data_3GKJ # _model_server_result.job_id UUj9OEoCwoUJ2-DMeksqww _model_server_result.datetime_utc '2025-02-17 22:53:11' _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 3gkj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":3}' # _entry.id 3GKJ # _exptl.entry_id 3GKJ _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 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 3GKJ _cell.length_a 65.926 _cell.length_b 65.926 _cell.length_c 82.988 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GKJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64' # _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 _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 C _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 B 1 NAG 2 n B NAG 2 B 2 NAG B 2 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 5 A CYS 25 1_555 A SG CYS 54 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf2 A SG CYS 11 A CYS 31 1_555 A SG CYS 22 A CYS 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf3 A SG CYS 43 A CYS 63 1_555 A SG CYS 89 A CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf4 A SG CYS 55 A CYS 75 1_555 A SG CYS 93 A CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf5 A SG CYS 77 A CYS 97 1_555 A SG CYS 218 A CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 A SG CYS 80 A CYS 100 1_555 A SG CYS 140 A CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 A SG CYS 157 A CYS 177 1_555 A SG CYS 164 A CYS 184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf8 A SG CYS 207 A CYS 227 1_555 A SG CYS 223 A CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf9 A SG CYS 220 A CYS 240 1_555 A SG CYS 227 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 C C1 NAG . A NAG 3 1_555 A ND2 ASN 138 A ASN 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 202 A ASN 222 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 315 n n C1 O1 NAG sing 316 n n C1 O5 NAG sing 317 n n C1 H1 NAG sing 318 n n C2 C3 NAG sing 319 n n C2 N2 NAG sing 320 n n C2 H2 NAG sing 321 n n C3 C4 NAG sing 322 n n C3 O3 NAG sing 323 n n C3 H3 NAG sing 324 n n C4 C5 NAG sing 325 n n C4 O4 NAG sing 326 n n C4 H4 NAG sing 327 n n C5 C6 NAG sing 328 n n C5 O5 NAG sing 329 n n C5 H5 NAG sing 330 n n C6 O6 NAG sing 331 n n C6 H61 NAG sing 332 n n C6 H62 NAG sing 333 n n C7 C8 NAG sing 334 n n C7 N2 NAG sing 335 n n C7 O7 NAG doub 336 n n C8 H81 NAG sing 337 n n C8 H82 NAG sing 338 n n C8 H83 NAG sing 339 n n N2 HN2 NAG sing 340 n n O1 HO1 NAG sing 341 n n O3 HO3 NAG sing 342 n n O4 HO4 NAG sing 343 n n O6 HO6 NAG sing 344 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 3GKJ _atom_sites.fract_transf_matrix[1][1] 0.015169 _atom_sites.fract_transf_matrix[1][2] 0.008758 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017515 _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] 0.01205 _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 C 3 NAG A 1 3 3 NAG NAG . D 4 HC3 A 1 253 1 HC3 HC3 . E 5 HOH A 1 4 4 HOH HOH . E 5 HOH A 2 5 5 HOH HOH . E 5 HOH A 3 6 6 HOH HOH . E 5 HOH A 4 7 7 HOH HOH . E 5 HOH A 5 8 8 HOH HOH . E 5 HOH A 6 9 9 HOH HOH . E 5 HOH A 7 10 10 HOH HOH . E 5 HOH A 8 11 11 HOH HOH . E 5 HOH A 9 12 12 HOH HOH . E 5 HOH A 10 13 13 HOH HOH . E 5 HOH A 11 14 14 HOH HOH . E 5 HOH A 12 15 15 HOH HOH . E 5 HOH A 13 16 16 HOH HOH . E 5 HOH A 14 17 17 HOH HOH . E 5 HOH A 15 18 18 HOH HOH . E 5 HOH A 16 19 19 HOH HOH . E 5 HOH A 17 20 20 HOH HOH . E 5 HOH A 18 254 1 HOH HOH . E 5 HOH A 19 255 2 HOH HOH . E 5 HOH A 20 256 3 HOH HOH . E 5 HOH A 21 257 21 HOH HOH . E 5 HOH A 22 258 22 HOH HOH . E 5 HOH A 23 259 23 HOH HOH . E 5 HOH A 24 260 24 HOH HOH . E 5 HOH A 25 261 25 HOH HOH . E 5 HOH A 26 262 26 HOH HOH . E 5 HOH A 27 263 27 HOH HOH . E 5 HOH A 28 264 28 HOH HOH . E 5 HOH A 29 265 29 HOH HOH . E 5 HOH A 30 266 30 HOH HOH . E 5 HOH A 31 267 31 HOH HOH . E 5 HOH A 32 268 32 HOH HOH . E 5 HOH A 33 269 33 HOH HOH . E 5 HOH A 34 270 34 HOH HOH . E 5 HOH A 35 271 35 HOH HOH . E 5 HOH A 36 272 36 HOH HOH . E 5 HOH A 37 273 37 HOH HOH . E 5 HOH A 38 274 38 HOH HOH . E 5 HOH A 39 275 39 HOH HOH . E 5 HOH A 40 276 40 HOH HOH . E 5 HOH A 41 277 41 HOH HOH . E 5 HOH A 42 278 42 HOH HOH . E 5 HOH A 43 279 43 HOH HOH . E 5 HOH A 44 280 44 HOH HOH . E 5 HOH A 45 281 45 HOH HOH . E 5 HOH A 46 282 46 HOH HOH . E 5 HOH A 47 283 47 HOH HOH . E 5 HOH A 48 284 48 HOH HOH . E 5 HOH A 49 285 49 HOH HOH . E 5 HOH A 50 286 50 HOH HOH . E 5 HOH A 51 287 51 HOH HOH . E 5 HOH A 52 288 52 HOH HOH . E 5 HOH A 53 289 53 HOH HOH . E 5 HOH A 54 290 54 HOH HOH . E 5 HOH A 55 291 55 HOH HOH . E 5 HOH A 56 292 56 HOH HOH . E 5 HOH A 57 293 57 HOH HOH . E 5 HOH A 58 294 58 HOH HOH . E 5 HOH A 59 295 59 HOH HOH . E 5 HOH A 60 296 60 HOH HOH . E 5 HOH A 61 297 61 HOH HOH . E 5 HOH A 62 298 62 HOH HOH . E 5 HOH A 63 299 63 HOH HOH . E 5 HOH A 64 300 64 HOH HOH . E 5 HOH A 65 301 65 HOH HOH . E 5 HOH A 66 302 66 HOH HOH . E 5 HOH A 67 303 67 HOH HOH . E 5 HOH A 68 304 68 HOH HOH . E 5 HOH A 69 305 69 HOH HOH . E 5 HOH A 70 306 70 HOH HOH . E 5 HOH A 71 307 71 HOH HOH . E 5 HOH A 72 308 72 HOH HOH . E 5 HOH A 73 309 73 HOH HOH . E 5 HOH A 74 310 74 HOH HOH . E 5 HOH A 75 311 75 HOH HOH . E 5 HOH A 76 312 76 HOH HOH . E 5 HOH A 77 313 77 HOH HOH . E 5 HOH A 78 314 78 HOH HOH . E 5 HOH A 79 315 79 HOH HOH . E 5 HOH A 80 316 80 HOH HOH . E 5 HOH A 81 317 81 HOH HOH . E 5 HOH A 82 318 82 HOH HOH . E 5 HOH A 83 319 83 HOH HOH . E 5 HOH A 84 320 84 HOH HOH . E 5 HOH A 85 321 85 HOH HOH . E 5 HOH A 86 322 86 HOH HOH . E 5 HOH A 87 323 87 HOH HOH . E 5 HOH A 88 324 88 HOH HOH . E 5 HOH A 89 325 89 HOH HOH . E 5 HOH A 90 326 90 HOH HOH . E 5 HOH A 91 327 91 HOH HOH . E 5 HOH A 92 328 92 HOH HOH . E 5 HOH A 93 329 93 HOH HOH . E 5 HOH A 94 330 94 HOH HOH . E 5 HOH A 95 331 95 HOH HOH . E 5 HOH A 96 332 96 HOH HOH . E 5 HOH A 97 333 97 HOH HOH . E 5 HOH A 98 334 98 HOH HOH . E 5 HOH A 99 335 99 HOH HOH . E 5 HOH A 100 336 100 HOH HOH . E 5 HOH A 101 337 101 HOH HOH . E 5 HOH A 102 338 102 HOH HOH . E 5 HOH A 103 339 103 HOH HOH . E 5 HOH A 104 340 104 HOH HOH . E 5 HOH A 105 341 105 HOH HOH . E 5 HOH A 106 342 106 HOH HOH . E 5 HOH A 107 343 107 HOH HOH . E 5 HOH A 108 344 108 HOH HOH . E 5 HOH A 109 345 109 HOH HOH . E 5 HOH A 110 346 110 HOH HOH . E 5 HOH A 111 347 111 HOH HOH . E 5 HOH A 112 348 112 HOH HOH . E 5 HOH A 113 349 113 HOH HOH . E 5 HOH A 114 350 114 HOH HOH . E 5 HOH A 115 351 115 HOH HOH . E 5 HOH A 116 352 116 HOH HOH . E 5 HOH A 117 353 117 HOH HOH . E 5 HOH A 118 354 118 HOH HOH . E 5 HOH A 119 355 119 HOH HOH . E 5 HOH A 120 356 120 HOH HOH . E 5 HOH A 121 357 121 HOH HOH . E 5 HOH A 122 358 122 HOH HOH . E 5 HOH A 123 359 123 HOH HOH . E 5 HOH A 124 360 124 HOH HOH . E 5 HOH A 125 361 125 HOH HOH . E 5 HOH A 126 362 126 HOH HOH . E 5 HOH A 127 363 127 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 . . . C 3 -18.182 -38.08 -10.592 1 31.19 ? C1 NAG 3 A 1 HETATM 2 C C2 NAG . . . C 3 -17.928 -37.279 -11.873 1 32.21 ? C2 NAG 3 A 1 HETATM 3 C C3 NAG . . . C 3 -17.345 -38.186 -12.966 1 33.07 ? C3 NAG 3 A 1 HETATM 4 C C4 NAG . . . C 3 -16.212 -39.095 -12.465 1 33.5 ? C4 NAG 3 A 1 HETATM 5 C C5 NAG . . . C 3 -16.499 -39.656 -11.071 1 33.4 ? C5 NAG 3 A 1 HETATM 6 C C6 NAG . . . C 3 -15.29 -40.353 -10.462 1 33.45 ? C6 NAG 3 A 1 HETATM 7 C C7 NAG . . . C 3 -20.315 -37.119 -12.533 1 32.96 ? C7 NAG 3 A 1 HETATM 8 C C8 NAG . . . C 3 -21.392 -36.259 -13.144 1 31.43 ? C8 NAG 3 A 1 HETATM 9 N N2 NAG . . . C 3 -19.109 -36.567 -12.36 1 31.84 ? N2 NAG 3 A 1 HETATM 10 O O3 NAG . . . C 3 -16.904 -37.4 -14.059 1 32.78 ? O3 NAG 3 A 1 HETATM 11 O O4 NAG . . . C 3 -16.079 -40.181 -13.348 1 33.21 ? O4 NAG 3 A 1 HETATM 12 O O5 NAG . . . C 3 -16.932 -38.633 -10.195 1 32.9 ? O5 NAG 3 A 1 HETATM 13 O O6 NAG . . . C 3 -15.644 -40.901 -9.206 1 33.34 ? O6 NAG 3 A 1 HETATM 14 O O7 NAG . . . C 3 -20.58 -38.279 -12.211 1 33.8 ? O7 NAG 3 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #