data_5YDJ # _model_server_result.job_id lpIYCvLNFbchufrnTOlOJA _model_server_result.datetime_utc '2025-03-06 03:26:22' _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 5ydj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 5YDJ # _exptl.entry_id 5YDJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _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 90 _cell.angle_gamma 120 _cell.entry_id 5YDJ _cell.length_a 147.65 _cell.length_b 147.65 _cell.length_c 224.18 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YDJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression B,D,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,MA 1 1 A,C,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,LA 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_564 y,-x+y+1,z-1/6 0.5 0.866025 0 -0.866025 0.5 0 0 0 1 -73.825 127.868651 -37.363333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 T N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 2 n C NAG 1 C 1 NAG D 1 NAG 2 n C NAG 2 C 2 NAG D 2 NAG 2 n D NAG 1 D 1 NAG E 1 NAG 2 n D NAG 2 D 2 NAG E 2 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 228 A CYS 228 1_555 A SG CYS 255 A CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 414 A CYS 414 1_555 A SG CYS 427 A CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 562 A CYS 562 1_555 A SG CYS 683 A CYS 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 B SG CYS 228 B CYS 228 1_555 B SG CYS 255 B CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 B SG CYS 414 B CYS 414 1_555 B SG CYS 427 B CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 B SG CYS 562 B CYS 562 1_555 B SG CYS 683 B CYS 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 220 A ASN 220 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A C GLU 359 A GLU 359 1_555 A N SEB 360 A SEB 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 A C SEB 360 A SEB 360 1_555 A N ALA 361 A ALA 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale4 A ND2 ASN 670 A ASN 670 1_555 E C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 B ND2 ASN 220 B ASN 220 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale6 B C GLU 359 B GLU 359 1_555 B N SEB 360 B SEB 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale7 B C SEB 360 B SEB 360 1_555 B N ALA 361 B ALA 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale8 B ND2 ASN 670 B ASN 670 1_555 T C1 NAG . B NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale9 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.52 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? metalc ? metalc1 A NE2 HIS 416 A HIS 416 1_555 S CO CO . A CO 815 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? metalc ? metalc2 S CO CO . A CO 815 1_555 LA O HOH . A HOH 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.734 ? metalc ? metalc3 S CO CO . A CO 815 1_555 LA O HOH . A HOH 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.753 ? metalc ? metalc4 B NE2 HIS 416 B HIS 416 1_555 KA CO CO . B CO 818 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? metalc ? metalc5 KA CO CO . B CO 818 1_555 MA O HOH . B HOH 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.735 ? metalc ? metalc6 KA CO CO . B CO 818 1_555 MA O HOH . B HOH 917 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.73 ? # _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 5YDJ _atom_sites.fract_transf_matrix[1][1] 0.006773 _atom_sites.fract_transf_matrix[1][2] 0.00391 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007821 _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] 0.004461 _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 E 3 NAG A 1 801 1 NAG NAG . F 4 SO4 A 1 802 2 SO4 SO4 . G 4 SO4 A 1 803 5 SO4 SO4 . H 4 SO4 A 1 804 6 SO4 SO4 . I 4 SO4 A 1 805 8 SO4 SO4 . J 4 SO4 A 1 806 12 SO4 SO4 . K 4 SO4 A 1 807 14 SO4 SO4 . L 4 SO4 A 1 808 18 SO4 SO4 . M 4 SO4 A 1 809 21 SO4 SO4 . N 4 SO4 A 1 810 23 SO4 SO4 . O 4 SO4 A 1 811 24 SO4 SO4 . P 4 SO4 A 1 812 27 SO4 SO4 . Q 4 SO4 A 1 813 29 SO4 SO4 . R 4 SO4 A 1 814 30 SO4 SO4 . S 5 CO A 1 815 2 CO CO . T 3 NAG B 1 801 1 NAG NAG . U 4 SO4 B 1 802 1 SO4 SO4 . V 4 SO4 B 1 803 3 SO4 SO4 . W 4 SO4 B 1 804 4 SO4 SO4 . X 4 SO4 B 1 805 7 SO4 SO4 . Y 4 SO4 B 1 806 9 SO4 SO4 . Z 4 SO4 B 1 807 10 SO4 SO4 . AA 4 SO4 B 1 808 13 SO4 SO4 . BA 4 SO4 B 1 809 15 SO4 SO4 . CA 4 SO4 B 1 810 16 SO4 SO4 . DA 4 SO4 B 1 811 17 SO4 SO4 . EA 4 SO4 B 1 812 19 SO4 SO4 . FA 4 SO4 B 1 813 20 SO4 SO4 . GA 4 SO4 B 1 814 22 SO4 SO4 . HA 4 SO4 B 1 815 25 SO4 SO4 . IA 4 SO4 B 1 816 26 SO4 SO4 . JA 4 SO4 B 1 817 28 SO4 SO4 . KA 5 CO B 1 818 1 CO CO . LA 6 HOH A 1 901 5 HOH HOH . LA 6 HOH A 2 902 41 HOH HOH . LA 6 HOH A 3 903 44 HOH HOH . LA 6 HOH A 4 904 40 HOH HOH . LA 6 HOH A 5 905 48 HOH HOH . LA 6 HOH A 6 906 3 HOH HOH . LA 6 HOH A 7 907 20 HOH HOH . LA 6 HOH A 8 908 23 HOH HOH . LA 6 HOH A 9 909 29 HOH HOH . LA 6 HOH A 10 910 7 HOH HOH . LA 6 HOH A 11 911 31 HOH HOH . LA 6 HOH A 12 912 8 HOH HOH . LA 6 HOH A 13 913 39 HOH HOH . LA 6 HOH A 14 914 25 HOH HOH . LA 6 HOH A 15 915 27 HOH HOH . LA 6 HOH A 16 916 4 HOH HOH . LA 6 HOH A 17 917 42 HOH HOH . LA 6 HOH A 18 918 19 HOH HOH . LA 6 HOH A 19 919 14 HOH HOH . LA 6 HOH A 20 920 38 HOH HOH . LA 6 HOH A 21 921 6 HOH HOH . LA 6 HOH A 22 922 34 HOH HOH . LA 6 HOH A 23 923 22 HOH HOH . MA 6 HOH B 1 901 26 HOH HOH . MA 6 HOH B 2 902 30 HOH HOH . MA 6 HOH B 3 903 28 HOH HOH . MA 6 HOH B 4 904 45 HOH HOH . MA 6 HOH B 5 905 47 HOH HOH . MA 6 HOH B 6 906 33 HOH HOH . MA 6 HOH B 7 907 10 HOH HOH . MA 6 HOH B 8 908 11 HOH HOH . MA 6 HOH B 9 909 9 HOH HOH . MA 6 HOH B 10 910 37 HOH HOH . MA 6 HOH B 11 911 46 HOH HOH . MA 6 HOH B 12 912 21 HOH HOH . MA 6 HOH B 13 913 35 HOH HOH . MA 6 HOH B 14 914 15 HOH HOH . MA 6 HOH B 15 915 24 HOH HOH . MA 6 HOH B 16 916 1 HOH HOH . MA 6 HOH B 17 917 2 HOH HOH . MA 6 HOH B 18 918 16 HOH HOH . MA 6 HOH B 19 919 17 HOH HOH . MA 6 HOH B 20 920 12 HOH HOH . MA 6 HOH B 21 921 13 HOH HOH . MA 6 HOH B 22 922 32 HOH HOH . MA 6 HOH B 23 923 36 HOH HOH . MA 6 HOH B 24 924 43 HOH HOH . MA 6 HOH B 25 925 18 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 . . . E 3 61.664 21.435 8.008 1 114.38 ? C1 NAG 801 A 1 HETATM 2 C C2 NAG . . . E 3 62.148 21.609 9.453 1 115.34 ? C2 NAG 801 A 1 HETATM 3 C C3 NAG . . . E 3 61.742 20.398 10.29 1 118.39 ? C3 NAG 801 A 1 HETATM 4 C C4 NAG . . . E 3 62.153 19.102 9.589 1 122.22 ? C4 NAG 801 A 1 HETATM 5 C C5 NAG . . . E 3 61.69 19.062 8.124 1 123.94 ? C5 NAG 801 A 1 HETATM 6 C C6 NAG . . . E 3 60.873 17.808 7.811 1 117.56 ? C6 NAG 801 A 1 HETATM 7 C C7 NAG . . . E 3 64.344 22.386 10.385 1 102.91 ? C7 NAG 801 A 1 HETATM 8 C C8 NAG . . . E 3 63.678 23.132 11.504 1 94.54 ? C8 NAG 801 A 1 HETATM 9 N N2 NAG . . . E 3 63.605 21.723 9.486 1 109.22 ? N2 NAG 801 A 1 HETATM 10 O O3 NAG . . . E 3 60.327 20.402 10.507 1 115.34 ? O3 NAG 801 A 1 HETATM 11 O O4 NAG . . . E 3 63.58 18.972 9.648 1 117.78 ? O4 NAG 801 A 1 HETATM 12 O O5 NAG . . . E 3 60.918 20.23 7.819 1 124.73 ? O5 NAG 801 A 1 HETATM 13 O O6 NAG . . . E 3 60.268 17.913 6.514 1 104.75 ? O6 NAG 801 A 1 HETATM 14 O O7 NAG . . . E 3 65.561 22.389 10.292 1 104.87 ? O7 NAG 801 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 14 #