data_8DN5
#
_model_server_result.job_id            nRqvKurR32B_v_PaRKQ-GQ 
_model_server_result.datetime_utc      '2024-11-22 20:27:35' 
_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          8dn5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"YA","auth_seq_id":503}' 
#
_entry.id    8DN5 
#
_exptl.entry_id    8DN5 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    5 
_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            8DN5 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DN5 
_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    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB 
_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    ? 
_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
? 4 G N N 
? 4 S N N 
? 4 GA N N 
? 4 PA N N 
? 4 YA 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 138 D CYS 138 1_555 A SG CYS 152 D CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 A SG CYS 198 D CYS 198 1_555 A SG CYS 209 D CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf3 B SG CYS 138 A CYS 138 1_555 B SG CYS 152 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 B SG CYS 198 A CYS 198 1_555 B SG CYS 209 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf5 C SG CYS 138 B CYS 138 1_555 C SG CYS 152 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf6 C SG CYS 198 B CYS 198 1_555 C SG CYS 209 B CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf7 D SG CYS 138 C CYS 138 1_555 D SG CYS 152 C CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf8 D SG CYS 198 C CYS 198 1_555 D SG CYS 209 C CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf9 E SG CYS 159 E CYS 161 1_555 E SG CYS 173 E CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf10 E SG CYS 219 E CYS 221 1_555 E SG CYS 231 E CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
covale ? covale1 A ND2 ASN 38 D ASN 38 1_555 G C1 NAG . D NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? 
covale ? covale2 B ND2 ASN 38 A ASN 38 1_555 S C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale3 C ND2 ASN 38 B ASN 38 1_555 GA C1 NAG . B NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale4 E ND2 ASN 218 E ASN 220 1_555 YA C1 NAG . E NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
#
_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 335 n n 
C1 O1 NAG sing 336 n n 
C1 O5 NAG sing 337 n n 
C1 H1 NAG sing 338 n n 
C2 C3 NAG sing 339 n n 
C2 N2 NAG sing 340 n n 
C2 H2 NAG sing 341 n n 
C3 C4 NAG sing 342 n n 
C3 O3 NAG sing 343 n n 
C3 H3 NAG sing 344 n n 
C4 C5 NAG sing 345 n n 
C4 O4 NAG sing 346 n n 
C4 H4 NAG sing 347 n n 
C5 C6 NAG sing 348 n n 
C5 O5 NAG sing 349 n n 
C5 H5 NAG sing 350 n n 
C6 O6 NAG sing 351 n n 
C6 H61 NAG sing 352 n n 
C6 H62 NAG sing 353 n n 
C7 C8 NAG sing 354 n n 
C7 N2 NAG sing 355 n n 
C7 O7 NAG doub 356 n n 
C8 H81 NAG sing 357 n n 
C8 H82 NAG sing 358 n n 
C8 H83 NAG sing 359 n n 
N2 HN2 NAG sing 360 n n 
O1 HO1 NAG sing 361 n n 
O3 HO3 NAG sing 362 n n 
O4 HO4 NAG sing 363 n n 
O6 HO6 NAG sing 364 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                     8DN5 
_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
F 3 GLY D 1 501 501 GLY GLY . 
G 4 NAG D 1 502 502 NAG NAG . 
H 5 DD9 D 1 503 503 DD9 DD9 . 
I 6 HP6 D 1 504 504 HP6 HP6 . 
J 7 HEX D 1 505 505 HEX HEX . 
K 6 HP6 D 1 506 506 HP6 HP6 . 
L 6 HP6 D 1 507 507 HP6 HP6 . 
M 7 HEX D 1 508 508 HEX HEX . 
N 7 HEX D 1 509 510 HEX HEX . 
O 7 HEX D 1 510 511 HEX HEX . 
P 7 HEX D 1 511 512 HEX HEX . 
Q 8 UND D 1 512 509 UND UND . 
R 3 GLY A 1 501 501 GLY GLY . 
S 4 NAG A 1 502 502 NAG NAG . 
T 8 UND A 1 503 503 UND UND . 
U 8 UND A 1 504 504 UND UND . 
V 5 DD9 A 1 505 505 DD9 DD9 . 
W 6 HP6 A 1 506 506 HP6 HP6 . 
X 7 HEX A 1 507 509 HEX HEX . 
Y 9 NBU A 1 508 510 NBU NBU . 
Z 5 DD9 A 1 509 511 DD9 DD9 . 
AA 9 NBU A 1 510 512 NBU NBU . 
BA 8 UND A 1 511 504 UND UND . 
CA 8 UND A 1 512 505 UND UND . 
DA 10 D10 B 1 501 507 D10 D10 . 
EA 5 DD9 B 1 502 508 DD9 DD9 . 
FA 3 GLY B 1 503 501 GLY GLY . 
GA 4 NAG B 1 504 502 NAG NAG . 
HA 7 HEX B 1 505 503 HEX HEX . 
IA 7 HEX B 1 506 504 HEX HEX . 
JA 9 NBU B 1 507 505 NBU NBU . 
KA 10 D10 B 1 508 506 D10 D10 . 
LA 9 NBU B 1 509 507 NBU NBU . 
MA 9 NBU B 1 510 508 NBU NBU . 
NA 7 HEX B 1 511 509 HEX HEX . 
OA 3 GLY C 1 501 501 GLY GLY . 
PA 4 NAG C 1 502 502 NAG NAG . 
QA 6 HP6 C 1 503 503 HP6 HP6 . 
RA 6 HP6 C 1 504 504 HP6 HP6 . 
SA 9 NBU C 1 505 505 NBU NBU . 
TA 7 HEX C 1 506 506 HEX HEX . 
UA 7 HEX C 1 507 507 HEX HEX . 
VA 9 NBU C 1 508 508 NBU NBU . 
WA 9 NBU E 1 501 509 NBU NBU . 
XA 3 GLY E 1 502 501 GLY GLY . 
YA 4 NAG E 1 503 502 NAG NAG . 
ZA 10 D10 E 1 504 503 D10 D10 . 
AB 8 UND E 1 505 506 UND UND . 
BB 11 OCT E 1 506 507 OCT OCT . 
CB 11 OCT E 1 507 508 OCT OCT . 
DB 7 HEX E 1 508 509 HEX HEX . 
EB 7 HEX E 1 509 510 HEX HEX . 
#
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 . . . YA 4 92.913 90.276 84.613 1 50 ? C1 NAG 503 E 1 
HETATM 2 C C2 NAG . . . YA 4 92.613 88.868 84.127 1 50 ? C2 NAG 503 E 1 
HETATM 3 C C3 NAG . . . YA 4 93.074 88.685 82.693 1 50 ? C3 NAG 503 E 1 
HETATM 4 C C4 NAG . . . YA 4 92.706 89.879 81.819 1 50 ? C4 NAG 503 E 1 
HETATM 5 C C5 NAG . . . YA 4 93.002 91.204 82.504 1 50 ? C5 NAG 503 E 1 
HETATM 6 C C6 NAG . . . YA 4 92.555 92.383 81.65 1 50 ? C6 NAG 503 E 1 
HETATM 7 C C7 NAG . . . YA 4 92.821 87.513 86.138 1 50 ? C7 NAG 503 E 1 
HETATM 8 C C8 NAG . . . YA 4 93.816 86.86 87.049 1 50 ? C8 NAG 503 E 1 
HETATM 9 N N2 NAG . . . YA 4 93.291 87.892 84.955 1 50 ? N2 NAG 503 E 1 
HETATM 10 O O3 NAG . . . YA 4 92.461 87.5 82.174 1 50 ? O3 NAG 503 E 1 
HETATM 11 O O4 NAG . . . YA 4 93.473 89.824 80.618 1 50 ? O4 NAG 503 E 1 
HETATM 12 O O5 NAG . . . YA 4 92.322 91.236 83.751 1 50 ? O5 NAG 503 E 1 
HETATM 13 O O6 NAG . . . YA 4 91.305 92.069 81.028 1 50 ? O6 NAG 503 E 1 
HETATM 14 O O7 NAG . . . YA 4 91.662 87.696 86.465 1 50 ? O7 NAG 503 E 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    16 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#