data_5B39 # _model_server_result.job_id qel8eTCnnZ0kPoam2nVWYQ _model_server_result.datetime_utc '2024-11-01 19:43:53' _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 5b39 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":302}' # _entry.id 5B39 # _exptl.entry_id 5B39 _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 95.56 _cell.angle_beta 98.5 _cell.angle_gamma 108.65 _cell.entry_id 5B39 _cell.length_a 51.568 _cell.length_b 61.118 _cell.length_c 65.089 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B39 _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,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 E N N ? 5 F N N ? 5 G N N # 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 101 A CYS 101 1_555 A SG CYS 164 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 203 A CYS 203 1_555 A SG CYS 259 A CYS 259 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 D SG CYS 28 G CYS 28 1_555 D SG CYS 74 G CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 D SG CYS 123 G CYS 123 1_555 D SG CYS 174 G CYS 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 D SG CYS 223 G CYS 223 1_555 D SG CYS 272 G CYS 272 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 D ND2 ASN 71 G ASN 71 1_555 E C1 NAG . G NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.558 ? covale ? covale2 D ND2 ASN 158 G ASN 158 1_555 F C1 NAG . G NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.6 sing covale ? covale3 D ND2 ASN 252 G ASN 252 1_555 G C1 NAG . G NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 sing # _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 5B39 _atom_sites.fract_transf_matrix[1][1] 0.019392 _atom_sites.fract_transf_matrix[1][2] 0.006545 _atom_sites.fract_transf_matrix[1][3] 0.003951 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017268 _atom_sites.fract_transf_matrix[2][3] 0.002688 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015721 _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 E 5 NAG G 1 301 1 NAG NAG . F 5 NAG G 1 302 2 NAG NAG . G 5 NAG G 1 303 3 NAG NAG . H 6 HOH A 1 301 83 HOH HOH . H 6 HOH A 2 302 140 HOH HOH . H 6 HOH A 3 303 89 HOH HOH . H 6 HOH A 4 304 48 HOH HOH . H 6 HOH A 5 305 146 HOH HOH . H 6 HOH A 6 306 112 HOH HOH . H 6 HOH A 7 307 13 HOH HOH . H 6 HOH A 8 308 19 HOH HOH . H 6 HOH A 9 309 40 HOH HOH . H 6 HOH A 10 310 141 HOH HOH . H 6 HOH A 11 311 1 HOH HOH . H 6 HOH A 12 312 49 HOH HOH . H 6 HOH A 13 313 95 HOH HOH . H 6 HOH A 14 314 53 HOH HOH . H 6 HOH A 15 315 65 HOH HOH . H 6 HOH A 16 316 86 HOH HOH . H 6 HOH A 17 317 15 HOH HOH . H 6 HOH A 18 318 76 HOH HOH . H 6 HOH A 19 319 92 HOH HOH . H 6 HOH A 20 320 67 HOH HOH . H 6 HOH A 21 321 74 HOH HOH . H 6 HOH A 22 322 20 HOH HOH . H 6 HOH A 23 323 4 HOH HOH . H 6 HOH A 24 324 17 HOH HOH . H 6 HOH A 25 325 102 HOH HOH . H 6 HOH A 26 326 18 HOH HOH . H 6 HOH A 27 327 98 HOH HOH . H 6 HOH A 28 328 87 HOH HOH . H 6 HOH A 29 329 47 HOH HOH . H 6 HOH A 30 330 12 HOH HOH . H 6 HOH A 31 331 45 HOH HOH . H 6 HOH A 32 332 50 HOH HOH . H 6 HOH A 33 333 30 HOH HOH . H 6 HOH A 34 334 84 HOH HOH . H 6 HOH A 35 335 81 HOH HOH . H 6 HOH A 36 336 14 HOH HOH . H 6 HOH A 37 337 57 HOH HOH . H 6 HOH A 38 338 111 HOH HOH . H 6 HOH A 39 339 62 HOH HOH . H 6 HOH A 40 340 37 HOH HOH . H 6 HOH A 41 341 36 HOH HOH . H 6 HOH A 42 342 52 HOH HOH . H 6 HOH A 43 343 88 HOH HOH . H 6 HOH A 44 344 70 HOH HOH . H 6 HOH A 45 345 105 HOH HOH . H 6 HOH A 46 346 9 HOH HOH . H 6 HOH A 47 347 23 HOH HOH . H 6 HOH A 48 348 56 HOH HOH . H 6 HOH A 49 349 6 HOH HOH . H 6 HOH A 50 350 142 HOH HOH . H 6 HOH A 51 351 68 HOH HOH . H 6 HOH A 52 352 147 HOH HOH . H 6 HOH A 53 353 66 HOH HOH . H 6 HOH A 54 354 80 HOH HOH . H 6 HOH A 55 355 124 HOH HOH . H 6 HOH A 56 356 131 HOH HOH . H 6 HOH A 57 357 129 HOH HOH . H 6 HOH A 58 358 104 HOH HOH . H 6 HOH A 59 359 2 HOH HOH . H 6 HOH A 60 360 54 HOH HOH . H 6 HOH A 61 361 75 HOH HOH . H 6 HOH A 62 362 100 HOH HOH . H 6 HOH A 63 363 61 HOH HOH . I 6 HOH B 1 101 90 HOH HOH . I 6 HOH B 2 102 128 HOH HOH . I 6 HOH B 3 103 96 HOH HOH . I 6 HOH B 4 104 22 HOH HOH . I 6 HOH B 5 105 44 HOH HOH . I 6 HOH B 6 106 127 HOH HOH . I 6 HOH B 7 107 3 HOH HOH . I 6 HOH B 8 108 11 HOH HOH . I 6 HOH B 9 109 29 HOH HOH . I 6 HOH B 10 110 38 HOH HOH . I 6 HOH B 11 111 121 HOH HOH . I 6 HOH B 12 112 71 HOH HOH . I 6 HOH B 13 113 94 HOH HOH . I 6 HOH B 14 114 109 HOH HOH . I 6 HOH B 15 115 32 HOH HOH . I 6 HOH B 16 116 33 HOH HOH . I 6 HOH B 17 117 64 HOH HOH . I 6 HOH B 18 118 46 HOH HOH . I 6 HOH B 19 119 59 HOH HOH . I 6 HOH B 20 120 136 HOH HOH . I 6 HOH B 21 121 135 HOH HOH . I 6 HOH B 22 122 58 HOH HOH . I 6 HOH B 23 123 115 HOH HOH . I 6 HOH B 24 124 107 HOH HOH . I 6 HOH B 25 125 126 HOH HOH . I 6 HOH B 26 126 101 HOH HOH . I 6 HOH B 27 127 113 HOH HOH . I 6 HOH B 28 128 130 HOH HOH . I 6 HOH B 29 129 134 HOH HOH . I 6 HOH B 30 130 133 HOH HOH . I 6 HOH B 31 131 125 HOH HOH . I 6 HOH B 32 132 27 HOH HOH . I 6 HOH B 33 133 119 HOH HOH . I 6 HOH B 34 134 116 HOH HOH . I 6 HOH B 35 135 122 HOH HOH . J 6 HOH C 1 101 55 HOH HOH . J 6 HOH C 2 102 106 HOH HOH . J 6 HOH C 3 103 60 HOH HOH . J 6 HOH C 4 104 103 HOH HOH . J 6 HOH C 5 105 91 HOH HOH . K 6 HOH G 1 401 132 HOH HOH . K 6 HOH G 2 402 108 HOH HOH . K 6 HOH G 3 403 41 HOH HOH . K 6 HOH G 4 404 97 HOH HOH . K 6 HOH G 5 405 8 HOH HOH . K 6 HOH G 6 406 114 HOH HOH . K 6 HOH G 7 407 72 HOH HOH . K 6 HOH G 8 408 79 HOH HOH . K 6 HOH G 9 409 10 HOH HOH . K 6 HOH G 10 410 143 HOH HOH . K 6 HOH G 11 411 118 HOH HOH . K 6 HOH G 12 412 85 HOH HOH . K 6 HOH G 13 413 82 HOH HOH . K 6 HOH G 14 414 43 HOH HOH . K 6 HOH G 15 415 39 HOH HOH . K 6 HOH G 16 416 78 HOH HOH . K 6 HOH G 17 417 69 HOH HOH . K 6 HOH G 18 418 139 HOH HOH . K 6 HOH G 19 419 73 HOH HOH . K 6 HOH G 20 420 93 HOH HOH . K 6 HOH G 21 421 42 HOH HOH . K 6 HOH G 22 422 137 HOH HOH . K 6 HOH G 23 423 5 HOH HOH . K 6 HOH G 24 424 110 HOH HOH . K 6 HOH G 25 425 138 HOH HOH . K 6 HOH G 26 426 99 HOH HOH . K 6 HOH G 27 427 25 HOH HOH . K 6 HOH G 28 428 145 HOH HOH . K 6 HOH G 29 429 7 HOH HOH . K 6 HOH G 30 430 51 HOH HOH . K 6 HOH G 31 431 123 HOH HOH . K 6 HOH G 32 432 16 HOH HOH . K 6 HOH G 33 433 28 HOH HOH . K 6 HOH G 34 434 24 HOH HOH . K 6 HOH G 35 435 26 HOH HOH . K 6 HOH G 36 436 21 HOH HOH . K 6 HOH G 37 437 35 HOH HOH . K 6 HOH G 38 438 63 HOH HOH . K 6 HOH G 39 439 120 HOH HOH . K 6 HOH G 40 440 144 HOH HOH . K 6 HOH G 41 441 34 HOH HOH . K 6 HOH G 42 442 31 HOH HOH . K 6 HOH G 43 443 77 HOH HOH . K 6 HOH G 44 444 117 HOH HOH . K 6 HOH G 45 445 148 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 . . . F 5 2.357 22.217 -30.066 1 66.9 ? C1 NAG 302 G 1 HETATM 2 C C2 NAG . . . F 5 2.802 21.786 -31.45 1 75.44 ? C2 NAG 302 G 1 HETATM 3 C C3 NAG . . . F 5 2.104 22.628 -32.518 1 72.04 ? C3 NAG 302 G 1 HETATM 4 C C4 NAG . . . F 5 0.816 23.255 -31.989 1 79.6 ? C4 NAG 302 G 1 HETATM 5 C C5 NAG . . . F 5 0.095 22.366 -30.965 1 72.99 ? C5 NAG 302 G 1 HETATM 6 C C6 NAG . . . F 5 -0.541 21.13 -31.568 1 69.22 ? C6 NAG 302 G 1 HETATM 7 C C7 NAG . . . F 5 5.04 20.799 -31.682 1 99.52 ? C7 NAG 302 G 1 HETATM 8 C C8 NAG . . . F 5 4.352 19.466 -31.639 1 95.02 ? C8 NAG 302 G 1 HETATM 9 N N2 NAG . . . F 5 4.248 21.873 -31.588 1 82.62 ? N2 NAG 302 G 1 HETATM 10 O O3 NAG . . . F 5 1.815 21.817 -33.651 1 79.17 ? O3 NAG 302 G 1 HETATM 11 O O4 NAG . . . F 5 1.056 24.554 -31.453 1 86.03 ? O4 NAG 302 G 1 HETATM 12 O O5 NAG . . . F 5 0.965 21.934 -29.9 1 74.82 ? O5 NAG 302 G 1 HETATM 13 O O6 NAG . . . F 5 0.207 19.955 -31.286 1 62.99 ? O6 NAG 302 G 1 HETATM 14 O O7 NAG . . . F 5 6.258 20.897 -31.796 1 89.9 ? O7 NAG 302 G 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #