data_6WXV # _model_server_result.job_id 5xDLlmJvKdh2iKDQMyKjIw _model_server_result.datetime_utc '2024-11-04 22:41:40' _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 6wxv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":406}' # _entry.id 6WXV # _exptl.entry_id 6WXV _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 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 6WXV _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6WXV _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 E N N ? 5 F N N ? 5 G N N ? 5 M N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 3 5 4 MAN MAN 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 B 500 NAG 3 n C NAG 2 C 2 NAG B 501 NAG 3 n C BMA 3 C 3 BMA B 502 BMA 3 n C MAN 4 C 4 MAN B 503 MAN 3 n C MAN 5 C 5 MAN B 505 MAN # 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 103 A CYS 118 1_555 A SG CYS 1150 A CYS 1165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 A SG CYS 330 A CYS 345 1_555 A SG CYS 550 A CYS 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 349 A CYS 364 1_555 A SG CYS 564 A CYS 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 167 B CYS 167 1_555 B SG CYS 234 B CYS 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 79 A ASN 94 1_555 E C1 NAG . A NAG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 327 A ASN 342 1_555 F C1 NAG . A NAG 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 A ND2 ASN 519 A ASN 534 1_555 G C1 NAG . A NAG 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale4 B ND2 ASN 84 B ASN 84 1_555 M C1 NAG . B NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale5 B ND2 ASN 109 B ASN 109 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale8 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale9 C O3 MAN . C MAN 4 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? metalc ? metalc1 A O ASP 94 A ASP 109 1_555 L CA CA . A CA 1609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc2 A OD1 ASP 94 A ASP 109 1_555 L CA CA . A CA 1609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc3 A O THR 155 A THR 170 1_555 L CA CA . A CA 1609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc4 A OG1 THR 155 A THR 170 1_555 L CA CA . A CA 1609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc5 A O TRP 157 A TRP 172 1_555 L CA CA . A CA 1609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc6 A OD1 ASP 159 A ASP 174 1_555 L CA CA . A CA 1609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.113 ? metalc ? metalc7 A NE2 HIS 1129 A HIS 1144 1_555 I FE HEB . A HEB 1606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.762 ? metalc ? metalc8 A NE2 HIS 1210 A HIS 1225 1_555 H FE HEB . A HEB 1605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? # _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_ _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 6WXV _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 D 4 FAD A 1 1601 1601 FAD FAD . E 5 NAG A 1 1602 1610 NAG NAG . F 5 NAG A 1 1603 1611 NAG NAG . G 5 NAG A 1 1604 1612 NAG NAG . H 6 HEB A 1 1605 1701 HEB LIG . I 6 HEB A 1 1606 1801 HEB LIG . J 7 NDP A 1 1607 2201 NDP NDP . K 8 PLC A 1 1608 2301 PLC PLC . L 9 CA A 1 1609 2401 CA CA . M 5 NAG B 1 406 506 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 . . . M 5 134.297 95.44 86.095 1 0 ? C1 NAG 406 B 1 HETATM 2 C C2 NAG . . . M 5 132.886 94.99 85.712 1 0 ? C2 NAG 406 B 1 HETATM 3 C C3 NAG . . . M 5 132.863 93.495 85.409 1 0 ? C3 NAG 406 B 1 HETATM 4 C C4 NAG . . . M 5 133.919 93.144 84.371 1 0 ? C4 NAG 406 B 1 HETATM 5 C C5 NAG . . . M 5 135.283 93.641 84.834 1 0 ? C5 NAG 406 B 1 HETATM 6 C C6 NAG . . . M 5 136.372 93.418 83.811 1 0 ? C6 NAG 406 B 1 HETATM 7 C C7 NAG . . . M 5 131.043 96.297 86.672 1 0 ? C7 NAG 406 B 1 HETATM 8 C C8 NAG . . . M 5 130.146 96.487 87.858 1 0 ? C8 NAG 406 B 1 HETATM 9 N N2 NAG . . . M 5 131.939 95.31 86.768 1 0 ? N2 NAG 406 B 1 HETATM 10 O O3 NAG . . . M 5 131.574 93.133 84.928 1 0 ? O3 NAG 406 B 1 HETATM 11 O O4 NAG . . . M 5 133.97 91.734 84.182 1 0 ? O4 NAG 406 B 1 HETATM 12 O O5 NAG . . . M 5 135.221 95.053 85.072 1 0 ? O5 NAG 406 B 1 HETATM 13 O O6 NAG . . . M 5 136.074 92.315 82.967 1 0 ? O6 NAG 406 B 1 HETATM 14 O O7 NAG . . . M 5 130.958 97.003 85.672 1 0 ? O7 NAG 406 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #