data_5B39
#
_model_server_result.job_id            ri5mQup_CsztgvwK43SSAg 
_model_server_result.datetime_utc      '2024-11-28 03:47:12' 
_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":"E","auth_seq_id":301}' 
#
_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 . . . E 5 15.886 23.06 -4.106 1 66.96 ? C1 NAG 301 G 1 
HETATM 2 C C2 NAG . . . E 5 16.173 23.001 -5.602 1 64.06 ? C2 NAG 301 G 1 
HETATM 3 C C3 NAG . . . E 5 16.967 21.738 -5.933 1 66.45 ? C3 NAG 301 G 1 
HETATM 4 C C4 NAG . . . E 5 18.209 21.643 -5.054 1 72.43 ? C4 NAG 301 G 1 
HETATM 5 C C5 NAG . . . E 5 17.822 21.764 -3.584 1 70.2 ? C5 NAG 301 G 1 
HETATM 6 C C6 NAG . . . E 5 19.014 21.785 -2.655 1 82.98 ? C6 NAG 301 G 1 
HETATM 7 C C7 NAG . . . E 5 14.657 24.033 -7.23 1 56.9 ? C7 NAG 301 G 1 
HETATM 8 C C8 NAG . . . E 5 13.343 23.924 -7.946 1 44.49 ? C8 NAG 301 G 1 
HETATM 9 N N2 NAG . . . E 5 14.945 23.049 -6.377 1 55.53 ? N2 NAG 301 G 1 
HETATM 10 O O3 NAG . . . E 5 17.333 21.76 -7.307 1 74.83 ? O3 NAG 301 G 1 
HETATM 11 O O4 NAG . . . E 5 18.865 20.397 -5.261 1 74.4 ? O4 NAG 301 G 1 
HETATM 12 O O5 NAG . . . E 5 17.109 22.993 -3.373 1 69.08 ? O5 NAG 301 G 1 
HETATM 13 O O6 NAG . . . E 5 18.944 22.868 -1.739 1 90.53 ? O6 NAG 301 G 1 
HETATM 14 O O7 NAG . . . E 5 15.422 24.974 -7.419 1 56.06 ? O7 NAG 301 G 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           302 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#