data_7YIX # _model_server_result.job_id 48lJVPxbXHb77dF0HZvoig _model_server_result.datetime_utc '2024-10-25 20:30:18' _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 7yix # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":602}' # _entry.id 7YIX # _exptl.entry_id 7YIX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 4 _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 7YIX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7YIX _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_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,O,P,Q,R,S,T _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 ? _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 ? 4 I N N ? 4 J N N ? 4 O N N ? 4 P N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 E NAG 1 E 1 NAG A 611 NAG 3 n E NAG 2 E 2 NAG A 612 NAG 3 n F NAG 1 F 1 NAG A 631 NAG 3 n F NAG 2 F 2 NAG A 632 NAG 3 n G NAG 1 G 1 NAG B 611 NAG 3 n G NAG 2 G 2 NAG B 612 NAG 3 n H NAG 1 H 1 NAG B 631 NAG 3 n H NAG 2 H 2 NAG B 632 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 141 A CYS 139 1_555 A SG CYS 203 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 491 A CYS 489 1_555 A SG CYS 499 A CYS 497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 B SG CYS 141 B CYS 139 1_555 B SG CYS 203 B CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 B SG CYS 491 B CYS 489 1_555 B SG CYS 499 B CYS 497 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 C SG CYS 49 C CYS 49 1_555 C SG CYS 123 C CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 C SG CYS 186 C CYS 186 1_555 C SG CYS 251 C CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf7 D SG CYS 49 D CYS 49 1_555 D SG CYS 123 D CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 D SG CYS 186 D CYS 186 1_555 D SG CYS 251 D CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 142 A ASN 140 1_555 I C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 273 A ASN 271 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 305 A ASN 303 1_555 J C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 432 A ASN 430 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 B ND2 ASN 142 B ASN 140 1_555 O C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 B ND2 ASN 273 B ASN 271 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 B ND2 ASN 305 B ASN 303 1_555 P C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 B ND2 ASN 432 B ASN 430 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale11 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale12 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 A OD2 ASP 62 A ASP 60 1_555 K MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc2 A OE1 GLU 237 A GLU 235 1_555 M CA CA . A CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc3 A OE2 GLU 237 A GLU 235 1_555 M CA CA . A CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc4 A O PHE 292 A PHE 290 1_555 M CA CA . A CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc5 A OE1 GLU 293 A GLU 291 1_555 M CA CA . A CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? metalc ? metalc6 A OD1 ASP 308 A ASP 306 1_555 M CA CA . A CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc7 A OD1 ASP 339 A ASP 337 1_555 L ZN ZN . A ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc8 A OD2 ASP 339 A ASP 337 1_555 L ZN ZN . A ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc9 A NE2 HIS 343 A HIS 341 1_555 L ZN ZN . A ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc10 A OD1 ASP 380 A ASP 378 1_555 N ZN ZN . A ZN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc11 A OD2 ASP 380 A ASP 378 1_555 N ZN ZN . A ZN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc12 A NE2 HIS 381 A HIS 379 1_555 N ZN ZN . A ZN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc13 A NE2 HIS 456 A HIS 454 1_555 L ZN ZN . A ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc14 B OD2 ASP 62 B ASP 60 1_555 Q MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc15 B OD1 ASP 62 B ASP 60 1_555 T ZN ZN . B ZN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc16 B OG1 THR 175 B THR 173 1_555 Q MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.773 ? metalc ? metalc17 B OE1 GLU 237 B GLU 235 1_555 S CA CA . B CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc18 B OE2 GLU 237 B GLU 235 1_555 S CA CA . B CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc19 B O PHE 292 B PHE 290 1_555 S CA CA . B CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc20 B OE2 GLU 293 B GLU 291 1_555 S CA CA . B CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc21 B OD1 ASP 308 B ASP 306 1_555 S CA CA . B CA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? metalc ? metalc22 B OD2 ASP 339 B ASP 337 1_555 R ZN ZN . B ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc23 B NE2 HIS 343 B HIS 341 1_555 R ZN ZN . B ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc24 B OD2 ASP 380 B ASP 378 1_555 T ZN ZN . B ZN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc25 B ND1 HIS 381 B HIS 379 1_555 T ZN ZN . B ZN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc26 B NE2 HIS 381 B HIS 379 1_555 T ZN ZN . B ZN 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc27 B NE2 HIS 456 B HIS 454 1_555 R ZN ZN . B ZN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 7YIX _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 I 4 NAG A 1 601 601 NAG NAG . J 4 NAG A 1 602 621 NAG NAG . K 5 MG A 1 603 701 MG MG . L 6 ZN A 1 604 702 ZN ZN . M 7 CA A 1 605 703 CA CA . N 6 ZN A 1 606 704 ZN ZN . O 4 NAG B 1 601 601 NAG NAG . P 4 NAG B 1 602 621 NAG NAG . Q 5 MG B 1 603 701 MG MG . R 6 ZN B 1 604 702 ZN ZN . S 7 CA B 1 605 703 CA CA . T 6 ZN B 1 606 704 ZN ZN . # 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 . . . J 4 153.408 171.934 164.488 1 82.51 ? C1 NAG 602 A 1 HETATM 2 C C2 NAG . . . J 4 152.721 173.117 165.177 1 82.51 ? C2 NAG 602 A 1 HETATM 3 C C3 NAG . . . J 4 151.259 172.791 165.472 1 82.51 ? C3 NAG 602 A 1 HETATM 4 C C4 NAG . . . J 4 150.552 172.33 164.204 1 82.51 ? C4 NAG 602 A 1 HETATM 5 C C5 NAG . . . J 4 151.318 171.173 163.568 1 82.51 ? C5 NAG 602 A 1 HETATM 6 C C6 NAG . . . J 4 150.734 170.736 162.245 1 82.51 ? C6 NAG 602 A 1 HETATM 7 C C7 NAG . . . J 4 153.585 172.728 167.464 1 82.51 ? C7 NAG 602 A 1 HETATM 8 C C8 NAG . . . J 4 154.334 173.336 168.61 1 82.51 ? C8 NAG 602 A 1 HETATM 9 N N2 NAG . . . J 4 153.419 173.515 166.392 1 82.51 ? N2 NAG 602 A 1 HETATM 10 O O3 NAG . . . J 4 150.613 173.944 165.998 1 82.51 ? O3 NAG 602 A 1 HETATM 11 O O4 NAG . . . J 4 149.229 171.906 164.51 1 82.51 ? O4 NAG 602 A 1 HETATM 12 O O5 NAG . . . J 4 152.673 171.569 163.312 1 82.51 ? O5 NAG 602 A 1 HETATM 13 O O6 NAG . . . J 4 151.615 171.026 161.168 1 82.51 ? O6 NAG 602 A 1 HETATM 14 O O7 NAG . . . J 4 153.153 171.579 167.509 1 82.51 ? O7 NAG 602 A 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #