data_5TDG # _model_server_result.job_id 7RJAvL0wVRy7l8BlolXxMw _model_server_result.datetime_utc '2024-11-05 01:27:30' _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 5tdg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":5001}' # _entry.id 5TDG # _exptl.entry_id 5TDG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _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 93.91 _cell.angle_gamma 90 _cell.entry_id 5TDG _cell.length_a 73.069 _cell.length_b 127.033 _cell.length_c 92.427 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5TDG _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 ? 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 12 A CYS 37 1_555 A SG CYS 414 A CYS 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 A SG CYS 44 A CYS 69 1_555 A SG CYS 187 A CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 130 A CYS 155 1_555 A SG CYS 265 A CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 A SG CYS 288 A CYS 313 1_555 A SG CYS 318 A CYS 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 297 A CYS 322 1_555 A SG CYS 308 A CYS 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 A SG CYS 333 A CYS 358 1_555 A SG CYS 342 A CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf7 A SG CYS 357 A CYS 382 1_555 A SG CYS 368 A CYS 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 A SG CYS 391 A CYS 416 1_555 A SG CYS 397 A CYS 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf9 B SG CYS 12 B CYS 37 1_555 B SG CYS 414 B CYS 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf10 B SG CYS 44 B CYS 69 1_555 B SG CYS 187 B CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 B SG CYS 130 B CYS 155 1_555 B SG CYS 265 B CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf12 B SG CYS 288 B CYS 313 1_555 B SG CYS 318 B CYS 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf13 B SG CYS 297 B CYS 322 1_555 B SG CYS 308 B CYS 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf14 B SG CYS 333 B CYS 358 1_555 B SG CYS 342 B CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf15 B SG CYS 357 B CYS 382 1_555 B SG CYS 368 B CYS 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf16 B SG CYS 391 B CYS 416 1_555 B SG CYS 397 B CYS 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf17 C SG CYS 12 C CYS 37 1_555 C SG CYS 414 C CYS 439 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf18 C SG CYS 44 C CYS 69 1_555 C SG CYS 187 C CYS 212 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf19 C SG CYS 130 C CYS 155 1_555 C SG CYS 265 C CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf20 C SG CYS 288 C CYS 313 1_555 C SG CYS 318 C CYS 343 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf21 C SG CYS 297 C CYS 322 1_555 C SG CYS 308 C CYS 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf22 C SG CYS 333 C CYS 358 1_555 C SG CYS 342 C CYS 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf23 C SG CYS 357 C CYS 382 1_555 C SG CYS 368 C CYS 393 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf24 C SG CYS 391 C CYS 416 1_555 C SG CYS 397 C CYS 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 475 A ASN 500 1_555 D C1 NAG . A NAG 5001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 B ND2 ASN 475 B ASN 500 1_555 E C1 NAG . B NAG 5001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale3 C ND2 ASN 475 C ASN 500 1_555 F C1 NAG . C NAG 5001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 5TDG _atom_sites.fract_transf_matrix[1][1] 0.013686 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000936 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007872 _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] 0.010845 _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 D 2 NAG A 1 5001 5001 NAG NAG . E 2 NAG B 1 5001 5001 NAG NAG . F 2 NAG C 1 5001 5001 NAG NAG . G 3 HOH A 1 5101 17 HOH HOH . G 3 HOH A 2 5102 24 HOH HOH . G 3 HOH A 3 5103 23 HOH HOH . G 3 HOH A 4 5104 13 HOH HOH . G 3 HOH A 5 5105 5 HOH HOH . G 3 HOH A 6 5106 21 HOH HOH . G 3 HOH A 7 5107 18 HOH HOH . H 3 HOH B 1 5101 29 HOH HOH . H 3 HOH B 2 5102 16 HOH HOH . H 3 HOH B 3 5103 14 HOH HOH . H 3 HOH B 4 5104 19 HOH HOH . H 3 HOH B 5 5105 9 HOH HOH . H 3 HOH B 6 5106 7 HOH HOH . H 3 HOH B 7 5107 2 HOH HOH . H 3 HOH B 8 5108 26 HOH HOH . H 3 HOH B 9 5109 8 HOH HOH . H 3 HOH B 10 5110 30 HOH HOH . H 3 HOH B 11 5111 27 HOH HOH . H 3 HOH B 12 5112 6 HOH HOH . H 3 HOH B 13 5113 33 HOH HOH . H 3 HOH B 14 5114 1 HOH HOH . H 3 HOH B 15 5115 34 HOH HOH . I 3 HOH C 1 5101 12 HOH HOH . I 3 HOH C 2 5102 32 HOH HOH . I 3 HOH C 3 5103 31 HOH HOH . I 3 HOH C 4 5104 22 HOH HOH . I 3 HOH C 5 5105 10 HOH HOH . I 3 HOH C 6 5106 25 HOH HOH . I 3 HOH C 7 5107 36 HOH HOH . I 3 HOH C 8 5108 35 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 . . . D 2 -26.982 4.686 -67.914 1 142.61 ? C1 NAG 5001 A 1 HETATM 2 C C2 NAG . . . D 2 -25.509 4.831 -67.523 1 141.65 ? C2 NAG 5001 A 1 HETATM 3 C C3 NAG . . . D 2 -25.009 6.239 -67.834 1 147.12 ? C3 NAG 5001 A 1 HETATM 4 C C4 NAG . . . D 2 -25.288 6.596 -69.288 1 149.75 ? C4 NAG 5001 A 1 HETATM 5 C C5 NAG . . . D 2 -26.77 6.412 -69.594 1 150.14 ? C5 NAG 5001 A 1 HETATM 6 C C6 NAG . . . D 2 -27.104 6.652 -71.049 1 145.5 ? C6 NAG 5001 A 1 HETATM 7 C C7 NAG . . . D 2 -24.243 3.85 -65.661 1 139.94 ? C7 NAG 5001 A 1 HETATM 8 C C8 NAG . . . D 2 -24.196 3.619 -64.181 1 131.81 ? C8 NAG 5001 A 1 HETATM 9 N N2 NAG . . . D 2 -25.308 4.519 -66.116 1 138.61 ? N2 NAG 5001 A 1 HETATM 10 O O3 NAG . . . D 2 -23.61 6.311 -67.579 1 148.13 ? O3 NAG 5001 A 1 HETATM 11 O O4 NAG . . . D 2 -24.921 7.946 -69.543 1 149.61 ? O4 NAG 5001 A 1 HETATM 12 O O5 NAG . . . D 2 -27.159 5.063 -69.293 1 149.08 ? O5 NAG 5001 A 1 HETATM 13 O O6 NAG . . . D 2 -28.305 5.996 -71.434 1 140.7 ? O6 NAG 5001 A 1 HETATM 14 O O7 NAG . . . D 2 -23.359 3.449 -66.41 1 150.2 ? O7 NAG 5001 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 14 #