data_4C53 # _model_server_result.job_id 3rrVbxOWy-Mu1m5sga-v9A _model_server_result.datetime_utc '2025-09-03 22:02:48' _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 4c53 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1407}' # _entry.id 4C53 # _exptl.entry_id 4C53 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 90 _cell.angle_gamma 90 _cell.entry_id 4C53 _cell.length_a 98.5 _cell.length_b 98.5 _cell.length_c 78.74 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4C53 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details 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 _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 ? 5 I N N ? 5 J N N ? 5 K N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 7 ? 4 5 4 MAN MAN C1 O1 . O3 HO3 . sing 8 ? 4 6 4 MAN MAN C1 O1 . O6 HO6 . sing 9 ? 4 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 2 n D NAG 1 D 1 NAG A 1404 NAG 2 n D NAG 2 D 2 NAG A 1405 NAG 2 n D BMA 3 D 3 BMA A 1406 BMA 3 n E NAG 1 E 1 NAG B 1408 NAG 3 n E NAG 2 E 2 NAG B 1409 NAG 4 n F NAG 1 F 1 NAG B 1410 NAG 4 n F NAG 2 F 2 NAG B 1411 NAG 4 n F BMA 3 F 3 BMA B 1412 BMA 4 n F MAN 4 F 4 MAN B 1413 MAN 4 n F MAN 5 F 5 MAN B 1415 MAN 4 n F MAN 6 F 6 MAN B 1414 MAN 4 n F MAN 7 F 7 MAN B 1416 MAN 4 n G NAG 1 G 1 NAG C 1407 NAG 4 n G NAG 2 G 2 NAG C 1408 NAG 4 n G BMA 3 G 3 BMA C 1409 BMA 4 n G MAN 4 G 4 MAN C 1410 MAN 4 n G MAN 5 G 5 MAN C 1412 MAN 4 n G MAN 6 G 6 MAN C 1411 MAN 4 n G MAN 7 G 7 MAN C 1413 MAN 4 n H NAG 1 H 1 NAG C 1414 NAG 4 n H NAG 2 H 2 NAG C 1415 NAG 4 n H BMA 3 H 3 BMA C 1416 BMA 4 n H MAN 4 H 4 MAN C 1417 MAN 4 n H MAN 5 H 5 MAN C 1419 MAN 4 n H MAN 6 H 6 MAN C 1418 MAN 4 n H MAN 7 H 7 MAN C 1420 MAN # 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 61 A CYS 350 1_555 A SG CYS 82 A CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? disulf ? disulf2 B SG CYS 61 B CYS 350 1_555 B SG CYS 82 B CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.726 ? disulf ? disulf3 C SG CYS 61 C CYS 350 1_555 C SG CYS 82 C CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? covale ? covale1 A ND2 ASN 25 A ASN 314 1_555 I C1 NAG . A NAG 1407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 A ND2 ASN 87 A ASN 376 1_555 J C1 NAG . A NAG 1408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale3 A ND2 ASN 92 A ASN 381 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 B ND2 ASN 25 B ASN 314 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale5 B ND2 ASN 62 B ASN 351 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 B ND2 ASN 92 B ASN 381 1_555 K C1 NAG . B NAG 1417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale7 C ND2 ASN 25 C ASN 314 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale8 C ND2 ASN 92 C ASN 381 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale10 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale11 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale12 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale13 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale14 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale15 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale16 F O3 MAN . F MAN 4 1_555 F C1 MAN . F MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale17 F O6 MAN . F MAN 4 1_555 F C1 MAN . F MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale18 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale19 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale20 G O6 BMA . G BMA 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale21 G O3 BMA . G BMA 3 1_555 G C1 MAN . G MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale22 G O3 MAN . G MAN 4 1_555 G C1 MAN . G MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale23 G O6 MAN . G MAN 4 1_555 G C1 MAN . G MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? covale ? covale24 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? covale ? covale25 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale26 H O6 BMA . H BMA 3 1_555 H C1 MAN . H MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale27 H O3 BMA . H BMA 3 1_555 H C1 MAN . H MAN 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale28 H O3 MAN . H MAN 4 1_555 H C1 MAN . H MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale29 H O6 MAN . H MAN 4 1_555 H C1 MAN . H MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? # _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 4C53 _atom_sites.fract_transf_matrix[1][1] 0.010152 _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] 0.010152 _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] 0.0127 _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 I 5 NAG A 1 1407 1407 NAG NAG . J 5 NAG A 1 1408 1408 NAG NAG . K 5 NAG B 1 1417 1417 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 5 -38.3 19.459 0.873 1 262.02 ? C1 NAG 1407 A 1 HETATM 2 C C2 NAG . . . I 5 -38.182 19.831 2.367 1 263.92 ? C2 NAG 1407 A 1 HETATM 3 C C3 NAG . . . I 5 -39.369 19.235 3.145 1 264.9 ? C3 NAG 1407 A 1 HETATM 4 C C4 NAG . . . I 5 -40.658 19.802 2.531 1 265.34 ? C4 NAG 1407 A 1 HETATM 5 C C5 NAG . . . I 5 -40.71 19.402 1.05 1 265.07 ? C5 NAG 1407 A 1 HETATM 6 C C6 NAG . . . I 5 -41.979 19.962 0.371 1 265.3 ? C6 NAG 1407 A 1 HETATM 7 C C7 NAG . . . I 5 -35.947 20.231 3.353 1 263.18 ? C7 NAG 1407 A 1 HETATM 8 C C8 NAG . . . I 5 -36.182 21.719 3.294 1 263.22 ? C8 NAG 1407 A 1 HETATM 9 N N2 NAG . . . I 5 -36.895 19.356 2.915 1 263.79 ? N2 NAG 1407 A 1 HETATM 10 O O3 NAG . . . I 5 -39.287 19.575 4.536 1 264.77 ? O3 NAG 1407 A 1 HETATM 11 O O4 NAG . . . I 5 -41.802 19.282 3.218 1 265.24 ? O4 NAG 1407 A 1 HETATM 12 O O5 NAG . . . I 5 -39.57 19.907 0.342 1 263.89 ? O5 NAG 1407 A 1 HETATM 13 O O6 NAG . . . I 5 -42.778 20.744 1.269 1 265.31 ? O6 NAG 1407 A 1 HETATM 14 O O7 NAG . . . I 5 -34.894 19.815 3.796 1 262.75 ? O7 NAG 1407 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #