data_1DE4 # _model_server_result.job_id QbW054foX2_IMGXMCP3PqQ _model_server_result.datetime_utc '2024-12-13 14:33:24' _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 1de4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":902}' # _entry.id 1DE4 # _exptl.entry_id 1DE4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.6 _cell.angle_gamma 90 _cell.entry_id 1DE4 _cell.length_a 110.4 _cell.length_b 144.4 _cell.length_c 327.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DE4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 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 PISA hexameric 6 author_and_software_defined_assembly 1 ? hexameric 6 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,E,F,J,K,L,M,Q,R 1 1 G,H,I,N,O,P,S 2 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' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 89.861221 0 326.454543 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 J N N ? 4 L N N ? 4 O 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 102 A CYS 102 1_555 A SG CYS 165 A CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 203 A CYS 203 1_555 A SG CYS 260 A CYS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 C SG CYS 233 C CYS 353 1_555 C SG CYS 243 C CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf5 C SG CYS 436 C CYS 556 1_555 C SG CYS 438 C CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf6 D SG CYS 102 D CYS 102 1_555 D SG CYS 165 D CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf7 D SG CYS 203 D CYS 203 1_555 D SG CYS 260 D CYS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 E SG CYS 25 E CYS 25 1_555 E SG CYS 80 E CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf9 F SG CYS 233 F CYS 353 1_555 F SG CYS 243 F CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf10 F SG CYS 436 F CYS 556 1_555 F SG CYS 438 F CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf11 G SG CYS 102 G CYS 102 1_555 G SG CYS 165 G CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf12 G SG CYS 203 G CYS 203 1_555 G SG CYS 260 G CYS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 H SG CYS 25 H CYS 25 1_555 H SG CYS 80 H CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf14 I SG CYS 233 I CYS 353 1_555 I SG CYS 243 I CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf15 I SG CYS 436 I CYS 556 1_555 I SG CYS 438 I CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? covale ? covale1 C ND2 ASN 197 C ASN 317 1_555 J C1 NAG . C NAG 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale2 F ND2 ASN 197 F ASN 317 1_555 L C1 NAG . F NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale3 I ND2 ASN 197 I ASN 317 1_555 O C1 NAG . I NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? metalc ? metalc1 C O THR 190 C THR 310 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc2 C OG1 THR 190 C THR 310 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc3 C O PHE 193 C PHE 313 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc4 C OE1 GLU 345 C GLU 465 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc5 C OE2 GLU 345 C GLU 465 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc6 C OE1 GLU 348 C GLU 468 1_555 K CA CA . C CA 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc7 F O THR 190 F THR 310 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc8 F OG1 THR 190 F THR 310 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.688 ? metalc ? metalc9 F O PHE 193 F PHE 313 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc10 F OE1 GLU 345 F GLU 465 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc11 F OE2 GLU 345 F GLU 465 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc12 F OE1 GLU 348 F GLU 468 1_555 M CA CA . F CA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc13 I OG1 THR 190 I THR 310 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc14 I O THR 190 I THR 310 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc15 I O PHE 193 I PHE 313 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc16 I OE2 GLU 345 I GLU 465 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? metalc ? metalc17 I OE1 GLU 345 I GLU 465 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc18 I OE1 GLU 348 I GLU 468 1_555 P CA CA . I CA 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? # _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 250 n n C1 O1 NAG sing 251 n n C1 O5 NAG sing 252 n n C1 H1 NAG sing 253 n n C2 C3 NAG sing 254 n n C2 N2 NAG sing 255 n n C2 H2 NAG sing 256 n n C3 C4 NAG sing 257 n n C3 O3 NAG sing 258 n n C3 H3 NAG sing 259 n n C4 C5 NAG sing 260 n n C4 O4 NAG sing 261 n n C4 H4 NAG sing 262 n n C5 C6 NAG sing 263 n n C5 O5 NAG sing 264 n n C5 H5 NAG sing 265 n n C6 O6 NAG sing 266 n n C6 H61 NAG sing 267 n n C6 H62 NAG sing 268 n n C7 C8 NAG sing 269 n n C7 N2 NAG sing 270 n n C7 O7 NAG doub 271 n n C8 H81 NAG sing 272 n n C8 H82 NAG sing 273 n n C8 H83 NAG sing 274 n n N2 HN2 NAG sing 275 n n O1 HO1 NAG sing 276 n n O3 HO3 NAG sing 277 n n O4 HO4 NAG sing 278 n n O6 HO6 NAG sing 279 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 1DE4 _atom_sites.fract_transf_matrix[1][1] 0.009058 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00057 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006925 _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] 0.003063 _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 4 NAG C 1 900 900 NAG NAG . K 5 CA C 1 801 1 CA CA . L 4 NAG F 1 901 901 NAG NAG . M 5 CA F 1 802 2 CA CA . N 6 GOL G 1 309 309 GOL CRY . O 4 NAG I 1 902 902 NAG NAG . P 5 CA I 1 803 3 CA CA . Q 7 HOH C 1 1 1 HOH TIP . Q 7 HOH C 2 2 2 HOH TIP . Q 7 HOH C 3 5 5 HOH TIP . Q 7 HOH C 4 6 6 HOH TIP . R 7 HOH F 1 7 7 HOH TIP . R 7 HOH F 2 8 8 HOH TIP . S 7 HOH I 1 3 3 HOH TIP . S 7 HOH I 2 4 4 HOH TIP . S 7 HOH I 3 9 9 HOH TIP . # 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 . . . O 4 49.107 70.222 135.714 1 61.58 ? C1 NAG 902 I 1 HETATM 2 C C2 NAG . . . O 4 48.837 70.077 134.22 1 72.4 ? C2 NAG 902 I 1 HETATM 3 C C3 NAG . . . O 4 50.149 70.314 133.471 1 76.56 ? C3 NAG 902 I 1 HETATM 4 C C4 NAG . . . O 4 50.629 71.732 133.793 1 75.57 ? C4 NAG 902 I 1 HETATM 5 C C5 NAG . . . O 4 50.82 71.852 135.313 1 69.64 ? C5 NAG 902 I 1 HETATM 6 C C6 NAG . . . O 4 51.209 73.248 135.719 1 64.98 ? C6 NAG 902 I 1 HETATM 7 C C7 NAG . . . O 4 46.964 68.662 133.695 1 72.08 ? C7 NAG 902 I 1 HETATM 8 C C8 NAG . . . O 4 46.415 67.286 133.356 1 68.25 ? C8 NAG 902 I 1 HETATM 9 N N2 NAG . . . O 4 48.276 68.775 133.906 1 72.98 ? N2 NAG 902 I 1 HETATM 10 O O3 NAG . . . O 4 49.943 70.171 132.077 1 90.72 ? O3 NAG 902 I 1 HETATM 11 O O4 NAG . . . O 4 51.841 72.032 133.104 1 68.62 ? O4 NAG 902 I 1 HETATM 12 O O5 NAG . . . O 4 49.58 71.545 135.995 1 59.88 ? O5 NAG 902 I 1 HETATM 13 O O6 NAG . . . O 4 50.794 74.184 134.739 1 80.45 ? O6 NAG 902 I 1 HETATM 14 O O7 NAG . . . O 4 46.189 69.619 133.772 1 66.76 ? O7 NAG 902 I 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 47 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #