data_5T33 # _model_server_result.job_id eXIV8xl_YsKtvE_ZcxYigQ _model_server_result.datetime_utc '2024-12-01 23:56:30' _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 5t33 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1088}' # _entry.id 5T33 # _exptl.entry_id 5T33 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _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 5T33 _cell.length_a 68.176 _cell.length_b 71.139 _cell.length_c 190.596 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5T33 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,J,K,L,M _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 ? 7 H N N ? 7 I N N ? 7 J N N ? 7 K N N ? 7 L N N ? 7 M N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide 6 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 5 4 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 7 ? 6 4 3 MAN BMA C1 O1 . O6 HO6 . sing 8 ? 6 5 4 MAN MAN C1 O1 . O3 HO3 . sing 9 ? 6 6 4 MAN MAN C1 O1 . O6 HO6 . sing 10 ? 6 7 3 MAN BMA C1 O1 . O3 HO3 . 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 4 n D NAG 1 A 1 NAG G 1234 NAG 4 n D NAG 2 A 2 NAG G 1235 NAG 5 n E NAG 1 B 1 NAG G 1262 NAG 5 n E NAG 2 B 2 NAG G 1263 NAG 5 n E BMA 3 B 3 BMA G 1264 BMA 5 n E MAN 4 B 4 MAN G 1265 MAN 6 n F NAG 1 C 1 NAG G 1276 NAG 6 n F NAG 2 C 2 NAG G 1277 NAG 6 n F BMA 3 C 3 BMA G 1278 BMA 6 n F MAN 4 C 4 MAN G 1280 MAN 6 n F MAN 5 C 5 MAN G 1281 MAN 6 n F MAN 6 C 6 MAN G 1282 MAN 6 n F MAN 7 C 7 MAN G 1279 MAN 4 n G NAG 1 D 1 NAG G 1295 NAG 4 n G NAG 2 D 2 NAG G 1296 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 22 H CYS 22 1_555 A SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 147 H CYS 140 1_555 A SG CYS 203 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 223 H CYS 216 1_555 B SG CYS 213 L CYS 211 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 22 L CYS 23 1_555 B SG CYS 87 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 B SG CYS 136 L CYS 134 1_555 B SG CYS 195 L CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 C SG CYS 11 G CYS 54 1_555 C SG CYS 31 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 C SG CYS 76 G CYS 119 1_555 C SG CYS 88 G CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf8 C SG CYS 101 G CYS 218 1_555 C SG CYS 130 G CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 C SG CYS 111 G CYS 228 1_555 C SG CYS 122 G CYS 239 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 C SG CYS 179 G CYS 296 1_555 C SG CYS 198 G CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf11 C SG CYS 244 G CYS 378 1_555 C SG CYS 311 G CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 C SG CYS 251 G CYS 385 1_555 C SG CYS 284 G CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 C ND2 ASN 6 G ASN 49 1_555 H C1 NAG . G NAG 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 C ND2 ASN 45 G ASN 88 1_555 I C1 NAG . G NAG 1088 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 C ND2 ASN 117 G ASN 234 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 C ND2 ASN 124 G ASN 241 1_555 J C1 NAG . G NAG 1241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 C ND2 ASN 145 G ASN 262 1_555 E C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 C ND2 ASN 159 G ASN 276 1_555 F C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 C ND2 ASN 172 G ASN 289 1_555 K C1 NAG . G NAG 1289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale8 C ND2 ASN 178 G ASN 295 1_555 G C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 C ND2 ASN 252 G ASN 386 1_555 L C1 NAG . G NAG 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 C ND2 ASN 314 G ASN 448 1_555 M C1 NAG . G NAG 1448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale12 E O4 NAG . B NAG 1 1_555 E C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale13 E O4 NAG . B NAG 2 1_555 E C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale14 E O6 BMA . B BMA 3 1_555 E C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale15 F O4 NAG . C NAG 1 1_555 F C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 F O4 NAG . C NAG 2 1_555 F C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale17 F O6 BMA . C BMA 3 1_555 F C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale18 F O3 BMA . C BMA 3 1_555 F C1 MAN . C MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale19 F O3 MAN . C MAN 4 1_555 F C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale20 F O6 MAN . C MAN 4 1_555 F C1 MAN . C MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale21 G O4 NAG . D NAG 1 1_555 G C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 5T33 _atom_sites.fract_transf_matrix[1][1] 0.014668 _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] 0.014057 _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] 0.005247 _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 H 7 NAG G 1 1049 1049 NAG NAG . I 7 NAG G 1 1088 1088 NAG NAG . J 7 NAG G 1 1241 1241 NAG NAG . K 7 NAG G 1 1289 1289 NAG NAG . L 7 NAG G 1 1386 1386 NAG NAG . M 7 NAG G 1 1448 1448 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 . . . I 7 -43.177 -24.817 -16.65 1 173.45 ? C1 NAG 1088 G 1 HETATM 2 C C2 NAG . . . I 7 -41.971 -25.735 -16.699 1 178.97 ? C2 NAG 1088 G 1 HETATM 3 C C3 NAG . . . I 7 -42.206 -27.04 -16.028 1 180.38 ? C3 NAG 1088 G 1 HETATM 4 C C4 NAG . . . I 7 -42.77 -26.883 -14.671 1 180.35 ? C4 NAG 1088 G 1 HETATM 5 C C5 NAG . . . I 7 -43.992 -25.999 -14.686 1 180.24 ? C5 NAG 1088 G 1 HETATM 6 C C6 NAG . . . I 7 -44.474 -25.81 -13.283 1 180.95 ? C6 NAG 1088 G 1 HETATM 7 C C7 NAG . . . I 7 -42.197 -26.604 -19.114 1 182.65 ? C7 NAG 1088 G 1 HETATM 8 C C8 NAG . . . I 7 -43.565 -27.217 -19.008 1 182.26 ? C8 NAG 1088 G 1 HETATM 9 N N2 NAG . . . I 7 -41.494 -25.942 -18.074 1 180.96 ? N2 NAG 1088 G 1 HETATM 10 O O3 NAG . . . I 7 -40.935 -27.764 -15.933 1 180.67 ? O3 NAG 1088 G 1 HETATM 11 O O4 NAG . . . I 7 -43.137 -28.195 -14.171 1 180.74 ? O4 NAG 1088 G 1 HETATM 12 O O5 NAG . . . I 7 -43.706 -24.687 -15.272 1 178.12 ? O5 NAG 1088 G 1 HETATM 13 O O6 NAG . . . I 7 -45.796 -25.319 -13.296 1 181.99 ? O6 NAG 1088 G 1 HETATM 14 O O7 NAG . . . I 7 -41.641 -26.68 -20.192 1 182.5 ? O7 NAG 1088 G 1 HETATM 15 H H1 NAG . . . I 7 -43.872 -25.179 -17.221 1 208.14 ? H1 NAG 1088 G 1 HETATM 16 H H2 NAG . . . I 7 -41.254 -25.29 -16.213 1 214.76 ? H2 NAG 1088 G 1 HETATM 17 H H3 NAG . . . I 7 -42.837 -27.572 -16.575 1 216.46 ? H3 NAG 1088 G 1 HETATM 18 H H4 NAG . . . I 7 -42.094 -26.489 -14.084 1 216.42 ? H4 NAG 1088 G 1 HETATM 19 H H5 NAG . . . I 7 -44.691 -26.432 -15.207 1 216.29 ? H5 NAG 1088 G 1 HETATM 20 H H61 NAG . . . I 7 -43.896 -25.17 -12.825 1 217.14 ? H61 NAG 1088 G 1 HETATM 21 H H62 NAG . . . I 7 -44.45 -26.662 -12.814 1 217.14 ? H62 NAG 1088 G 1 HETATM 22 H H81 NAG . . . I 7 -43.862 -27.508 -19.891 1 218.71 ? H81 NAG 1088 G 1 HETATM 23 H H82 NAG . . . I 7 -44.191 -26.556 -18.657 1 218.71 ? H82 NAG 1088 G 1 HETATM 24 H H83 NAG . . . I 7 -43.531 -27.989 -18.403 1 218.71 ? H83 NAG 1088 G 1 HETATM 25 H HN2 NAG . . . I 7 -40.663 -25.614 -18.279 1 217.15 ? HN2 NAG 1088 G 1 HETATM 26 H HO3 NAG . . . I 7 -40.889 -28.37 -16.586 1 216.81 ? HO3 NAG 1088 G 1 HETATM 27 H HO4 NAG . . . I 7 -43.053 -28.21 -13.297 1 216.89 ? HO4 NAG 1088 G 1 HETATM 28 H HO6 NAG . . . I 7 -46.194 -25.518 -12.526 1 218.39 ? HO6 NAG 1088 G 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #