data_2YDM # _model_server_result.job_id x3bFxgHeqFE-hPF9gjeujg _model_server_result.datetime_utc '2025-08-31 02:35:08' _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 2ydm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1622}' # _entry.id 2YDM # _exptl.entry_id 2YDM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _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 2YDM _cell.length_a 56.143 _cell.length_b 84.533 _cell.length_c 132.27 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YDM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . 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 B NAG 1 B 1 NAG A 1623 NAG 2 n B NAG 2 B 2 NAG A 1624 NAG 2 n B BMA 3 B 3 BMA A 1625 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 116 A CYS 152 1_555 A SG CYS 122 A CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf2 A SG CYS 316 A CYS 352 1_555 A SG CYS 334 A CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? disulf ? disulf3 A SG CYS 502 A CYS 538 1_555 A SG CYS 514 A CYS 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? covale ? covale1 A ND2 ASN 36 A ASN 72 1_555 F C1 NAG . A NAG 1622 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 73 A ASN 109 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A NH1 ARG 312 A ARG 348 1_555 F C8 NAG . A NAG 1622 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? metalc ? metalc1 A NE2 HIS 347 A HIS 383 1_555 C ZN ZN . A ZN 1619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc2 A NE2 HIS 351 A HIS 387 1_555 C ZN ZN . A ZN 1619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc3 A OE1 GLU 375 A GLU 411 1_555 C ZN ZN . A ZN 1619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc4 C ZN ZN . A ZN 1619 1_555 G SE SLC . A SLC 1626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 2YDM _atom_sites.fract_transf_matrix[1][1] 0.017812 _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] 0.01183 _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] 0.00756 _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 3 ZN A 1 1619 1619 ZN ZN . D 4 CL A 1 1620 1620 CL CL . E 4 CL A 1 1621 1621 CL CL . F 5 NAG A 1 1622 1622 NAG NAG . G 6 SLC A 1 1626 1626 SLC SLC . H 7 HOH A 1 2001 2001 HOH HOH . H 7 HOH A 2 2002 2002 HOH HOH . H 7 HOH A 3 2003 2003 HOH HOH . H 7 HOH A 4 2004 2004 HOH HOH . H 7 HOH A 5 2005 2005 HOH HOH . H 7 HOH A 6 2006 2006 HOH HOH . H 7 HOH A 7 2007 2007 HOH HOH . H 7 HOH A 8 2008 2008 HOH HOH . H 7 HOH A 9 2009 2009 HOH HOH . H 7 HOH A 10 2010 2010 HOH HOH . H 7 HOH A 11 2011 2011 HOH HOH . H 7 HOH A 12 2012 2012 HOH HOH . H 7 HOH A 13 2013 2013 HOH HOH . H 7 HOH A 14 2014 2014 HOH HOH . H 7 HOH A 15 2015 2015 HOH HOH . H 7 HOH A 16 2016 2016 HOH HOH . H 7 HOH A 17 2017 2017 HOH HOH . H 7 HOH A 18 2018 2018 HOH HOH . H 7 HOH A 19 2019 2019 HOH HOH . H 7 HOH A 20 2020 2020 HOH HOH . H 7 HOH A 21 2021 2021 HOH HOH . H 7 HOH A 22 2022 2022 HOH HOH . H 7 HOH A 23 2023 2023 HOH HOH . H 7 HOH A 24 2024 2024 HOH HOH . H 7 HOH A 25 2025 2025 HOH HOH . H 7 HOH A 26 2026 2026 HOH HOH . H 7 HOH A 27 2027 2027 HOH HOH . H 7 HOH A 28 2028 2028 HOH HOH . H 7 HOH A 29 2029 2029 HOH HOH . H 7 HOH A 30 2030 2030 HOH HOH . H 7 HOH A 31 2031 2031 HOH HOH . H 7 HOH A 32 2032 2032 HOH HOH . H 7 HOH A 33 2033 2033 HOH HOH . H 7 HOH A 34 2034 2034 HOH HOH . H 7 HOH A 35 2035 2035 HOH HOH . H 7 HOH A 36 2036 2036 HOH HOH . H 7 HOH A 37 2037 2037 HOH HOH . H 7 HOH A 38 2038 2038 HOH HOH . H 7 HOH A 39 2039 2039 HOH HOH . H 7 HOH A 40 2040 2040 HOH HOH . H 7 HOH A 41 2041 2041 HOH HOH . H 7 HOH A 42 2042 2042 HOH HOH . H 7 HOH A 43 2043 2043 HOH HOH . H 7 HOH A 44 2044 2044 HOH HOH . H 7 HOH A 45 2045 2045 HOH HOH . H 7 HOH A 46 2046 2046 HOH HOH . H 7 HOH A 47 2047 2047 HOH HOH . H 7 HOH A 48 2048 2048 HOH HOH . H 7 HOH A 49 2049 2049 HOH HOH . H 7 HOH A 50 2050 2050 HOH HOH . H 7 HOH A 51 2051 2051 HOH HOH . H 7 HOH A 52 2052 2052 HOH HOH . H 7 HOH A 53 2053 2053 HOH HOH . H 7 HOH A 54 2054 2054 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 . . . F 5 10.585 -20.088 0.388 0.5 39.24 ? C1 NAG 1622 A 1 HETATM 2 C C2 NAG . . . F 5 12.047 -19.868 0.819 0.5 41.03 ? C2 NAG 1622 A 1 HETATM 3 C C3 NAG . . . F 5 12.268 -20.174 2.299 0.5 40.51 ? C3 NAG 1622 A 1 HETATM 4 C C4 NAG . . . F 5 11.12 -19.692 3.178 0.5 39.8 ? C4 NAG 1622 A 1 HETATM 5 C C5 NAG . . . F 5 9.81 -20.218 2.615 0.5 39.05 ? C5 NAG 1622 A 1 HETATM 6 C C6 NAG . . . F 5 8.631 -19.904 3.535 0.5 37.75 ? C6 NAG 1622 A 1 HETATM 7 C C7 NAG . . . F 5 14.151 -20.168 -0.429 0.5 45.71 ? C7 NAG 1622 A 1 HETATM 8 C C8 NAG . . . F 5 15.07 -21.091 -1.166 0.5 46.97 ? C8 NAG 1622 A 1 HETATM 9 N N2 NAG . . . F 5 12.995 -20.666 0.037 0.5 42.66 ? N2 NAG 1622 A 1 HETATM 10 O O3 NAG . . . F 5 13.461 -19.55 2.727 0.5 41.99 ? O3 NAG 1622 A 1 HETATM 11 O O4 NAG . . . F 5 11.29 -20.15 4.504 0.5 38.99 ? O4 NAG 1622 A 1 HETATM 12 O O5 NAG . . . F 5 9.638 -19.635 1.343 0.5 38.82 ? O5 NAG 1622 A 1 HETATM 13 O O6 NAG . . . F 5 7.959 -18.741 3.105 0.5 37.02 ? O6 NAG 1622 A 1 HETATM 14 O O7 NAG . . . F 5 14.502 -19.022 -0.152 0.5 45.13 ? O7 NAG 1622 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #