data_7XM9 # _model_server_result.job_id N5-kjl3OKqjtUdCkwd8YzQ _model_server_result.datetime_utc '2024-11-21 14:29:16' _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 7xm9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":504}' # _entry.id 7XM9 # _exptl.entry_id 7XM9 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _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 7XM9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7XM9 _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 5 F N N ? 5 I N N ? 5 J N N ? 5 K N N ? 5 L N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n D NAG 1 D 1 NAG D 1 NAG 4 n D NAG 2 D 2 NAG D 2 NAG 4 n E NAG 1 E 1 NAG E 1 NAG 4 n E NAG 2 E 2 NAG E 2 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 315 A CYS 315 1_555 A SG CYS 330 A CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? disulf ? disulf2 A SG CYS 884 A CYS 895 1_555 C SG CYS 55 C CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.813 ? disulf ? disulf3 A SG CYS 886 A CYS 897 1_555 A SG CYS 892 A CYS 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 A SG CYS 924 A CYS 935 1_555 A SG CYS 933 A CYS 944 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 A SG CYS 1339 A CYS 1350 1_555 A SG CYS 1359 A CYS 1370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 A SG CYS 1704 A CYS 1715 1_555 A SG CYS 1719 A CYS 1730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 B SG CYS 21 B CYS 21 1_555 B SG CYS 43 B CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? disulf ? disulf8 B SG CYS 40 B CYS 40 1_555 B SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 C SG CYS 50 C CYS 50 1_555 C SG CYS 127 C CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? disulf ? disulf10 C SG CYS 72 C CYS 72 1_555 C SG CYS 75 C CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 1341 A ASN 1352 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 1355 A ASN 1366 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 1364 A ASN 1375 1_555 F C1 NAG . A NAG 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 B ND2 ASN 93 B ASN 93 1_555 I C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 B ND2 ASN 110 B ASN 110 1_555 J C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 B ND2 ASN 114 B ASN 114 1_555 K C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 B ND2 ASN 135 B ASN 135 1_555 L C1 NAG . B NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _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 410 n n C1 O1 NAG sing 411 n n C1 O5 NAG sing 412 n n C1 H1 NAG sing 413 n n C2 C3 NAG sing 414 n n C2 N2 NAG sing 415 n n C2 H2 NAG sing 416 n n C3 C4 NAG sing 417 n n C3 O3 NAG sing 418 n n C3 H3 NAG sing 419 n n C4 C5 NAG sing 420 n n C4 O4 NAG sing 421 n n C4 H4 NAG sing 422 n n C5 C6 NAG sing 423 n n C5 O5 NAG sing 424 n n C5 H5 NAG sing 425 n n C6 O6 NAG sing 426 n n C6 H61 NAG sing 427 n n C6 H62 NAG sing 428 n n C7 C8 NAG sing 429 n n C7 N2 NAG sing 430 n n C7 O7 NAG doub 431 n n C8 H81 NAG sing 432 n n C8 H82 NAG sing 433 n n C8 H83 NAG sing 434 n n N2 HN2 NAG sing 435 n n O1 HO1 NAG sing 436 n n O3 HO3 NAG sing 437 n n O4 HO4 NAG sing 438 n n O6 HO6 NAG sing 439 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 7XM9 _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 F 5 NAG A 1 2301 2005 NAG NAG . G 6 G2E A 1 2302 2101 G2E LIG . H 7 6OU A 1 2303 2201 6OU 6OU . I 5 NAG B 1 501 301 NAG NAG . J 5 NAG B 1 502 302 NAG NAG . K 5 NAG B 1 503 303 NAG NAG . L 5 NAG B 1 504 304 NAG NAG . # 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 . . . L 5 130.438 122.354 185.82 1 77.29 ? C1 NAG 504 B 1 HETATM 2 C C2 NAG . . . L 5 129.751 120.997 185.909 1 77.29 ? C2 NAG 504 B 1 HETATM 3 C C3 NAG . . . L 5 130.273 120.235 187.121 1 77.29 ? C3 NAG 504 B 1 HETATM 4 C C4 NAG . . . L 5 131.794 120.147 187.077 1 77.29 ? C4 NAG 504 B 1 HETATM 5 C C5 NAG . . . L 5 132.411 121.532 186.884 1 77.29 ? C5 NAG 504 B 1 HETATM 6 C C6 NAG . . . L 5 133.906 121.491 186.673 1 77.29 ? C6 NAG 504 B 1 HETATM 7 C C7 NAG . . . L 5 127.519 121.142 184.899 1 77.29 ? C7 NAG 504 B 1 HETATM 8 C C8 NAG . . . L 5 126.05 121.297 185.156 1 77.29 ? C8 NAG 504 B 1 HETATM 9 N N2 NAG . . . L 5 128.306 121.141 185.98 1 77.29 ? N2 NAG 504 B 1 HETATM 10 O O3 NAG . . . L 5 129.704 118.931 187.145 1 77.29 ? O3 NAG 504 B 1 HETATM 11 O O4 NAG . . . L 5 132.277 119.595 188.296 1 77.29 ? O4 NAG 504 B 1 HETATM 12 O O5 NAG . . . L 5 131.85 122.169 185.725 1 77.29 ? O5 NAG 504 B 1 HETATM 13 O O6 NAG . . . L 5 134.389 122.718 186.143 1 77.29 ? O6 NAG 504 B 1 HETATM 14 O O7 NAG . . . L 5 127.972 121.025 183.765 1 77.29 ? O7 NAG 504 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #