data_3O8X # _model_server_result.job_id t-Kywn6WgykCyO5ruFNV7Q _model_server_result.datetime_utc '2024-10-30 07:22:15' _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 3o8x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":500}' # _entry.id 3O8X # _exptl.entry_id 3O8X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 8 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 3O8X _cell.length_a 79 _cell.length_b 191.2 _cell.length_c 151.2 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3O8X _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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,F,G,H,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 8 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 1 FUC NAG C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 5 n E NAG 1 E 1 NAG F 501 NAG 5 n E NAG 2 E 2 NAG F 502 NAG 6 n F NAG 1 F 1 NAG F 511 NAG 6 n F NAG 2 F 2 NAG F 512 NAG 6 n F FUC 3 F 3 FUC F 513 FUC # 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 104 A CYS 104 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? disulf ? disulf2 A SG CYS 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf4 C SG CYS 24 C CYS 22 1_555 C SG CYS 91 C CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf5 C SG CYS 138 C CYS 139 1_555 C SG CYS 188 C CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf6 C SG CYS 163 C CYS 164 1_555 D SG CYS 169 D CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf7 D SG CYS 24 D CYS 23 1_555 D SG CYS 92 D CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf8 D SG CYS 143 D CYS 142 1_555 D SG CYS 208 D CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 H C1 NAG . A NAG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 F O6 NAG . F NAG 1 1_555 F C1 FUC . F FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 381 n n C1 O1 NAG sing 382 n n C1 O5 NAG sing 383 n n C1 H1 NAG sing 384 n n C2 C3 NAG sing 385 n n C2 N2 NAG sing 386 n n C2 H2 NAG sing 387 n n C3 C4 NAG sing 388 n n C3 O3 NAG sing 389 n n C3 H3 NAG sing 390 n n C4 C5 NAG sing 391 n n C4 O4 NAG sing 392 n n C4 H4 NAG sing 393 n n C5 C6 NAG sing 394 n n C5 O5 NAG sing 395 n n C5 H5 NAG sing 396 n n C6 O6 NAG sing 397 n n C6 H61 NAG sing 398 n n C6 H62 NAG sing 399 n n C7 C8 NAG sing 400 n n C7 N2 NAG sing 401 n n C7 O7 NAG doub 402 n n C8 H81 NAG sing 403 n n C8 H82 NAG sing 404 n n C8 H83 NAG sing 405 n n N2 HN2 NAG sing 406 n n O1 HO1 NAG sing 407 n n O3 HO3 NAG sing 408 n n O4 HO4 NAG sing 409 n n O6 HO6 NAG sing 410 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3O8X _atom_sites.fract_transf_matrix[1][1] 0.012669 _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] 0.005229 _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] 0.006613 _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 G 7 GSL A 1 501 501 GSL GSL . H 8 NAG A 1 500 500 NAG NAG . I 9 HOH A 1 287 6 HOH HOH . I 9 HOH A 2 288 8 HOH HOH . I 9 HOH A 3 289 10 HOH HOH . I 9 HOH A 4 290 11 HOH HOH . I 9 HOH A 5 291 14 HOH HOH . I 9 HOH A 6 292 15 HOH HOH . I 9 HOH A 7 293 16 HOH HOH . I 9 HOH A 8 294 17 HOH HOH . I 9 HOH A 9 295 18 HOH HOH . I 9 HOH A 10 296 28 HOH HOH . I 9 HOH A 11 297 33 HOH HOH . I 9 HOH A 12 298 35 HOH HOH . I 9 HOH A 13 299 37 HOH HOH . I 9 HOH A 14 300 45 HOH HOH . I 9 HOH A 15 301 50 HOH HOH . I 9 HOH A 16 302 56 HOH HOH . I 9 HOH A 17 303 62 HOH HOH . I 9 HOH A 18 304 64 HOH HOH . I 9 HOH A 19 305 67 HOH HOH . I 9 HOH A 20 306 80 HOH HOH . I 9 HOH A 21 307 84 HOH HOH . I 9 HOH A 22 308 89 HOH HOH . I 9 HOH A 23 309 90 HOH HOH . I 9 HOH A 24 310 91 HOH HOH . I 9 HOH A 25 311 93 HOH HOH . I 9 HOH A 26 312 94 HOH HOH . I 9 HOH A 27 313 101 HOH HOH . I 9 HOH A 28 314 103 HOH HOH . I 9 HOH A 29 315 107 HOH HOH . I 9 HOH A 30 316 110 HOH HOH . I 9 HOH A 31 317 118 HOH HOH . I 9 HOH A 32 318 123 HOH HOH . I 9 HOH A 33 319 126 HOH HOH . I 9 HOH A 34 320 135 HOH HOH . I 9 HOH A 35 321 137 HOH HOH . I 9 HOH A 36 322 138 HOH HOH . I 9 HOH A 37 323 143 HOH HOH . I 9 HOH A 38 324 149 HOH HOH . I 9 HOH A 39 325 155 HOH HOH . I 9 HOH A 40 326 156 HOH HOH . I 9 HOH A 41 327 157 HOH HOH . J 9 HOH B 1 100 5 HOH HOH . J 9 HOH B 2 101 21 HOH HOH . J 9 HOH B 3 102 22 HOH HOH . J 9 HOH B 4 103 24 HOH HOH . J 9 HOH B 5 104 42 HOH HOH . J 9 HOH B 6 105 46 HOH HOH . J 9 HOH B 7 106 47 HOH HOH . J 9 HOH B 8 107 54 HOH HOH . J 9 HOH B 9 108 72 HOH HOH . J 9 HOH B 10 109 96 HOH HOH . J 9 HOH B 11 158 158 HOH HOH . K 9 HOH C 1 102 102 HOH HOH . K 9 HOH C 2 211 7 HOH HOH . K 9 HOH C 3 212 25 HOH HOH . K 9 HOH C 4 213 49 HOH HOH . K 9 HOH C 5 214 52 HOH HOH . K 9 HOH C 6 215 76 HOH HOH . K 9 HOH C 7 216 77 HOH HOH . K 9 HOH C 8 217 78 HOH HOH . K 9 HOH C 9 218 87 HOH HOH . K 9 HOH C 10 219 104 HOH HOH . K 9 HOH C 11 220 115 HOH HOH . K 9 HOH C 12 221 119 HOH HOH . K 9 HOH C 13 222 122 HOH HOH . K 9 HOH C 14 223 124 HOH HOH . K 9 HOH C 15 224 128 HOH HOH . K 9 HOH C 16 225 142 HOH HOH . K 9 HOH C 17 226 162 HOH HOH . K 9 HOH C 18 227 163 HOH HOH . K 9 HOH C 19 228 164 HOH HOH . L 9 HOH D 1 241 1 HOH HOH . L 9 HOH D 2 242 3 HOH HOH . L 9 HOH D 3 243 19 HOH HOH . L 9 HOH D 4 244 23 HOH HOH . L 9 HOH D 5 245 26 HOH HOH . L 9 HOH D 6 246 29 HOH HOH . L 9 HOH D 7 247 30 HOH HOH . L 9 HOH D 8 248 31 HOH HOH . L 9 HOH D 9 249 32 HOH HOH . L 9 HOH D 10 250 34 HOH HOH . L 9 HOH D 11 251 43 HOH HOH . L 9 HOH D 12 252 44 HOH HOH . L 9 HOH D 13 253 48 HOH HOH . L 9 HOH D 14 254 58 HOH HOH . L 9 HOH D 15 255 61 HOH HOH . L 9 HOH D 16 256 63 HOH HOH . L 9 HOH D 17 257 71 HOH HOH . L 9 HOH D 18 258 73 HOH HOH . L 9 HOH D 19 259 74 HOH HOH . L 9 HOH D 20 260 86 HOH HOH . L 9 HOH D 21 261 88 HOH HOH . L 9 HOH D 22 262 95 HOH HOH . L 9 HOH D 23 263 97 HOH HOH . L 9 HOH D 24 264 98 HOH HOH . L 9 HOH D 25 265 100 HOH HOH . L 9 HOH D 26 266 106 HOH HOH . L 9 HOH D 27 267 111 HOH HOH . L 9 HOH D 28 268 112 HOH HOH . L 9 HOH D 29 269 120 HOH HOH . L 9 HOH D 30 270 146 HOH HOH . L 9 HOH D 31 271 147 HOH HOH . L 9 HOH D 32 272 152 HOH HOH . L 9 HOH D 33 273 161 HOH HOH . L 9 HOH D 34 274 165 HOH HOH . L 9 HOH D 35 275 166 HOH HOH . L 9 HOH D 36 276 167 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 NAG . . . H 8 -33.746 41.949 -17.752 1 55.87 ? C1 NAG 500 A 1 HETATM 2 C C2 NAG . . . H 8 -33.098 43.308 -18.062 1 60.95 ? C2 NAG 500 A 1 HETATM 3 C C3 NAG . . . H 8 -31.962 43.274 -19.08 1 62.35 ? C3 NAG 500 A 1 HETATM 4 C C4 NAG . . . H 8 -30.989 42.143 -18.75 1 60.94 ? C4 NAG 500 A 1 HETATM 5 C C5 NAG . . . H 8 -31.761 40.807 -18.749 1 56.11 ? C5 NAG 500 A 1 HETATM 6 C C6 NAG . . . H 8 -30.849 39.598 -18.469 1 54.41 ? C6 NAG 500 A 1 HETATM 7 C C7 NAG . . . H 8 -34.596 45.214 -17.834 1 67.1 ? C7 NAG 500 A 1 HETATM 8 C C8 NAG . . . H 8 -35.621 46.07 -18.526 1 68.66 ? C8 NAG 500 A 1 HETATM 9 N N2 NAG . . . H 8 -34.1 44.219 -18.568 1 63.95 ? N2 NAG 500 A 1 HETATM 10 O O3 NAG . . . H 8 -31.311 44.531 -19.092 1 65.29 ? O3 NAG 500 A 1 HETATM 11 O O4 NAG . . . H 8 -29.91 42.151 -19.675 1 61.78 ? O4 NAG 500 A 1 HETATM 12 O O5 NAG . . . H 8 -32.868 40.813 -17.841 1 53.78 ? O5 NAG 500 A 1 HETATM 13 O O6 NAG . . . H 8 -30.362 39.574 -17.139 1 52.94 ? O6 NAG 500 A 1 HETATM 14 O O7 NAG . . . H 8 -34.26 45.441 -16.664 1 67.8 ? O7 NAG 500 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #