data_2YQ2 # _model_server_result.job_id vZdjWZH9cgkk6tF5h88GeA _model_server_result.datetime_utc '2025-03-06 01:11:06' _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 2yq2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1002}' # _entry.id 2YQ2 # _exptl.entry_id 2YQ2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 108.15 _cell.angle_gamma 90 _cell.entry_id 2YQ2 _cell.length_a 132.18 _cell.length_b 47.593 _cell.length_c 159.29 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YQ2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _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 _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 ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H N N # 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 4 A CYS 4 1_555 A SG CYS 48 A CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 A SG CYS 59 A CYS 59 1_555 A SG CYS 106 A CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf3 A SG CYS 104 A CYS 104 1_555 A SG CYS 140 A CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 130 A CYS 130 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf5 A SG CYS 181 A CYS 181 1_555 A SG CYS 189 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 A SG CYS 205 A CYS 205 1_555 A SG CYS 226 A CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 A SG CYS 208 A CYS 208 1_555 A SG CYS 242 A CYS 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf8 A SG CYS 257 A CYS 257 1_555 A SG CYS 278 A CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 A SG CYS 295 A CYS 295 1_555 B SG CYS 295 B CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf10 B SG CYS 4 B CYS 4 1_555 B SG CYS 48 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 B SG CYS 59 B CYS 59 1_555 B SG CYS 106 B CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf12 B SG CYS 104 B CYS 104 1_555 B SG CYS 140 B CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf13 B SG CYS 130 B CYS 130 1_555 B SG CYS 168 B CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf14 B SG CYS 181 B CYS 181 1_555 B SG CYS 189 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf15 B SG CYS 205 B CYS 205 1_555 B SG CYS 226 B CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf16 B SG CYS 208 B CYS 208 1_555 B SG CYS 242 B CYS 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 B SG CYS 257 B CYS 257 1_555 B SG CYS 278 B CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 117 A ASN 117 1_555 D C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 186 A ASN 186 1_555 C C1 NAG . A NAG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A ND2 ASN 230 A ASN 230 1_555 E C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 B ND2 ASN 117 B ASN 117 1_555 H C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale5 B ND2 ASN 186 B ASN 186 1_555 G C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale6 B ND2 ASN 230 B ASN 230 1_555 F C1 NAG . B NAG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 2YQ2 _atom_sites.fract_transf_matrix[1][1] 0.007565 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00248 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021011 _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] 0.006607 _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 C 2 NAG A 1 1000 1000 NAG NAG . D 2 NAG A 1 1001 1001 NAG NAG . E 2 NAG A 1 1002 1002 NAG NAG . F 2 NAG B 1 1000 1000 NAG NAG . G 2 NAG B 1 1001 1001 NAG NAG . H 2 NAG B 1 1002 1002 NAG NAG . I 3 HOH A 1 2001 2001 HOH HOH . I 3 HOH A 2 2002 2002 HOH HOH . I 3 HOH A 3 2003 2003 HOH HOH . I 3 HOH A 4 2004 2004 HOH HOH . I 3 HOH A 5 2005 2005 HOH HOH . I 3 HOH A 6 2006 2006 HOH HOH . I 3 HOH A 7 2007 2007 HOH HOH . I 3 HOH A 8 2008 2008 HOH HOH . I 3 HOH A 9 2009 2009 HOH HOH . I 3 HOH A 10 2010 2010 HOH HOH . I 3 HOH A 11 2011 2011 HOH HOH . I 3 HOH A 12 2012 2012 HOH HOH . I 3 HOH A 13 2013 2013 HOH HOH . I 3 HOH A 14 2014 2014 HOH HOH . I 3 HOH A 15 2015 2015 HOH HOH . I 3 HOH A 16 2016 2016 HOH HOH . I 3 HOH A 17 2017 2017 HOH HOH . I 3 HOH A 18 2018 2018 HOH HOH . I 3 HOH A 19 2019 2019 HOH HOH . I 3 HOH A 20 2020 2020 HOH HOH . I 3 HOH A 21 2021 2021 HOH HOH . I 3 HOH A 22 2022 2022 HOH HOH . I 3 HOH A 23 2023 2023 HOH HOH . I 3 HOH A 24 2024 2024 HOH HOH . I 3 HOH A 25 2025 2025 HOH HOH . J 3 HOH B 1 2001 2001 HOH HOH . J 3 HOH B 2 2002 2002 HOH HOH . J 3 HOH B 3 2003 2003 HOH HOH . J 3 HOH B 4 2004 2004 HOH HOH . J 3 HOH B 5 2005 2005 HOH HOH . J 3 HOH B 6 2006 2006 HOH HOH . J 3 HOH B 7 2007 2007 HOH HOH . J 3 HOH B 8 2008 2008 HOH HOH . J 3 HOH B 9 2009 2009 HOH HOH . J 3 HOH B 10 2010 2010 HOH HOH . J 3 HOH B 11 2011 2011 HOH HOH . J 3 HOH B 12 2012 2012 HOH HOH . J 3 HOH B 13 2013 2013 HOH HOH . J 3 HOH B 14 2014 2014 HOH HOH . J 3 HOH B 15 2015 2015 HOH HOH . J 3 HOH B 16 2016 2016 HOH HOH . J 3 HOH B 17 2017 2017 HOH HOH . J 3 HOH B 18 2018 2018 HOH HOH . J 3 HOH B 19 2019 2019 HOH HOH . J 3 HOH B 20 2020 2020 HOH HOH . J 3 HOH B 21 2021 2021 HOH HOH . J 3 HOH B 22 2022 2022 HOH HOH . J 3 HOH B 23 2023 2023 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 2 110.384 47.787 -116.081 1 64.49 ? C1 NAG 1002 B 1 HETATM 2 C C2 NAG . . . H 2 110.528 47.351 -114.617 1 65.13 ? C2 NAG 1002 B 1 HETATM 3 C C3 NAG . . . H 2 111.957 47.027 -114.184 1 65.08 ? C3 NAG 1002 B 1 HETATM 4 C C4 NAG . . . H 2 112.6 46.084 -115.184 1 65.01 ? C4 NAG 1002 B 1 HETATM 5 C C5 NAG . . . H 2 112.622 46.757 -116.552 1 65.61 ? C5 NAG 1002 B 1 HETATM 6 C C6 NAG . . . H 2 113.217 45.874 -117.629 1 65.71 ? C6 NAG 1002 B 1 HETATM 7 C C7 NAG . . . H 2 109.253 47.819 -112.559 1 66.75 ? C7 NAG 1002 B 1 HETATM 8 C C8 NAG . . . H 2 109.158 48.801 -111.43 1 67.04 ? C8 NAG 1002 B 1 HETATM 9 N N2 NAG . . . H 2 109.901 48.246 -113.657 1 66.32 ? N2 NAG 1002 B 1 HETATM 10 O O3 NAG . . . H 2 111.957 46.427 -112.893 1 65.34 ? O3 NAG 1002 B 1 HETATM 11 O O4 NAG . . . H 2 113.914 45.738 -114.761 1 64.39 ? O4 NAG 1002 B 1 HETATM 12 O O5 NAG . . . H 2 111.277 47.069 -116.968 1 65.36 ? O5 NAG 1002 B 1 HETATM 13 O O6 NAG . . . H 2 112.936 44.488 -117.439 1 65.76 ? O6 NAG 1002 B 1 HETATM 14 O O7 NAG . . . H 2 108.828 46.672 -112.457 1 66.93 ? O7 NAG 1002 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #