data_4NYR # _model_server_result.job_id GjfUPtuFi6ibeBEAFYvFkg _model_server_result.datetime_utc '2025-07-02 00:17:59' _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 4nyr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":205}' # _entry.id 4NYR # _exptl.entry_id 4NYR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 99.5 _cell.angle_beta 100.28 _cell.angle_gamma 104.11 _cell.entry_id 4NYR _cell.length_a 32.28 _cell.length_b 33.22 _cell.length_c 40.18 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NYR _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 2 n B NAG 1 B 1 NAG A 154 NAG 2 n B NAG 2 B 2 NAG A 155 NAG 2 n C NAG 1 C 1 NAG A 157 NAG 2 n C NAG 2 C 2 NAG A 158 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 13 A CYS 4 1_555 A SG CYS 146 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf2 A SG CYS 129 A CYS 120 1_555 A SG CYS 160 A CYS 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 A ND2 ASN 44 A ASN 35 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 A ND2 ASN 88 A ASN 79 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale3 A ND2 ASN 154 A ASN 145 1_555 D C1 NAG . A NAG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C 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 250 n n C1 O1 NAG sing 251 n n C1 O5 NAG sing 252 n n C1 H1 NAG sing 253 n n C2 C3 NAG sing 254 n n C2 N2 NAG sing 255 n n C2 H2 NAG sing 256 n n C3 C4 NAG sing 257 n n C3 O3 NAG sing 258 n n C3 H3 NAG sing 259 n n C4 C5 NAG sing 260 n n C4 O4 NAG sing 261 n n C4 H4 NAG sing 262 n n C5 C6 NAG sing 263 n n C5 O5 NAG sing 264 n n C5 H5 NAG sing 265 n n C6 O6 NAG sing 266 n n C6 H61 NAG sing 267 n n C6 H62 NAG sing 268 n n C7 C8 NAG sing 269 n n C7 N2 NAG sing 270 n n C7 O7 NAG doub 271 n n C8 H81 NAG sing 272 n n C8 H82 NAG sing 273 n n C8 H83 NAG sing 274 n n N2 HN2 NAG sing 275 n n O1 HO1 NAG sing 276 n n O3 HO3 NAG sing 277 n n O4 HO4 NAG sing 278 n n O6 HO6 NAG sing 279 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 4NYR _atom_sites.fract_transf_matrix[1][1] 0.030979 _atom_sites.fract_transf_matrix[1][2] 0.007786 _atom_sites.fract_transf_matrix[1][3] 0.007503 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.031039 _atom_sites.fract_transf_matrix[2][3] 0.006949 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.02592 _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 3 NAG A 1 205 159 NAG NAG . E 4 GOL A 1 206 1 GOL GOL . F 5 HOH A 1 301 1 HOH HOH . F 5 HOH A 2 302 2 HOH HOH . F 5 HOH A 3 303 3 HOH HOH . F 5 HOH A 4 304 4 HOH HOH . F 5 HOH A 5 305 5 HOH HOH . F 5 HOH A 6 306 6 HOH HOH . F 5 HOH A 7 307 7 HOH HOH . F 5 HOH A 8 308 8 HOH HOH . F 5 HOH A 9 309 9 HOH HOH . F 5 HOH A 10 310 10 HOH HOH . F 5 HOH A 11 311 11 HOH HOH . F 5 HOH A 12 312 12 HOH HOH . F 5 HOH A 13 313 13 HOH HOH . F 5 HOH A 14 314 14 HOH HOH . F 5 HOH A 15 315 15 HOH HOH . F 5 HOH A 16 316 16 HOH HOH . F 5 HOH A 17 317 17 HOH HOH . F 5 HOH A 18 318 18 HOH HOH . F 5 HOH A 19 319 19 HOH HOH . F 5 HOH A 20 320 20 HOH HOH . F 5 HOH A 21 321 21 HOH HOH . F 5 HOH A 22 322 22 HOH HOH . F 5 HOH A 23 323 23 HOH HOH . F 5 HOH A 24 324 24 HOH HOH . F 5 HOH A 25 325 25 HOH HOH . F 5 HOH A 26 326 26 HOH HOH . F 5 HOH A 27 327 27 HOH HOH . F 5 HOH A 28 328 28 HOH HOH . F 5 HOH A 29 329 29 HOH HOH . F 5 HOH A 30 330 30 HOH HOH . F 5 HOH A 31 331 31 HOH HOH . F 5 HOH A 32 332 32 HOH HOH . F 5 HOH A 33 333 33 HOH HOH . F 5 HOH A 34 334 34 HOH HOH . F 5 HOH A 35 335 35 HOH HOH . F 5 HOH A 36 336 36 HOH HOH . F 5 HOH A 37 337 37 HOH HOH . F 5 HOH A 38 338 38 HOH HOH . F 5 HOH A 39 339 39 HOH HOH . F 5 HOH A 40 340 40 HOH HOH . F 5 HOH A 41 341 41 HOH HOH . F 5 HOH A 42 342 42 HOH HOH . F 5 HOH A 43 343 43 HOH HOH . F 5 HOH A 44 344 44 HOH HOH . F 5 HOH A 45 345 45 HOH HOH . F 5 HOH A 46 346 46 HOH HOH . F 5 HOH A 47 347 47 HOH HOH . F 5 HOH A 48 348 48 HOH HOH . F 5 HOH A 49 349 49 HOH HOH . F 5 HOH A 50 350 50 HOH HOH . F 5 HOH A 51 351 51 HOH HOH . F 5 HOH A 52 352 53 HOH HOH . F 5 HOH A 53 353 54 HOH HOH . F 5 HOH A 54 354 55 HOH HOH . F 5 HOH A 55 355 56 HOH HOH . F 5 HOH A 56 356 57 HOH HOH . F 5 HOH A 57 357 58 HOH HOH . F 5 HOH A 58 358 59 HOH HOH . F 5 HOH A 59 359 60 HOH HOH . F 5 HOH A 60 360 61 HOH HOH . F 5 HOH A 61 361 62 HOH HOH . F 5 HOH A 62 362 63 HOH HOH . F 5 HOH A 63 363 64 HOH HOH . F 5 HOH A 64 364 65 HOH HOH . F 5 HOH A 65 365 66 HOH HOH . F 5 HOH A 66 366 67 HOH HOH . F 5 HOH A 67 367 68 HOH HOH . F 5 HOH A 68 368 69 HOH HOH . F 5 HOH A 69 369 70 HOH HOH . F 5 HOH A 70 370 71 HOH HOH . F 5 HOH A 71 371 72 HOH HOH . F 5 HOH A 72 372 73 HOH HOH . F 5 HOH A 73 373 74 HOH HOH . F 5 HOH A 74 374 75 HOH HOH . F 5 HOH A 75 375 76 HOH HOH . F 5 HOH A 76 376 77 HOH HOH . F 5 HOH A 77 377 78 HOH HOH . F 5 HOH A 78 378 79 HOH HOH . F 5 HOH A 79 379 81 HOH HOH . F 5 HOH A 80 380 83 HOH HOH . F 5 HOH A 81 381 85 HOH HOH . F 5 HOH A 82 382 87 HOH HOH . F 5 HOH A 83 383 88 HOH HOH . F 5 HOH A 84 384 89 HOH HOH . F 5 HOH A 85 385 90 HOH HOH . F 5 HOH A 86 386 91 HOH HOH . F 5 HOH A 87 387 92 HOH HOH . F 5 HOH A 88 388 93 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 3 -14.817 12.041 22.448 1 26.69 ? C1 NAG 205 A 1 HETATM 2 C C2 NAG . . . D 3 -14.227 10.997 21.498 1 29.82 ? C2 NAG 205 A 1 HETATM 3 C C3 NAG . . . D 3 -14.255 11.526 20.062 1 29.53 ? C3 NAG 205 A 1 HETATM 4 C C4 NAG . . . D 3 -15.636 12.016 19.643 1 28.73 ? C4 NAG 205 A 1 HETATM 5 C C5 NAG . . . D 3 -16.13 13.035 20.663 1 28.5 ? C5 NAG 205 A 1 HETATM 6 C C6 NAG . . . D 3 -17.561 13.519 20.369 1 27.48 ? C6 NAG 205 A 1 HETATM 7 C C7 NAG . . . D 3 -12.667 9.209 22.133 1 31.57 ? C7 NAG 205 A 1 HETATM 8 C C8 NAG . . . D 3 -11.257 8.766 22.447 1 32.05 ? C8 NAG 205 A 1 HETATM 9 N N2 NAG . . . D 3 -12.88 10.502 21.826 1 30.14 ? N2 NAG 205 A 1 HETATM 10 O O3 NAG . . . D 3 -13.882 10.446 19.242 1 32.39 ? O3 NAG 205 A 1 HETATM 11 O O4 NAG . . . D 3 -15.67 12.486 18.295 1 29.54 ? O4 NAG 205 A 1 HETATM 12 O O5 NAG . . . D 3 -16.084 12.437 21.957 1 28.08 ? O5 NAG 205 A 1 HETATM 13 O O6 NAG . . . D 3 -18.507 12.522 20.683 1 27.61 ? O6 NAG 205 A 1 HETATM 14 O O7 NAG . . . D 3 -13.577 8.374 22.191 1 31.06 ? O7 NAG 205 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 443 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #