data_8DYA
#
_model_server_result.job_id            sWNQQRFmP78MX8MWg-5PfA 
_model_server_result.datetime_utc      '2024-11-21 08:51:15' 
_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          8dya 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":1305}' 
#
_entry.id    8DYA 
#
_exptl.entry_id    8DYA 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    18 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_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 
_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
? 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 
#
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 54 A CYS 707 1_555 B SG CYS 230 B CYS 883 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
disulf ? disulf2 A SG CYS 230 A CYS 883 1_555 C SG CYS 54 C CYS 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
disulf ? disulf3 A SG CYS 379 A CYS 1032 1_555 A SG CYS 390 A CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
disulf ? disulf4 A SG CYS 429 A CYS 1082 1_555 A SG CYS 473 A CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
disulf ? disulf5 B SG CYS 54 B CYS 707 1_555 C SG CYS 230 C CYS 883 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
disulf ? disulf6 B SG CYS 379 B CYS 1032 1_555 B SG CYS 390 B CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? 
disulf ? disulf7 B SG CYS 429 B CYS 1082 1_555 B SG CYS 473 B CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
disulf ? disulf8 C SG CYS 379 C CYS 1032 1_555 C SG CYS 390 C CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
disulf ? disulf9 C SG CYS 429 C CYS 1082 1_555 C SG CYS 473 C CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
covale ? covale1 A ND2 ASN 56 A ASN 709 1_555 G C1 NAG . A NAG 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.505 ? 
covale ? covale2 A ND2 ASN 148 A ASN 801 1_555 D C1 NAG . A NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.496 ? 
covale ? covale3 A ND2 ASN 421 A ASN 1074 1_555 H C1 NAG . A NAG 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? 
covale ? covale4 A ND2 ASN 445 A ASN 1098 1_555 F C1 NAG . A NAG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.501 ? 
covale ? covale5 A ND2 ASN 481 A ASN 1134 1_555 E C1 NAG . A NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? 
covale ? covale6 B ND2 ASN 56 B ASN 709 1_555 M C1 NAG . B NAG 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.505 ? 
covale ? covale7 B ND2 ASN 148 B ASN 801 1_555 J C1 NAG . B NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.497 ? 
covale ? covale8 B ND2 ASN 421 B ASN 1074 1_555 N C1 NAG . B NAG 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? 
covale ? covale9 B ND2 ASN 445 B ASN 1098 1_555 L C1 NAG . B NAG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.502 ? 
covale ? covale10 B ND2 ASN 481 B ASN 1134 1_555 K C1 NAG . B NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? 
covale ? covale11 C ND2 ASN 56 C ASN 709 1_555 S C1 NAG . C NAG 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.505 ? 
covale ? covale12 C ND2 ASN 148 C ASN 801 1_555 P C1 NAG . C NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.497 ? 
covale ? covale13 C ND2 ASN 421 C ASN 1074 1_555 T C1 NAG . C NAG 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? 
covale ? covale14 C ND2 ASN 445 C ASN 1098 1_555 R C1 NAG . C NAG 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.501 ? 
covale ? covale15 C ND2 ASN 481 C ASN 1134 1_555 Q C1 NAG . C NAG 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 ? 
#
_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                     8DYA 
_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 1301 1300 NAG NAG . 
E 2 NAG A 1 1302 1306 NAG NAG . 
F 2 NAG A 1 1303 1310 NAG NAG . 
G 2 NAG A 1 1304 1315 NAG NAG . 
H 2 NAG A 1 1305 1316 NAG NAG . 
I 2 NAG A 1 1306 1401 NAG NAG . 
J 2 NAG B 1 1301 1300 NAG NAG . 
K 2 NAG B 1 1302 1306 NAG NAG . 
L 2 NAG B 1 1303 1310 NAG NAG . 
M 2 NAG B 1 1304 1315 NAG NAG . 
N 2 NAG B 1 1305 1316 NAG NAG . 
O 2 NAG B 1 1306 1401 NAG NAG . 
P 2 NAG C 1 1301 1300 NAG NAG . 
Q 2 NAG C 1 1302 1306 NAG NAG . 
R 2 NAG C 1 1303 1310 NAG NAG . 
S 2 NAG C 1 1304 1315 NAG NAG . 
T 2 NAG C 1 1305 1316 NAG NAG . 
U 2 NAG C 1 1306 1401 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 . . . N 2 162.818 180.343 137.542 1 17.81 ? C1 NAG 1305 B 1 
HETATM 2 C C2 NAG . . . N 2 164.323 180.753 137.707 1 18.11 ? C2 NAG 1305 B 1 
HETATM 3 C C3 NAG . . . N 2 164.555 181.17 139.175 1 18.08 ? C3 NAG 1305 B 1 
HETATM 4 C C4 NAG . . . N 2 163.618 182.343 139.529 1 18.46 ? C4 NAG 1305 B 1 
HETATM 5 C C5 NAG . . . N 2 162.157 181.892 139.313 1 18.48 ? C5 NAG 1305 B 1 
HETATM 6 C C6 NAG . . . N 2 161.187 183.027 139.583 1 18.6 ? C6 NAG 1305 B 1 
HETATM 7 C C7 NAG . . . N 2 166.163 179.668 136.547 1 17.45 ? C7 NAG 1305 B 1 
HETATM 8 C C8 NAG . . . N 2 166.999 178.455 136.266 1 16.69 ? C8 NAG 1305 B 1 
HETATM 9 N N2 NAG . . . N 2 165.154 179.583 137.405 1 17.63 ? N2 NAG 1305 B 1 
HETATM 10 O O3 NAG . . . N 2 165.917 181.566 139.353 1 18.14 ? O3 NAG 1305 B 1 
HETATM 11 O O4 NAG . . . N 2 163.806 182.704 140.888 1 18.67 ? O4 NAG 1305 B 1 
HETATM 12 O O5 NAG . . . N 2 161.971 181.453 137.924 1 18.12 ? O5 NAG 1305 B 1 
HETATM 13 O O6 NAG . . . N 2 161.476 184.173 138.795 1 18.73 ? O6 NAG 1305 B 1 
HETATM 14 O O7 NAG . . . N 2 166.421 180.735 135.979 1 18.03 ? O7 NAG 1305 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#