data_7XGD # _model_server_result.job_id YXbwGap0R3RZofIenFPbYg _model_server_result.datetime_utc '2024-11-22 22:25:13' _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 7xgd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 7XGD # _exptl.entry_id 7XGD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 4 _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 7XGD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7XGD _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 ? _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 ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F 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 3 A CYS 3 1_555 A SG CYS 22 A CYS 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 120 A CYS 120 1_555 A SG CYS 148 A CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 152 A CYS 152 1_555 A SG CYS 175 A CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 A SG CYS 162 A CYS 162 1_555 A SG CYS 181 A CYS 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 A SG CYS 185 A CYS 185 1_555 A SG CYS 194 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 A SG CYS 189 A CYS 189 1_555 A SG CYS 200 A CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 A SG CYS 201 A CYS 201 1_555 A SG CYS 209 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 A SG CYS 205 A CYS 205 1_555 A SG CYS 218 A CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 A SG CYS 221 A CYS 221 1_555 A SG CYS 230 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 A SG CYS 234 A CYS 234 1_555 A SG CYS 246 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 A SG CYS 252 A CYS 252 1_555 A SG CYS 273 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 A SG CYS 277 A CYS 277 1_555 A SG CYS 291 A CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf13 A SG CYS 294 A CYS 294 1_555 A SG CYS 298 A CYS 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf14 A SG CYS 302 A CYS 302 1_555 A SG CYS 323 A CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf15 A SG CYS 633 A CYS 633 1_555 A SG CYS 849 A CYS 849 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf16 A SG CYS 669 A CYS 669 1_555 A SG CYS 672 A CYS 672 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf17 A SG CYS 670 A CYS 670 1_555 B SG CYS 670 B CYS 670 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf18 A SG CYS 776 A CYS 776 1_555 A SG CYS 785 A CYS 785 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf19 B SG CYS 3 B CYS 3 1_555 B SG CYS 22 B CYS 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf20 B SG CYS 120 B CYS 120 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf21 B SG CYS 152 B CYS 152 1_555 B SG CYS 175 B CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf22 B SG CYS 162 B CYS 162 1_555 B SG CYS 181 B CYS 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf23 B SG CYS 185 B CYS 185 1_555 B SG CYS 194 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf24 B SG CYS 189 B CYS 189 1_555 B SG CYS 200 B CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf25 B SG CYS 201 B CYS 201 1_555 B SG CYS 209 B CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf26 B SG CYS 205 B CYS 205 1_555 B SG CYS 218 B CYS 218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf27 B SG CYS 221 B CYS 221 1_555 B SG CYS 230 B CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf28 B SG CYS 234 B CYS 234 1_555 B SG CYS 246 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf29 B SG CYS 252 B CYS 252 1_555 B SG CYS 273 B CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf30 B SG CYS 277 B CYS 277 1_555 B SG CYS 291 B CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf31 B SG CYS 294 B CYS 294 1_555 B SG CYS 298 B CYS 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf32 B SG CYS 302 B CYS 302 1_555 B SG CYS 323 B CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf33 B SG CYS 425 B CYS 425 1_555 B SG CYS 458 B CYS 458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf34 B SG CYS 633 B CYS 633 1_555 B SG CYS 849 B CYS 849 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf35 B SG CYS 669 B CYS 669 1_555 B SG CYS 672 B CYS 672 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf36 B SG CYS 776 B CYS 776 1_555 B SG CYS 785 B CYS 785 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 21 A ASN 21 1_555 C C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 105 A ASN 105 1_555 D C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 B ND2 ASN 21 B ASN 21 1_555 E C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 B ND2 ASN 105 B ASN 105 1_555 F C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 7XGD _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 2 NAG A 1 1001 1001 NAG NAG . D 2 NAG A 1 1002 1003 NAG NAG . E 2 NAG B 1 1001 1001 NAG NAG . F 2 NAG B 1 1002 1003 NAG NAG . # 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 . . . C 2 257.076 195.28 185.92 1 313.02 ? C1 NAG 1001 A 1 HETATM 2 C C2 NAG . . . C 2 256.764 194.47 184.662 1 313.02 ? C2 NAG 1001 A 1 HETATM 3 C C3 NAG . . . C 2 258.009 193.721 184.194 1 313.02 ? C3 NAG 1001 A 1 HETATM 4 C C4 NAG . . . C 2 259.177 194.683 184.028 1 313.02 ? C4 NAG 1001 A 1 HETATM 5 C C5 NAG . . . C 2 259.388 195.483 185.309 1 313.02 ? C5 NAG 1001 A 1 HETATM 6 C C6 NAG . . . C 2 260.456 196.543 185.175 1 313.02 ? C6 NAG 1001 A 1 HETATM 7 C C7 NAG . . . C 2 254.382 193.9 184.832 1 313.02 ? C7 NAG 1001 A 1 HETATM 8 C C8 NAG . . . C 2 253.384 192.816 185.105 1 313.02 ? C8 NAG 1001 A 1 HETATM 9 N N2 NAG . . . C 2 255.669 193.543 184.898 1 313.02 ? N2 NAG 1001 A 1 HETATM 10 O O3 NAG . . . C 2 257.733 193.073 182.958 1 313.02 ? O3 NAG 1001 A 1 HETATM 11 O O4 NAG . . . C 2 260.364 193.958 183.726 1 313.02 ? O4 NAG 1001 A 1 HETATM 12 O O5 NAG . . . C 2 258.174 196.162 185.664 1 313.02 ? O5 NAG 1001 A 1 HETATM 13 O O6 NAG . . . C 2 260.133 197.481 184.159 1 313.02 ? O6 NAG 1001 A 1 HETATM 14 O O7 NAG . . . C 2 254.039 195.049 184.568 1 313.02 ? O7 NAG 1001 A 1 HETATM 15 H H1 NAG . . . C 2 257.319 194.667 186.639 1 313.02 ? H1 NAG 1001 A 1 HETATM 16 H H2 NAG . . . C 2 256.501 195.09 183.956 1 313.02 ? H2 NAG 1001 A 1 HETATM 17 H H3 NAG . . . C 2 258.244 193.047 184.86 1 313.02 ? H3 NAG 1001 A 1 HETATM 18 H H4 NAG . . . C 2 258.983 195.297 183.295 1 313.02 ? H4 NAG 1001 A 1 HETATM 19 H H5 NAG . . . C 2 259.634 194.872 186.029 1 313.02 ? H5 NAG 1001 A 1 HETATM 20 H H61 NAG . . . C 2 260.548 197.013 186.026 1 313.02 ? H61 NAG 1001 A 1 HETATM 21 H H62 NAG . . . C 2 261.305 196.114 184.954 1 313.02 ? H62 NAG 1001 A 1 HETATM 22 H H81 NAG . . . C 2 252.597 192.95 184.544 1 313.02 ? H81 NAG 1001 A 1 HETATM 23 H H82 NAG . . . C 2 253.783 191.948 184.906 1 313.02 ? H82 NAG 1001 A 1 HETATM 24 H H83 NAG . . . C 2 253.121 192.846 186.044 1 313.02 ? H83 NAG 1001 A 1 HETATM 25 H HN2 NAG . . . C 2 255.869 192.676 185.098 1 313.02 ? HN2 NAG 1001 A 1 HETATM 26 H HO3 NAG . . . C 2 257.131 193.542 182.504 1 313.02 ? HO3 NAG 1001 A 1 HETATM 27 H HO4 NAG . . . C 2 260.396 193.792 182.855 1 313.02 ? HO4 NAG 1001 A 1 HETATM 28 H HO6 NAG . . . C 2 259.279 197.391 183.932 1 313.02 ? HO6 NAG 1001 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #