data_4Y4F # _model_server_result.job_id 7jCzPjq7Qqbh9YoBEU3wkQ _model_server_result.datetime_utc '2025-03-13 17:47:47' _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 4y4f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 4Y4F # _exptl.entry_id 4Y4F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.46 _cell.angle_gamma 90 _cell.entry_id 4Y4F _cell.length_a 78.589 _cell.length_b 149.728 _cell.length_c 101.386 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Y4F _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 ? tetrameric 4 author_defined_assembly 1 ? tetrameric 4 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,I,K,L 1 1 E,F,G,H,J,M,N 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 K N N ? 6 M N N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 5 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 5 n I NAG 1 I 1 NAG A 503 NAG 5 n I NAG 2 I 2 NAG A 504 NAG 5 n J NAG 1 J 1 NAG E 503 NAG 5 n J NAG 2 J 2 NAG E 504 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 104 A CYS 104 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 A SG CYS 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 C SG CYS 24 C CYS 23 1_555 C SG CYS 91 C CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 C SG CYS 138 C CYS 137 1_555 C SG CYS 188 C CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 C SG CYS 163 C CYS 162 1_555 D SG CYS 169 D CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf7 D SG CYS 24 D CYS 23 1_555 D SG CYS 92 D CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 D SG CYS 143 D CYS 142 1_555 D SG CYS 208 D CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf9 E SG CYS 104 E CYS 104 1_555 E SG CYS 168 E CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf10 E SG CYS 208 E CYS 208 1_555 E SG CYS 263 E CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 F SG CYS 25 F CYS 25 1_555 F SG CYS 80 F CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 G SG CYS 24 G CYS 23 1_555 G SG CYS 91 G CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 G SG CYS 138 G CYS 137 1_555 G SG CYS 188 G CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf14 G SG CYS 163 G CYS 162 1_555 H SG CYS 169 H CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf15 H SG CYS 24 H CYS 23 1_555 H SG CYS 92 H CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf16 H SG CYS 143 H CYS 142 1_555 H SG CYS 208 H CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? covale ? covale1 A ND2 ASN 42 A ASN 42 1_555 K C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A ND2 ASN 165 A ASN 165 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 E ND2 ASN 42 E ASN 42 1_555 M C1 NAG . E NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 E ND2 ASN 165 E ASN 165 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 403 n n C1 O1 NAG sing 404 n n C1 O5 NAG sing 405 n n C1 H1 NAG sing 406 n n C2 C3 NAG sing 407 n n C2 N2 NAG sing 408 n n C2 H2 NAG sing 409 n n C3 C4 NAG sing 410 n n C3 O3 NAG sing 411 n n C3 H3 NAG sing 412 n n C4 C5 NAG sing 413 n n C4 O4 NAG sing 414 n n C4 H4 NAG sing 415 n n C5 C6 NAG sing 416 n n C5 O5 NAG sing 417 n n C5 H5 NAG sing 418 n n C6 O6 NAG sing 419 n n C6 H61 NAG sing 420 n n C6 H62 NAG sing 421 n n C7 C8 NAG sing 422 n n C7 N2 NAG sing 423 n n C7 O7 NAG doub 424 n n C8 H81 NAG sing 425 n n C8 H82 NAG sing 426 n n C8 H83 NAG sing 427 n n N2 HN2 NAG sing 428 n n O1 HO1 NAG sing 429 n n O3 HO3 NAG sing 430 n n O4 HO4 NAG sing 431 n n O6 HO6 NAG sing 432 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 4Y4F _atom_sites.fract_transf_matrix[1][1] 0.012724 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00144 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006679 _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] 0.009926 _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 K 6 NAG A 1 501 501 NAG NAG . L 7 49M A 1 504 600 49M GCK . M 6 NAG E 1 501 501 NAG NAG . N 7 49M E 1 504 600 49M GCK . # 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 19.151 7.594 16.049 1 88.75 ? C1 NAG 501 A 1 HETATM 2 C C2 NAG . . . K 6 18.367 7.753 14.743 1 89.36 ? C2 NAG 501 A 1 HETATM 3 C C3 NAG . . . K 6 19.282 7.585 13.531 1 89.79 ? C3 NAG 501 A 1 HETATM 4 C C4 NAG . . . K 6 20.473 8.537 13.627 1 90.15 ? C4 NAG 501 A 1 HETATM 5 C C5 NAG . . . K 6 21.178 8.363 14.977 1 90.29 ? C5 NAG 501 A 1 HETATM 6 C C6 NAG . . . K 6 22.277 9.406 15.162 1 91.14 ? C6 NAG 501 A 1 HETATM 7 C C7 NAG . . . K 6 16.024 7.201 14.356 1 87.99 ? C7 NAG 501 A 1 HETATM 8 C C8 NAG . . . K 6 14.983 6.13 14.33 1 87.72 ? C8 NAG 501 A 1 HETATM 9 N N2 NAG . . . K 6 17.26 6.816 14.678 1 88.4 ? N2 NAG 501 A 1 HETATM 10 O O3 NAG . . . K 6 18.558 7.834 12.348 1 89.92 ? O3 NAG 501 A 1 HETATM 11 O O4 NAG . . . K 6 21.37 8.302 12.561 1 90.44 ? O4 NAG 501 A 1 HETATM 12 O O5 NAG . . . K 6 20.261 8.477 16.056 1 89.1 ? O5 NAG 501 A 1 HETATM 13 O O6 NAG . . . K 6 21.71 10.629 15.583 1 92.57 ? O6 NAG 501 A 1 HETATM 14 O O7 NAG . . . K 6 15.706 8.358 14.089 1 88.42 ? O7 NAG 501 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #