data_3A79 # _model_server_result.job_id G4jQTD3YrS1YnhE_gxI5Qw _model_server_result.datetime_utc '2025-06-27 23:28:47' _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 3a79 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":821}' # _entry.id 3A79 # _exptl.entry_id 3A79 _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 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 120 _cell.entry_id 3A79 _cell.length_a 168.901 _cell.length_b 168.901 _cell.length_c 231.353 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3A79 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,K,L,M,N,O _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 ? 6 J N N ? 6 K N N ? 6 L N N ? 6 M N N ? 6 N N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 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 4 n D NAG 1 D 1 NAG A 831 NAG 4 n D NAG 2 D 2 NAG A 832 NAG 4 n E NAG 1 E 1 NAG B 931 NAG 4 n E NAG 2 E 2 NAG B 932 NAG 5 n F NAG 1 F 1 NAG B 941 NAG 5 n F NAG 2 F 2 NAG B 942 NAG 5 n F BMA 3 F 3 BMA B 943 BMA 5 n G NAG 1 G 1 NAG B 951 NAG 5 n G NAG 2 G 2 NAG B 952 NAG 5 n G BMA 3 G 3 BMA B 953 BMA 5 n H NAG 1 H 1 NAG B 961 NAG 5 n H NAG 2 H 2 NAG B 962 NAG 5 n H BMA 3 H 3 BMA B 963 BMA 4 n I NAG 1 I 1 NAG B 971 NDG 4 n I NAG 2 I 2 NAG B 972 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 30 A CYS 30 1_555 A SG CYS 36 A CYS 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 353 A CYS 353 1_555 A SG CYS 382 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf3 A SG CYS 432 A CYS 432 1_555 A SG CYS 454 A CYS 454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 A SG CYS 537 A CYS 537 1_555 A SG CYS 562 A CYS 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 539 A CYS 539 1_555 A SG CYS 574 A CYS 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 117 B CYS 117 1_555 B SG CYS 139 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf7 B SG CYS 235 B CYS 235 1_555 B SG CYS 265 B CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf8 B SG CYS 348 B CYS 348 1_555 B SG CYS 373 B CYS 373 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 B SG CYS 424 B CYS 424 1_555 B SG CYS 447 B CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf10 B SG CYS 511 B CYS 511 1_555 B SG CYS 544 B CYS 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 B SG CYS 513 B CYS 513 1_555 B SG CYS 556 B CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 147 A ASN 147 1_555 J C1 NAG . A NAG 811 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale2 A ND2 ASN 414 A ASN 414 1_555 K C1 NAG . A NAG 821 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 442 A ASN 442 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 B ND2 ASN 144 B ASN 144 1_555 L C1 NAG . B NAG 911 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale5 B ND2 ASN 195 B ASN 195 1_555 N C1 NAG . B NAG 981 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale6 B ND2 ASN 214 B ASN 214 1_555 M C1 NAG . B NAG 921 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale7 B ND2 ASN 253 B ASN 253 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale8 B ND2 ASN 285 B ASN 285 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale9 B ND2 ASN 359 B ASN 359 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale10 B ND2 ASN 401 B ASN 401 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale11 B ND2 ASN 434 B ASN 434 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale12 C SG CYS 1 C CYS 11 1_555 O C20 PXS . C PXS 581 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.784 ? covale ? covale13 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale14 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale15 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale16 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale17 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale18 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale19 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale20 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale21 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 3A79 _atom_sites.fract_transf_matrix[1][1] 0.005921 _atom_sites.fract_transf_matrix[1][2] 0.003418 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006837 _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] 0.004322 _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 J 6 NAG A 1 811 811 NAG NAG . K 6 NAG A 1 821 821 NAG NAG . L 6 NAG B 1 911 911 NAG NAG . M 6 NAG B 1 921 921 NAG NAG . N 6 NAG B 1 981 981 NAG NAG . O 7 PXS C 1 581 581 PXS PXS . # 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 . . . K 6 20.957 -62.836 24.638 1 95.81 ? C1 NAG 821 A 1 HETATM 2 C C2 NAG . . . K 6 21.358 -63.693 25.845 1 109.41 ? C2 NAG 821 A 1 HETATM 3 C C3 NAG . . . K 6 20.276 -64.706 26.22 1 117.09 ? C3 NAG 821 A 1 HETATM 4 C C4 NAG . . . K 6 18.916 -64.015 26.31 1 115.06 ? C4 NAG 821 A 1 HETATM 5 C C5 NAG . . . K 6 18.62 -63.263 25.019 1 109.03 ? C5 NAG 821 A 1 HETATM 6 C C6 NAG . . . K 6 17.298 -62.52 25.149 1 109.82 ? C6 NAG 821 A 1 HETATM 7 C C7 NAG . . . K 6 22.97 -64.951 24.457 1 114.13 ? C7 NAG 821 A 1 HETATM 8 C C8 NAG . . . K 6 24.298 -64.577 23.857 1 96.61 ? C8 NAG 821 A 1 HETATM 9 N N2 NAG . . . K 6 22.632 -64.373 25.619 1 114.5 ? N2 NAG 821 A 1 HETATM 10 O O3 NAG . . . K 6 20.615 -65.306 27.455 1 122.65 ? O3 NAG 821 A 1 HETATM 11 O O4 NAG . . . K 6 17.864 -64.928 26.573 1 114.04 ? O4 NAG 821 A 1 HETATM 12 O O5 NAG . . . K 6 19.637 -62.326 24.731 1 97.63 ? O5 NAG 821 A 1 HETATM 13 O O6 NAG . . . K 6 17.317 -61.794 26.357 1 104.29 ? O6 NAG 821 A 1 HETATM 14 O O7 NAG . . . K 6 22.251 -65.771 23.878 1 122.19 ? O7 NAG 821 A 1 # _model_server_stats.io_time_ms 110 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 14 #