data_5WY8 # _model_server_result.job_id 9ydfQcpq8fwrmVuknUcQew _model_server_result.datetime_utc '2025-03-01 19:32:13' _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 5wy8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1103}' # _entry.id 5WY8 # _exptl.entry_id 5WY8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 5WY8 _cell.length_a 110.416 _cell.length_b 110.416 _cell.length_c 210.536 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WY8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 153 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 1 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,M,N _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 H N N ? 6 I N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide 5 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 ? 3 2 1 FUC NAG C1 O1 . O3 HO3 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 5 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . 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 3 n C NAG 1 C 1 NAG N 1101 NAG 3 n C FUC 2 C 2 FUC N 1112 FUC 4 n D NAG 1 D 1 NAG N 350 NAG 4 n D NAG 2 D 2 NAG N 351 NAG 4 n E NAG 1 E 1 NAG N 1401 NAG 4 n E NAG 2 E 2 NAG N 1402 NAG 5 n F NAG 1 F 1 NAG N 1501 NAG 5 n F NAG 2 F 2 NAG N 1502 NAG 5 n F BMA 3 F 3 BMA N 1503 BMA 5 n F MAN 4 F 4 MAN N 1504 MAN 4 n G NAG 1 G 1 NAG N 1601 NAG 4 n G NAG 2 G 2 NAG N 1602 NAG # 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 25 A CYS 45 1_555 A SG CYS 78 A CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 127 A CYS 147 1_555 A SG CYS 187 A CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 237 A CYS 257 1_555 A SG CYS 282 A CYS 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 B SG CYS 5 B CYS 31 1_555 B SG CYS 100 B CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 B SG CYS 27 B CYS 53 1_555 B SG CYS 92 B CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 B SG CYS 117 B CYS 143 1_555 B SG CYS 159 B CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf7 B SG CYS 138 B CYS 164 1_555 B SG CYS 190 B CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 B SG CYS 241 B CYS 267 1_555 B SG CYS 308 B CYS 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? covale ? covale1 A ND2 ASN 234 A ASN 254 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 279 A ASN 299 1_555 H C1 NAG . A NAG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 B ND2 ASN 37 B ASN 63 1_555 I C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B ND2 ASN 96 B ASN 122 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 B ND2 ASN 112 B ASN 138 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale6 B ND2 ASN 187 B ASN 213 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 sing covale ? covale7 B ND2 ASN 238 B ASN 264 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.639 sing covale ? covale8 C O3 NAG . C NAG 1 1_555 C C1 FUC . C FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale12 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale14 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? metalc ? metalc1 A OE1 GLU 86 A GLU 106 1_555 J ZN ZN . B ZN 412 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.789 ? metalc ? metalc2 A OE2 GLU 86 A GLU 106 1_555 J ZN ZN . B ZN 412 5_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc3 B OE1 GLU 182 B GLU 208 1_555 L ZN ZN . B ZN 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc4 B OE2 GLU 182 B GLU 208 1_555 L ZN ZN . B ZN 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.849 ? metalc ? metalc5 B OD1 ASP 183 B ASP 209 1_555 L ZN ZN . B ZN 414 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc6 B OD2 ASP 183 B ASP 209 1_555 L ZN ZN . B ZN 414 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.812 ? metalc ? metalc7 B NE2 HIS 283 B HIS 309 1_555 L ZN ZN . B ZN 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc8 B NE2 HIS 318 B HIS 344 1_555 J ZN ZN . B ZN 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? # _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 308 n n C1 O1 NAG sing 309 n n C1 O5 NAG sing 310 n n C1 H1 NAG sing 311 n n C2 C3 NAG sing 312 n n C2 N2 NAG sing 313 n n C2 H2 NAG sing 314 n n C3 C4 NAG sing 315 n n C3 O3 NAG sing 316 n n C3 H3 NAG sing 317 n n C4 C5 NAG sing 318 n n C4 O4 NAG sing 319 n n C4 H4 NAG sing 320 n n C5 C6 NAG sing 321 n n C5 O5 NAG sing 322 n n C5 H5 NAG sing 323 n n C6 O6 NAG sing 324 n n C6 H61 NAG sing 325 n n C6 H62 NAG sing 326 n n C7 C8 NAG sing 327 n n C7 N2 NAG sing 328 n n C7 O7 NAG doub 329 n n C8 H81 NAG sing 330 n n C8 H82 NAG sing 331 n n C8 H83 NAG sing 332 n n N2 HN2 NAG sing 333 n n O1 HO1 NAG sing 334 n n O3 HO3 NAG sing 335 n n O4 HO4 NAG sing 336 n n O6 HO6 NAG sing 337 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 5WY8 _atom_sites.fract_transf_matrix[1][1] 0.009057 _atom_sites.fract_transf_matrix[1][2] 0.005229 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010458 _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] 0.00475 _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 H 6 NAG A 1 1103 1201 NAG NAG . I 6 NAG B 1 403 1301 NAG NAG . J 7 ZN B 1 412 1 ZN ZN . K 7 ZN B 1 413 2 ZN ZN . L 7 ZN B 1 414 3 ZN ZN . M 8 HOH A 1 1201 1 HOH HOH . M 8 HOH A 2 1202 2 HOH HOH . N 8 HOH B 1 501 8 HOH HOH . N 8 HOH B 2 502 5 HOH HOH . N 8 HOH B 3 503 3 HOH HOH . N 8 HOH B 4 504 4 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 6 -43.849 29.96 -64.606 1 122.95 ? C1 NAG 1103 A 1 HETATM 2 C C2 NAG . . . H 6 -43.19 31.319 -64.868 1 124.2 ? C2 NAG 1103 A 1 HETATM 3 C C3 NAG . . . H 6 -42.932 31.51 -66.362 1 123.36 ? C3 NAG 1103 A 1 HETATM 4 C C4 NAG . . . H 6 -42.116 30.348 -66.91 1 120.87 ? C4 NAG 1103 A 1 HETATM 5 C C5 NAG . . . H 6 -42.827 29.031 -66.611 1 127.71 ? C5 NAG 1103 A 1 HETATM 6 C C6 NAG . . . H 6 -42.035 27.814 -67.036 1 120.71 ? C6 NAG 1103 A 1 HETATM 7 C C7 NAG . . . H 6 -43.727 33.035 -63.196 1 122.76 ? C7 NAG 1103 A 1 HETATM 8 C C8 NAG . . . H 6 -44.667 34.135 -62.806 1 113.56 ? C8 NAG 1103 A 1 HETATM 9 N N2 NAG . . . H 6 -44.002 32.407 -64.345 1 121.6 ? N2 NAG 1103 A 1 HETATM 10 O O3 NAG . . . H 6 -42.239 32.734 -66.578 1 130.92 ? O3 NAG 1103 A 1 HETATM 11 O O4 NAG . . . H 6 -41.937 30.495 -68.315 1 112.2 ? O4 NAG 1103 A 1 HETATM 12 O O5 NAG . . . H 6 -43.05 28.908 -65.197 1 128.8 ? O5 NAG 1103 A 1 HETATM 13 O O6 NAG . . . H 6 -41.108 27.405 -66.039 1 110.53 ? O6 NAG 1103 A 1 HETATM 14 O O7 NAG . . . H 6 -42.761 32.729 -62.503 1 126.62 ? O7 NAG 1103 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #