data_1E05 # _model_server_result.job_id H34LyURPK6gObcitjn4KNQ _model_server_result.datetime_utc '2024-11-30 01:39:21' _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 1e05 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":821}' # _entry.id 1E05 # _exptl.entry_id 1E05 _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.32 _cell.angle_gamma 90 _cell.entry_id 1E05 _cell.length_a 61.41 _cell.length_b 98.31 _cell.length_c 90.41 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1E05 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS monomeric 1 author_and_software_defined_assembly 1 PQS monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,E,F,K,L,M,N,O,P,R 1 1 A,C,D,G,H,I,J,Q 2 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 ? 6 L N N ? 6 M N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 4 3 2 GUP NAG C1 O1 . O4 HO4 . sing 6 ? 4 4 3 MAN GUP C1 O1 . O6 HO6 . sing 7 ? 4 5 4 NAG MAN C1 O1 . O2 HO2 . sing 8 ? 4 6 5 GAL NAG C1 O1 . O4 HO4 . sing 9 ? 4 7 3 MAN GUP C1 O1 . O3 HO3 . sing 10 ? 4 8 7 BMA MAN C1 O1 . O2 HO2 . 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 2 n C NAG 1 A 1 NAG I 801 NAG 2 n C NAG 2 A 2 NAG I 802 NAG 3 n D NAG 1 B 1 NAG I 841 NAG 3 n D NAG 2 B 2 NAG I 842 NAG 3 n D BMA 3 B 3 BMA I 843 BMA 2 n E NAG 1 C 1 NAG L 841 NAG 2 n E NAG 2 C 2 NAG L 842 NAG 4 n F NAG 1 D 1 NAG L 861 NAG 4 n F NAG 2 D 2 NAG L 862 NAG 4 n F GUP 3 D 3 GUP L 863 GUP 4 n F MAN 4 D 4 MAN L 864 MAN 4 n F NAG 5 D 5 NAG L 865 NAG 4 n F GAL 6 D 6 GAL L 866 GAL 4 n F MAN 7 D 7 MAN L 868 MAN 4 n F BMA 8 D 8 BMA L 869 BMA # 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 8 I CYS 8 1_555 A SG CYS 128 I CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 21 I CYS 21 1_555 A SG CYS 95 I CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 247 I CYS 247 1_555 A SG CYS 430 I CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 B SG CYS 8 L CYS 8 1_555 B SG CYS 128 L CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 B SG CYS 21 L CYS 21 1_555 B SG CYS 95 L CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 B SG CYS 247 L CYS 247 1_555 B SG CYS 430 L CYS 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? covale ? covale1 A ND2 ASN 96 I ASN 96 1_555 C C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale2 A ND2 ASN 135 I ASN 135 1_555 H C1 NAG . I NAG 821 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale3 A ND2 ASN 155 I ASN 155 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale4 A ND2 ASN 192 I ASN 192 1_555 I C1 NAG . I NAG 861 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.307 ? covale ? covale5 B ND2 ASN 96 L ASN 96 1_555 L C1 NAG . L NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale6 B ND2 ASN 135 L ASN 135 1_555 M C1 NAG . L NAG 821 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.357 ? covale ? covale7 B ND2 ASN 155 L ASN 155 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale8 B ND2 ASN 192 L ASN 192 1_555 F C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.386 ? covale ? covale9 C O4 NAG . A NAG 1 1_555 C C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.369 ? covale ? covale10 D O4 NAG . B NAG 1 1_555 D C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale11 D O4 NAG . B NAG 2 1_555 D C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale12 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale13 F O4 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale14 F O4 NAG . D NAG 2 1_555 F C1 GUP . D GUP 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? covale ? covale15 F O6 GUP . D GUP 3 1_555 F C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale16 F O3 GUP . D GUP 3 1_555 F C1 MAN . D MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale17 F O2 MAN . D MAN 4 1_555 F C1 NAG . D NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale18 F O4 NAG . D NAG 5 1_555 F C1 GAL . D GAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale19 F O2 MAN . D MAN 7 1_555 F C1 BMA . D BMA 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? # _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 346 n n C1 O1 NAG sing 347 n n C1 O5 NAG sing 348 n n C1 H1 NAG sing 349 n n C2 C3 NAG sing 350 n n C2 N2 NAG sing 351 n n C2 H2 NAG sing 352 n n C3 C4 NAG sing 353 n n C3 O3 NAG sing 354 n n C3 H3 NAG sing 355 n n C4 C5 NAG sing 356 n n C4 O4 NAG sing 357 n n C4 H4 NAG sing 358 n n C5 C6 NAG sing 359 n n C5 O5 NAG sing 360 n n C5 H5 NAG sing 361 n n C6 O6 NAG sing 362 n n C6 H61 NAG sing 363 n n C6 H62 NAG sing 364 n n C7 C8 NAG sing 365 n n C7 N2 NAG sing 366 n n C7 O7 NAG doub 367 n n C8 H81 NAG sing 368 n n C8 H82 NAG sing 369 n n C8 H83 NAG sing 370 n n N2 HN2 NAG sing 371 n n O1 HO1 NAG sing 372 n n O3 HO3 NAG sing 373 n n O4 HO4 NAG sing 374 n n O6 HO6 NAG sing 375 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 1E05 _atom_sites.fract_transf_matrix[1][1] 0.016284 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003855 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010172 _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] 0.011366 _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 5 MAN I 1 803 803 MAN MAN . H 6 NAG I 1 821 821 NAG NAG . I 6 NAG I 1 861 861 NAG NAG . J 7 GOL I 1 901 901 GOL GOL . K 8 PO4 L 1 501 501 PO4 PO4 . L 6 NAG L 1 801 801 NAG NAG . M 6 NAG L 1 821 821 NAG NAG . N 5 MAN L 1 843 843 MAN MAN . O 5 MAN L 1 844 844 MAN MAN . P 7 GOL L 1 901 901 GOL GOL . Q 9 HOH I 1 2001 2001 HOH HOH . Q 9 HOH I 2 2002 2002 HOH HOH . Q 9 HOH I 3 2003 2003 HOH HOH . Q 9 HOH I 4 2004 2004 HOH HOH . Q 9 HOH I 5 2005 2005 HOH HOH . Q 9 HOH I 6 2006 2006 HOH HOH . Q 9 HOH I 7 2007 2007 HOH HOH . Q 9 HOH I 8 2008 2008 HOH HOH . Q 9 HOH I 9 2009 2009 HOH HOH . Q 9 HOH I 10 2010 2010 HOH HOH . Q 9 HOH I 11 2011 2011 HOH HOH . Q 9 HOH I 12 2012 2012 HOH HOH . Q 9 HOH I 13 2013 2013 HOH HOH . Q 9 HOH I 14 2014 2014 HOH HOH . Q 9 HOH I 15 2015 2015 HOH HOH . Q 9 HOH I 16 2016 2016 HOH HOH . Q 9 HOH I 17 2017 2017 HOH HOH . Q 9 HOH I 18 2018 2018 HOH HOH . Q 9 HOH I 19 2019 2019 HOH HOH . Q 9 HOH I 20 2020 2020 HOH HOH . Q 9 HOH I 21 2021 2021 HOH HOH . Q 9 HOH I 22 2022 2022 HOH HOH . Q 9 HOH I 23 2023 2023 HOH HOH . Q 9 HOH I 24 2024 2024 HOH HOH . Q 9 HOH I 25 2025 2025 HOH HOH . Q 9 HOH I 26 2026 2026 HOH HOH . Q 9 HOH I 27 2027 2027 HOH HOH . Q 9 HOH I 28 2028 2028 HOH HOH . Q 9 HOH I 29 2029 2029 HOH HOH . Q 9 HOH I 30 2030 2030 HOH HOH . Q 9 HOH I 31 2031 2031 HOH HOH . Q 9 HOH I 32 2032 2032 HOH HOH . Q 9 HOH I 33 2033 2033 HOH HOH . Q 9 HOH I 34 2034 2034 HOH HOH . Q 9 HOH I 35 2035 2035 HOH HOH . Q 9 HOH I 36 2036 2036 HOH HOH . Q 9 HOH I 37 2037 2037 HOH HOH . Q 9 HOH I 38 2038 2038 HOH HOH . Q 9 HOH I 39 2039 2039 HOH HOH . Q 9 HOH I 40 2040 2040 HOH HOH . Q 9 HOH I 41 2041 2041 HOH HOH . Q 9 HOH I 42 2042 2042 HOH HOH . Q 9 HOH I 43 2043 2043 HOH HOH . Q 9 HOH I 44 2044 2044 HOH HOH . Q 9 HOH I 45 2045 2045 HOH HOH . Q 9 HOH I 46 2046 2046 HOH HOH . R 9 HOH L 1 2001 2001 HOH HOH . R 9 HOH L 2 2002 2002 HOH HOH . R 9 HOH L 3 2003 2003 HOH HOH . R 9 HOH L 4 2004 2004 HOH HOH . R 9 HOH L 5 2005 2005 HOH HOH . R 9 HOH L 6 2006 2006 HOH HOH . R 9 HOH L 7 2007 2007 HOH HOH . R 9 HOH L 8 2008 2008 HOH HOH . R 9 HOH L 9 2009 2009 HOH HOH . R 9 HOH L 10 2010 2010 HOH HOH . R 9 HOH L 11 2011 2011 HOH HOH . R 9 HOH L 12 2012 2012 HOH HOH . R 9 HOH L 13 2013 2013 HOH HOH . R 9 HOH L 14 2014 2014 HOH HOH . R 9 HOH L 15 2015 2015 HOH HOH . R 9 HOH L 16 2016 2016 HOH HOH . R 9 HOH L 17 2017 2017 HOH HOH . R 9 HOH L 18 2018 2018 HOH HOH . R 9 HOH L 19 2019 2019 HOH HOH . R 9 HOH L 20 2020 2020 HOH HOH . R 9 HOH L 21 2021 2021 HOH HOH . R 9 HOH L 22 2022 2022 HOH HOH . R 9 HOH L 23 2023 2023 HOH HOH . R 9 HOH L 24 2024 2024 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 . . . M 6 -6.478 12.685 -42.308 1 120.33 ? C1 NAG 821 L 1 HETATM 2 C C2 NAG . . . M 6 -7.138 13.653 -43.259 1 122.34 ? C2 NAG 821 L 1 HETATM 3 C C3 NAG . . . M 6 -6.514 13.531 -44.631 1 123.67 ? C3 NAG 821 L 1 HETATM 4 C C4 NAG . . . M 6 -5.142 12.862 -44.604 1 122.38 ? C4 NAG 821 L 1 HETATM 5 C C5 NAG . . . M 6 -4.322 12.931 -43.313 1 120.39 ? C5 NAG 821 L 1 HETATM 6 C C6 NAG . . . M 6 -3.412 14.151 -43.332 1 119.03 ? C6 NAG 821 L 1 HETATM 7 C C7 NAG . . . M 6 -9.543 14.243 -43.557 1 124.29 ? C7 NAG 821 L 1 HETATM 8 C C8 NAG . . . M 6 -10.916 13.854 -43.153 1 123.36 ? C8 NAG 821 L 1 HETATM 9 N N2 NAG . . . M 6 -8.584 13.306 -43.387 1 122.96 ? N2 NAG 821 L 1 HETATM 10 O O3 NAG . . . M 6 -6.427 14.835 -45.203 1 126.5 ? O3 NAG 821 L 1 HETATM 11 O O4 NAG . . . M 6 -5.23 11.475 -44.986 1 122.08 ? O4 NAG 821 L 1 HETATM 12 O O5 NAG . . . M 6 -5.097 13.038 -42.151 1 119.92 ? O5 NAG 821 L 1 HETATM 13 O O6 NAG . . . M 6 -2.408 14.073 -44.275 1 117.28 ? O6 NAG 821 L 1 HETATM 14 O O7 NAG . . . M 6 -9.294 15.273 -43.988 1 126.67 ? O7 NAG 821 L 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 355 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #