data_4YH6 # _model_server_result.job_id 2AQiNCaGSCaetQvWQKoQVw _model_server_result.datetime_utc '2025-02-26 06:00:33' _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 4yh6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":404}' # _entry.id 4YH6 # _exptl.entry_id 4YH6 _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 1 _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 4YH6 _cell.length_a 102.454 _cell.length_b 102.454 _cell.length_c 222.712 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YH6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 5 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 6 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing 7 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 8 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 9 ? 4 4 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 C NAG 1 C 1 NAG A 1221 NAG 2 n C NAG 2 C 2 NAG A 1222 NAG 2 n C BMA 3 C 3 BMA A 1223 BMA 3 n D NAG 1 D 1 NAG A 2131 NAG 3 n D NAG 2 D 2 NAG A 2132 NAG 3 n D BMA 3 D 3 BMA A 2133 BMA 3 n D MAN 4 D 4 MAN A 2134 MAN 3 n D MAN 5 D 5 MAN A 2135 MAN 3 n E NAG 1 E 1 NAG A 2641 NAG 3 n E NAG 2 E 2 NAG A 2642 NAG 3 n E BMA 3 E 3 BMA A 2643 BMA 3 n E MAN 4 E 4 MAN A 2644 MAN 3 n E MAN 5 E 5 MAN A 2645 MAN 2 n F NAG 1 F 1 NAG B 1381 NAG 2 n F NAG 2 F 2 NAG B 1382 NAG 2 n F BMA 3 F 3 BMA B 1383 BMA 3 n G NAG 1 G 1 NAG B 2131 NAG 3 n G NAG 2 G 2 NAG B 2132 NAG 3 n G BMA 3 G 3 BMA B 2133 BMA 3 n G MAN 4 G 4 MAN B 2134 MAN 3 n G MAN 5 G 5 MAN B 2135 MAN 4 n H NAG 1 H 1 NAG B 2641 NAG 4 n H NAG 2 H 2 NAG B 2642 NAG 4 n H BMA 3 H 3 BMA B 2643 BMA 4 n H MAN 4 H 4 MAN B 2644 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 20 A CYS 31 1_555 A SG CYS 115 A CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 42 A CYS 53 1_555 A SG CYS 107 A CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 132 A CYS 143 1_555 A SG CYS 174 A CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 A SG CYS 153 A CYS 164 1_555 A SG CYS 205 A CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 256 A CYS 267 1_555 A SG CYS 323 A CYS 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 20 B CYS 31 1_555 B SG CYS 115 B CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf7 B SG CYS 42 B CYS 53 1_555 B SG CYS 107 B CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 B SG CYS 132 B CYS 143 1_555 B SG CYS 174 B CYS 185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 B SG CYS 153 B CYS 164 1_555 B SG CYS 205 B CYS 216 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 B SG CYS 256 B CYS 267 1_555 B SG CYS 323 B CYS 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 111 A ASN 122 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 127 A ASN 138 1_555 I C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 202 A ASN 213 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 A ND2 ASN 253 A ASN 264 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 B ND2 ASN 127 B ASN 138 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 B ND2 ASN 202 B ASN 213 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale7 B ND2 ASN 253 B ASN 264 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale9 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale11 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale12 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale13 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale14 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale15 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale16 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale17 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale18 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale19 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale20 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale21 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale22 G O3 BMA . G BMA 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale23 G O6 BMA . G BMA 3 1_555 G C1 MAN . G MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale24 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale25 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale26 H O3 BMA . H BMA 3 1_555 H C1 MAN . H MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 4YH6 _atom_sites.fract_transf_matrix[1][1] 0.00976 _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] 0.00976 _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] 0.00449 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id I _pdbx_nonpoly_scheme.entity_id 5 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 404 _pdbx_nonpoly_scheme.auth_seq_num 1381 _pdbx_nonpoly_scheme.pdb_mon_id NAG _pdbx_nonpoly_scheme.auth_mon_id NAG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 9.765 -2.137 34.91 1 107.29 ? C1 NAG 404 A 1 HETATM 2 C C2 NAG . . . I 5 9.201 -3.553 34.819 1 114.6 ? C2 NAG 404 A 1 HETATM 3 C C3 NAG . . . I 5 7.92 -3.662 35.642 1 125.46 ? C3 NAG 404 A 1 HETATM 4 C C4 NAG . . . I 5 8.165 -3.191 37.07 1 120.68 ? C4 NAG 404 A 1 HETATM 5 C C5 NAG . . . I 5 8.782 -1.795 37.068 1 122.81 ? C5 NAG 404 A 1 HETATM 6 C C6 NAG . . . I 5 9.163 -1.318 38.45 1 130.76 ? C6 NAG 404 A 1 HETATM 7 C C7 NAG . . . I 5 8.922 -5.202 33.021 1 115.23 ? C7 NAG 404 A 1 HETATM 8 C C8 NAG . . . I 5 8.657 -5.408 31.56 1 119.87 ? C8 NAG 404 A 1 HETATM 9 N N2 NAG . . . I 5 8.956 -3.931 33.437 1 113.64 ? N2 NAG 404 A 1 HETATM 10 O O3 NAG . . . I 5 7.471 -5.013 35.651 1 133.03 ? O3 NAG 404 A 1 HETATM 11 O O4 NAG . . . I 5 6.937 -3.162 37.789 1 116.97 ? O4 NAG 404 A 1 HETATM 12 O O5 NAG . . . I 5 9.984 -1.792 36.281 1 111.87 ? O5 NAG 404 A 1 HETATM 13 O O6 NAG . . . I 5 9.427 0.078 38.466 1 132.07 ? O6 NAG 404 A 1 HETATM 14 O O7 NAG . . . I 5 9.092 -6.142 33.791 1 116.73 ? O7 NAG 404 A 1 # _model_server_stats.io_time_ms 75 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 407 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #