A 1 5158 5158 NAG NAG . K 2 SIO B 1 1001 1001 SIO SIO . L 3 ACY B 1 2001 2001 ACY ACY . M 4 NAG B 1 5154 5154 NAG NAG . N 4 NAG B 1 5155 5155 NAG NAG . O 4 NAG B 1 5156 5156 NAG NAG . P 4 NAG B 1 5157 5157 NAG NAG . Q 4 NAG B 1 5158 5158 NAG NAG . R 4 NAG B 1 5159 5159 NAG NAG . S 2 SIO C 1 1001 1001 SIO SIO . T 3 ACY C 1 2001 2001 ACY ACY . U 4 NAG C 1 5154 5154 NAG NAG . V 4 NAG C 1 5155 5155 NAG NAG . W 4 NAG C 1 5156 5156 NAG NAG . X 4 NAG C 1 5157 5157 NAG NAG . Y 4 NAG C 1 5158 5158 NAG NAG . Z 5 HOH A 1 4 4 HOH HOH . Z 5 HOH A 2 9 9 HOH HOH . Z 5 HOH A 3 11 11 HOH HOH . AA 5 HOH B 1 2 2 HOH HOH . AA 5 HOH B 2 5 5 HOH HOH . AA 5 HOH B 3 8 8 HOH HOH . BA 5 HOH C 1 1 1 HOH HOH . BA 5 HOH C 2 3 3 HOH HOH . BA 5 HOH C 3 6 6 HOH HOH . BA 5 HOH C 4 7 7 HOH HOH . BA 5 HOH C 5 10 10 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 OA4 SIO . . . D 2 -10.481 -13.215 18.823 1 56.83 ? OA4 SIO 1001 A 1 HETATM 2 C CA4 SIO . . . D 2 -11.617 -13.114 19.255 1 56.5 ? CA4 SIO 1001 A 1 HETATM 3 C CM4 SIO . . . D 2 -12.136 -13.992 20.362 1 57.21 ? CM4 SIO 1001 A 1 HETATM 4 O O4 SIO . . . D 2 -12.484 -12.091 18.687 1 55.8 ? O4 SIO 1001 A 1 HETATM 5 C C4 SIO . . . D 2 -12.934 -12.328 17.356 1 54.2 ? C4 SIO 1001 A 1 HETATM 6 C C5 SIO . . . D 2 -13.11 -10.96 16.674 1 53.71 ? C5 SIO 1001 A 1 HETATM 7 N N5 SIO . . . D 2 -11.77 -10.542 16.241 1 52.72 ? N5 SIO 1001 A 1 HETATM 8 C C10 SIO . . . D 2 -10.995 -9.624 16.843 1 51.96 ? C10 SIO 1001 A 1 HETATM 9 O O10 SIO . . . D 2 -11.303 -8.996 17.847 1 51.18 ? O10 SIO 1001 A 1 HETATM 10 C C11 SIO . . . D 2 -9.666 -9.391 16.19 1 51.26 ? C11 SIO 1001 A 1 HETATM 11 C C3 SIO . . . D 2 -14.205 -13.176 17.447 1 53.55 ? C3 SIO 1001 A 1 HETATM 12 C C2 SIO . . . D 2 -15.189 -13.061 16.272 1 54.19 ? C2 SIO 1001 A 1 HETATM 13 O O2 SIO . . . D 2 -16.495 -13.299 16.777 1 54.29 ? O2 SIO 1001 A 1 HETATM 14 C CM2 SIO . . . D 2 -17.517 -12.892 15.88 1 53.75 ? CM2 SIO 1001 A 1 HETATM 15 C C1 SIO . . . D 2 -14.868 -14.137 15.248 1 54.12 ? C1 SIO 1001 A 1 HETATM 16 O O1B SIO . . . D 2 -14.418 -15.22 15.678 1 54.62 ? O1B SIO 1001 A 1 HETATM 17 O O1A SIO . . . D 2 -15.072 -13.938 14.025 1 53.42 ? O1A SIO 1001 A 1 HETATM 18 O O6 SIO . . . D 2 -15.19 -11.742 15.697 1 54.42 ? O6 SIO 1001 A 1 HETATM 19 C C6 SIO . . . D 2 -13.939 -11.119 15.397 1 53.94 ? C6 SIO 1001 A 1 HETATM 20 C C7 SIO . . . D 2 -14.297 -9.821 14.672 1 54.38 ? C7 SIO 1001 A 1 HETATM 21 O O7 SIO . . . D 2 -14.684 -8.778 15.576 1 53.72 ? O7 SIO 1001 A 1 HETATM 22 C C8 SIO . . . D 2 -15.462 -10.049 13.713 1 54.27 ? C8 SIO 1001 A 1 HETATM 23 O O8 SIO . . . D 2 -15.24 -11.251 12.969 1 54.52 ? O8 SIO 1001 A 1 HETATM 24 C C9 SIO . . . D 2 -15.602 -8.887 12.742 1 54.72 ? C9 SIO 1001 A 1 HETATM 25 O O9 SIO . . . D 2 -14.354 -8.671 12.085 1 54.9 ? O9 SIO 1001 A 1 HETATM 26 C CA9 SIO . . . D 2 -14.215 -7.588 11.13 1 55.7 ? CA9 SIO 1001 A 1 HETATM 27 O OA9 SIO . . . D 2 -15.073 -6.717 11.113 1 56.02 ? OA9 SIO 1001 A 1 HETATM 28 C CM9 SIO . . . D 2 -13.034 -7.582 10.205 1 55.27 ? CM9 SIO 1001 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #