data_5X59
#
_model_server_result.job_id            aNmakf7gEwb4gQvz65OaFw 
_model_server_result.datetime_utc      '2024-11-17 01:46:34' 
_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          5x59 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":1401}' 
#
_entry.id    5X59 
#
_exptl.entry_id    5X59 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          2 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    30 
_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         90 
_cell.entry_id            5X59 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5X59 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA 
_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
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 Q N N 
? 2 R N N 
? 2 S N N 
? 2 T N N 
? 2 U N N 
? 2 V N N 
? 2 W N N 
? 2 X N N 
? 2 Y N N 
? 2 Z N N 
? 2 AA N N 
? 2 BA N N 
? 2 CA N N 
? 2 DA N N 
? 2 EA N N 
? 2 FA N N 
? 2 GA 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 13 A CYS 30 1_555 A SG CYS 178 A CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf2 A SG CYS 159 A CYS 176 1_555 A SG CYS 197 A CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf3 A SG CYS 168 A CYS 185 1_555 A SG CYS 220 A CYS 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf4 A SG CYS 322 A CYS 339 1_555 A SG CYS 332 A CYS 349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf5 A SG CYS 366 A CYS 383 1_555 A SG CYS 390 A CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf6 A SG CYS 408 A CYS 425 1_555 A SG CYS 461 A CYS 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf7 A SG CYS 420 A CYS 437 1_555 A SG CYS 568 A CYS 585 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf8 A SG CYS 486 A CYS 503 1_555 A SG CYS 509 A CYS 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf9 A SG CYS 603 A CYS 620 1_555 A SG CYS 633 A CYS 650 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf10 A SG CYS 662 A CYS 679 1_555 A SG CYS 696 A CYS 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
disulf ? disulf11 A SG CYS 794 A CYS 811 1_555 A SG CYS 800 A CYS 817 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
disulf ? disulf12 A SG CYS 1089 A CYS 1106 1_555 A SG CYS 1100 A CYS 1117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf13 B SG CYS 13 B CYS 30 1_555 B SG CYS 178 B CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf14 B SG CYS 159 B CYS 176 1_555 B SG CYS 197 B CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf15 B SG CYS 168 B CYS 185 1_555 B SG CYS 220 B CYS 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf16 B SG CYS 322 B CYS 339 1_555 B SG CYS 332 B CYS 349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf17 B SG CYS 366 B CYS 383 1_555 B SG CYS 390 B CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf18 B SG CYS 408 B CYS 425 1_555 B SG CYS 461 B CYS 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf19 B SG CYS 420 B CYS 437 1_555 B SG CYS 568 B CYS 585 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf20 B SG CYS 486 B CYS 503 1_555 B SG CYS 509 B CYS 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf21 B SG CYS 603 B CYS 620 1_555 B SG CYS 633 B CYS 650 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf22 B SG CYS 662 B CYS 679 1_555 B SG CYS 696 B CYS 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
disulf ? disulf23 B SG CYS 794 B CYS 811 1_555 B SG CYS 800 B CYS 817 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
disulf ? disulf24 B SG CYS 1089 B CYS 1106 1_555 B SG CYS 1100 B CYS 1117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf25 C SG CYS 13 C CYS 30 1_555 C SG CYS 178 C CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
disulf ? disulf26 C SG CYS 159 C CYS 176 1_555 C SG CYS 197 C CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf27 C SG CYS 168 C CYS 185 1_555 C SG CYS 220 C CYS 237 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf28 C SG CYS 322 C CYS 339 1_555 C SG CYS 332 C CYS 349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf29 C SG CYS 366 C CYS 383 1_555 C SG CYS 390 C CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf30 C SG CYS 408 C CYS 425 1_555 C SG CYS 461 C CYS 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf31 C SG CYS 420 C CYS 437 1_555 C SG CYS 568 C CYS 585 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf32 C SG CYS 486 C CYS 503 1_555 C SG CYS 509 C CYS 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf33 C SG CYS 603 C CYS 620 1_555 C SG CYS 633 C CYS 650 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf34 C SG CYS 662 C CYS 679 1_555 C SG CYS 696 C CYS 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
disulf ? disulf35 C SG CYS 794 C CYS 811 1_555 C SG CYS 800 C CYS 817 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
disulf ? disulf36 C SG CYS 1089 C CYS 1106 1_555 C SG CYS 1100 C CYS 1117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
#
_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 235 n n 
C1 O1 NAG sing 236 n n 
C1 O5 NAG sing 237 n n 
C1 H1 NAG sing 238 n n 
C2 C3 NAG sing 239 n n 
C2 N2 NAG sing 240 n n 
C2 H2 NAG sing 241 n n 
C3 C4 NAG sing 242 n n 
C3 O3 NAG sing 243 n n 
C3 H3 NAG sing 244 n n 
C4 C5 NAG sing 245 n n 
C4 O4 NAG sing 246 n n 
C4 H4 NAG sing 247 n n 
C5 C6 NAG sing 248 n n 
C5 O5 NAG sing 249 n n 
C5 H5 NAG sing 250 n n 
C6 O6 NAG sing 251 n n 
C6 H61 NAG sing 252 n n 
C6 H62 NAG sing 253 n n 
C7 C8 NAG sing 254 n n 
C7 N2 NAG sing 255 n n 
C7 O7 NAG doub 256 n n 
C8 H81 NAG sing 257 n n 
C8 H82 NAG sing 258 n n 
C8 H83 NAG sing 259 n n 
N2 HN2 NAG sing 260 n n 
O1 HO1 NAG sing 261 n n 
O3 HO3 NAG sing 262 n n 
O4 HO4 NAG sing 263 n n 
O6 HO6 NAG sing 264 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                     5X59 
_atom_sites.fract_transf_matrix[1][1]    1 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    1 
_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]    1 
_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 2 NAG A 1 1401 1401 NAG NAG . 
E 2 NAG A 1 1402 1402 NAG NAG . 
F 2 NAG A 1 1403 1403 NAG NAG . 
G 2 NAG A 1 1404 1404 NAG NAG . 
H 2 NAG A 1 1405 1405 NAG NAG . 
I 2 NAG A 1 1406 1406 NAG NAG . 
J 2 NAG A 1 1407 1407 NAG NAG . 
K 2 NAG A 1 1408 1408 NAG NAG . 
L 2 NAG A 1 1409 1409 NAG NAG . 
M 2 NAG A 1 1410 1410 NAG NAG . 
N 2 NAG B 1 1401 1401 NAG NAG . 
O 2 NAG B 1 1402 1402 NAG NAG . 
P 2 NAG B 1 1403 1403 NAG NAG . 
Q 2 NAG B 1 1404 1404 NAG NAG . 
R 2 NAG B 1 1405 1405 NAG NAG . 
S 2 NAG B 1 1406 1406 NAG NAG . 
T 2 NAG B 1 1407 1407 NAG NAG . 
U 2 NAG B 1 1408 1408 NAG NAG . 
V 2 NAG B 1 1409 1409 NAG NAG . 
W 2 NAG B 1 1410 1410 NAG NAG . 
X 2 NAG C 1 1401 1401 NAG NAG . 
Y 2 NAG C 1 1402 1402 NAG NAG . 
Z 2 NAG C 1 1403 1403 NAG NAG . 
AA 2 NAG C 1 1404 1404 NAG NAG . 
BA 2 NAG C 1 1405 1405 NAG NAG . 
CA 2 NAG C 1 1406 1406 NAG NAG . 
DA 2 NAG C 1 1407 1407 NAG NAG . 
EA 2 NAG C 1 1408 1408 NAG NAG . 
FA 2 NAG C 1 1409 1409 NAG NAG . 
GA 2 NAG C 1 1410 1410 NAG NAG . 
#
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 . . . X 2 -57.7 -8.795 31.222 1 46.08 ? C1 NAG 1401 C 1 
HETATM 2 C C2 NAG . . . X 2 -58.666 -9.497 32.169 1 36.3 ? C2 NAG 1401 C 1 
HETATM 3 C C3 NAG . . . X 2 -58.445 -9.039 33.605 1 33.36 ? C3 NAG 1401 C 1 
HETATM 4 C C4 NAG . . . X 2 -56.971 -9.124 33.983 1 30.79 ? C4 NAG 1401 C 1 
HETATM 5 C C5 NAG . . . X 2 -56.091 -8.471 32.924 1 35.98 ? C5 NAG 1401 C 1 
HETATM 6 C C6 NAG . . . X 2 -54.614 -8.65 33.256 1 54.93 ? C6 NAG 1401 C 1 
HETATM 7 C C7 NAG . . . X 2 -60.638 -9.858 30.741 1 37.44 ? C7 NAG 1401 C 1 
HETATM 8 C C8 NAG . . . X 2 -59.843 -10.869 29.963 1 26.32 ? C8 NAG 1401 C 1 
HETATM 9 N N2 NAG . . . X 2 -60.039 -9.243 31.766 1 26.69 ? N2 NAG 1401 C 1 
HETATM 10 O O3 NAG . . . X 2 -59.218 -9.857 34.493 1 25.69 ? O3 NAG 1401 C 1 
HETATM 11 O O4 NAG . . . X 2 -56.762 -8.476 35.244 1 34.34 ? O4 NAG 1401 C 1 
HETATM 12 O O5 NAG . . . X 2 -56.361 -9.045 31.648 1 40.82 ? O5 NAG 1401 C 1 
HETATM 13 O O6 NAG . . . X 2 -54.151 -9.899 32.733 1 52.64 ? O6 NAG 1401 C 1 
HETATM 14 O O7 NAG . . . X 2 -61.795 -9.605 30.447 1 40.31 ? O7 NAG 1401 C 1 
HETATM 15 H H1 NAG . . . X 2 -57.901 -7.716 31.262 1 55.29 ? H1 NAG 1401 C 1 
HETATM 16 H H2 NAG . . . X 2 -58.479 -10.58 32.116 1 43.56 ? H2 NAG 1401 C 1 
HETATM 17 H H3 NAG . . . X 2 -58.768 -7.993 33.691 1 40.03 ? H3 NAG 1401 C 1 
HETATM 18 H H4 NAG . . . X 2 -56.692 -10.184 34.063 1 36.95 ? H4 NAG 1401 C 1 
HETATM 19 H H5 NAG . . . X 2 -56.315 -7.395 32.899 1 43.17 ? H5 NAG 1401 C 1 
HETATM 20 H H61 NAG . . . X 2 -54.037 -7.831 32.822 1 65.92 ? H61 NAG 1401 C 1 
HETATM 21 H H62 NAG . . . X 2 -54.476 -8.628 34.339 1 65.92 ? H62 NAG 1401 C 1 
HETATM 22 H H81 NAG . . . X 2 -59.435 -11.586 30.628 1 31.59 ? H81 NAG 1401 C 1 
HETATM 23 H H82 NAG . . . X 2 -59.059 -10.381 29.445 1 31.59 ? H82 NAG 1401 C 1 
HETATM 24 H H83 NAG . . . X 2 -60.476 -11.356 29.267 1 31.59 ? H83 NAG 1401 C 1 
HETATM 25 H HN2 NAG . . . X 2 -60.56 -8.561 32.297 1 32.03 ? HN2 NAG 1401 C 1 
HETATM 26 H HO3 NAG . . . X 2 -58.845 -9.807 35.383 1 30.83 ? HO3 NAG 1401 C 1 
HETATM 27 H HO4 NAG . . . X 2 -55.816 -8.322 35.374 1 41.21 ? HO4 NAG 1401 C 1 
HETATM 28 H HO6 NAG . . . X 2 -53.63 -9.741 31.935 1 63.17 ? HO6 NAG 1401 C 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           669 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           28 
#