data_3R4D # _model_server_result.job_id nI9tj9aJtN2s84wkSR-Lew _model_server_result.datetime_utc '2025-07-27 12:45:27' _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 3r4d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":300}' # _entry.id 3R4D # _exptl.entry_id 3R4D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _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 120 _cell.entry_id 3R4D _cell.length_a 76.38 _cell.length_b 76.38 _cell.length_c 942.09 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3R4D _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,G,H,I,M,N 1 1 C,D,F,J,K,L,O,P 2 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 ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 3 n E NAG 1 E 1 NAG A 301 NAG 3 n E NAG 2 E 2 NAG A 302 NAG 3 n F NAG 1 F 1 NAG C 301 NAG 3 n F NAG 2 F 2 NAG C 302 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 132 A CYS 132 1_555 A SG CYS 180 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? disulf ? disulf2 B SG CYS 7 B CYS 21 1_555 B SG CYS 144 B CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 B SG CYS 139 B CYS 153 1_555 B SG CYS 173 B CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? disulf ? disulf4 B SG CYS 151 B CYS 165 1_555 B SG CYS 232 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? disulf ? disulf5 C SG CYS 132 C CYS 132 1_555 C SG CYS 180 C CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf6 D SG CYS 7 D CYS 21 1_555 D SG CYS 144 D CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf7 D SG CYS 139 D CYS 153 1_555 D SG CYS 173 D CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf8 D SG CYS 151 D CYS 165 1_555 D SG CYS 232 D CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? covale ? covale1 A ND2 ASN 37 A ASN 37 1_555 G C1 NAG . A NAG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 A ND2 ASN 55 A ASN 55 1_555 H C1 NAG . A NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 70 A ASN 70 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 B ND2 ASN 178 B ASN 192 1_555 I C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale5 C ND2 ASN 37 C ASN 37 1_555 J C1 NAG . C NAG 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 C ND2 ASN 55 C ASN 55 1_555 K C1 NAG . C NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale7 C ND2 ASN 70 C ASN 70 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale8 D ND2 ASN 178 D ASN 192 1_555 L C1 NAG . D NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.769 ? covale ? covale10 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.564 ? # _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 3R4D _atom_sites.fract_transf_matrix[1][1] 0.013092 _atom_sites.fract_transf_matrix[1][2] 0.007559 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015118 _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] 0.001061 _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 G 4 NAG A 1 300 300 NAG NAG . H 4 NAG A 1 304 304 NAG NAG . I 4 NAG B 1 303 300 NAG NAG . J 4 NAG C 1 300 300 NAG NAG . K 4 NAG C 1 304 304 NAG NAG . L 4 NAG D 1 303 300 NAG NAG . M 5 HOH A 1 209 33 HOH HOH . M 5 HOH A 2 210 39 HOH HOH . M 5 HOH A 3 211 42 HOH HOH . M 5 HOH A 4 212 44 HOH HOH . M 5 HOH A 5 213 45 HOH HOH . M 5 HOH A 6 214 46 HOH HOH . M 5 HOH A 7 215 178 HOH HOH . M 5 HOH A 8 216 185 HOH HOH . M 5 HOH A 9 217 187 HOH HOH . M 5 HOH A 10 218 199 HOH HOH . M 5 HOH A 11 219 53 HOH HOH . N 5 HOH B 1 305 56 HOH HOH . N 5 HOH B 2 306 57 HOH HOH . N 5 HOH B 3 307 62 HOH HOH . N 5 HOH B 4 308 63 HOH HOH . N 5 HOH B 5 309 64 HOH HOH . N 5 HOH B 6 310 65 HOH HOH . N 5 HOH B 7 311 66 HOH HOH . N 5 HOH B 8 312 71 HOH HOH . N 5 HOH B 9 313 157 HOH HOH . N 5 HOH B 10 314 159 HOH HOH . N 5 HOH B 11 315 167 HOH HOH . N 5 HOH B 12 316 170 HOH HOH . N 5 HOH B 13 317 183 HOH HOH . N 5 HOH B 14 318 184 HOH HOH . N 5 HOH B 15 319 192 HOH HOH . N 5 HOH B 16 320 201 HOH HOH . N 5 HOH B 17 321 202 HOH HOH . O 5 HOH C 1 209 87 HOH HOH . O 5 HOH C 2 210 92 HOH HOH . O 5 HOH C 3 211 93 HOH HOH . O 5 HOH C 4 212 98 HOH HOH . O 5 HOH C 5 213 101 HOH HOH . O 5 HOH C 6 214 102 HOH HOH . O 5 HOH C 7 215 107 HOH HOH . O 5 HOH C 8 216 142 HOH HOH . O 5 HOH C 9 217 174 HOH HOH . O 5 HOH C 10 218 179 HOH HOH . O 5 HOH C 11 219 180 HOH HOH . O 5 HOH C 12 220 190 HOH HOH . O 5 HOH C 13 221 193 HOH HOH . O 5 HOH C 14 222 200 HOH HOH . P 5 HOH D 1 304 76 HOH HOH . P 5 HOH D 2 305 112 HOH HOH . P 5 HOH D 3 306 120 HOH HOH . P 5 HOH D 4 307 121 HOH HOH . P 5 HOH D 5 308 122 HOH HOH . P 5 HOH D 6 309 124 HOH HOH . P 5 HOH D 7 310 125 HOH HOH . P 5 HOH D 8 311 126 HOH HOH . P 5 HOH D 9 312 127 HOH HOH . P 5 HOH D 10 313 132 HOH HOH . P 5 HOH D 11 314 146 HOH HOH . P 5 HOH D 12 315 148 HOH HOH . P 5 HOH D 13 316 150 HOH HOH . P 5 HOH D 14 317 151 HOH HOH . P 5 HOH D 15 318 153 HOH HOH . P 5 HOH D 16 319 154 HOH HOH . P 5 HOH D 17 320 156 HOH HOH . P 5 HOH D 18 321 160 HOH HOH . P 5 HOH D 19 322 161 HOH HOH . P 5 HOH D 20 323 171 HOH HOH . P 5 HOH D 21 324 173 HOH HOH . P 5 HOH D 22 325 195 HOH HOH . P 5 HOH D 23 326 196 HOH HOH . P 5 HOH D 24 327 197 HOH HOH . P 5 HOH D 25 328 203 HOH HOH . P 5 HOH D 26 329 204 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 . . . J 4 -15.416 -32.972 -75.783 1 53.44 ? C1 NAG 300 C 1 HETATM 2 C C2 NAG . . . J 4 -16.199 -34.096 -75.107 1 68.33 ? C2 NAG 300 C 1 HETATM 3 C C3 NAG . . . J 4 -17.696 -33.814 -75.365 1 70.75 ? C3 NAG 300 C 1 HETATM 4 C C4 NAG . . . J 4 -18.044 -32.421 -74.797 1 71.46 ? C4 NAG 300 C 1 HETATM 5 C C5 NAG . . . J 4 -17.094 -31.339 -75.369 1 69.42 ? C5 NAG 300 C 1 HETATM 6 C C6 NAG . . . J 4 -17.397 -29.918 -74.858 1 72.09 ? C6 NAG 300 C 1 HETATM 7 C C7 NAG . . . J 4 -15.936 -36.271 -76.439 1 74.3 ? C7 NAG 300 C 1 HETATM 8 C C8 NAG . . . J 4 -17.075 -36.012 -77.393 1 75.28 ? C8 NAG 300 C 1 HETATM 9 N N2 NAG . . . J 4 -15.625 -35.399 -75.473 1 71.43 ? N2 NAG 300 C 1 HETATM 10 O O3 NAG . . . J 4 -18.531 -34.821 -74.817 1 73.08 ? O3 NAG 300 C 1 HETATM 11 O O4 NAG . . . J 4 -19.404 -32.143 -75.076 1 72.89 ? O4 NAG 300 C 1 HETATM 12 O O5 NAG . . . J 4 -15.729 -31.725 -75.15 1 62.27 ? O5 NAG 300 C 1 HETATM 13 O O6 NAG . . . J 4 -16.346 -29.383 -74.066 1 75.97 ? O6 NAG 300 C 1 HETATM 14 O O7 NAG . . . J 4 -15.286 -37.309 -76.55 1 74.67 ? O7 NAG 300 C 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #