data_7YVK
#
_model_server_result.job_id            miVb1w_DXM3foK4wh3qe2Q 
_model_server_result.datetime_utc      '2024-11-21 09:00:15' 
_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          7yvk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"LA","auth_seq_id":1306}' 
#
_entry.id    7YVK 
#
_exptl.entry_id    7YVK 
_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    36 
_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            7YVK 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7YVK 
_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    nonameric 
_pdbx_struct_assembly.oligomeric_count      9 
_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 
_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 J N N 
? 4 K N N 
? 4 L N N 
? 4 M N N 
? 4 N N N 
? 4 O N N 
? 4 P N N 
? 4 Q N N 
? 4 R N N 
? 4 S N N 
? 4 T N N 
? 4 U N N 
? 4 V N N 
? 4 W N N 
? 4 X N N 
? 4 Y N N 
? 4 Z N N 
? 4 AA N N 
? 4 BA N N 
? 4 CA N N 
? 4 DA N N 
? 4 EA N N 
? 4 FA N N 
? 4 GA N N 
? 4 HA N N 
? 4 IA N N 
? 4 JA N N 
? 4 KA N N 
? 4 LA N N 
? 4 MA N N 
? 4 NA N N 
? 4 OA N N 
? 4 PA N N 
? 4 QA N N 
? 4 RA N N 
? 4 SA 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 131 A CYS 131 1_555 A SG CYS 166 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
disulf ? disulf2 A SG CYS 291 A CYS 291 1_555 A SG CYS 301 A CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf3 A SG CYS 336 A CYS 336 1_555 A SG CYS 361 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
disulf ? disulf4 A SG CYS 379 A CYS 379 1_555 A SG CYS 432 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf5 A SG CYS 391 A CYS 391 1_555 A SG CYS 525 A CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf6 A SG CYS 480 A CYS 480 1_555 A SG CYS 488 A CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf7 A SG CYS 538 A CYS 538 1_555 A SG CYS 590 A CYS 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf8 A SG CYS 617 A CYS 617 1_555 A SG CYS 649 A CYS 649 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
disulf ? disulf9 A SG CYS 662 A CYS 662 1_555 A SG CYS 671 A CYS 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf10 A SG CYS 738 A CYS 738 1_555 A SG CYS 760 A CYS 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf11 A SG CYS 743 A CYS 743 1_555 A SG CYS 749 A CYS 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
disulf ? disulf12 A SG CYS 1032 A CYS 1032 1_555 A SG CYS 1043 A CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf13 A SG CYS 1082 A CYS 1082 1_555 A SG CYS 1126 A CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf14 B SG CYS 131 C CYS 131 1_555 B SG CYS 166 C CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf15 B SG CYS 291 C CYS 291 1_555 B SG CYS 301 C CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf16 B SG CYS 336 C CYS 336 1_555 B SG CYS 361 C CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf17 B SG CYS 379 C CYS 379 1_555 B SG CYS 432 C CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf18 B SG CYS 391 C CYS 391 1_555 B SG CYS 525 C CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf19 B SG CYS 480 C CYS 480 1_555 B SG CYS 488 C CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf20 B SG CYS 538 C CYS 538 1_555 B SG CYS 590 C CYS 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf21 B SG CYS 617 C CYS 617 1_555 B SG CYS 649 C CYS 649 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
disulf ? disulf22 B SG CYS 662 C CYS 662 1_555 B SG CYS 671 C CYS 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf23 B SG CYS 738 C CYS 738 1_555 B SG CYS 760 C CYS 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf24 B SG CYS 743 C CYS 743 1_555 B SG CYS 749 C CYS 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf25 B SG CYS 1032 C CYS 1032 1_555 B SG CYS 1043 C CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf26 B SG CYS 1082 C CYS 1082 1_555 B SG CYS 1126 C CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf27 C SG CYS 131 B CYS 131 1_555 C SG CYS 166 B CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
disulf ? disulf28 C SG CYS 291 B CYS 291 1_555 C SG CYS 301 B CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf29 C SG CYS 336 B CYS 336 1_555 C SG CYS 361 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf30 C SG CYS 379 B CYS 379 1_555 C SG CYS 432 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf31 C SG CYS 391 B CYS 391 1_555 C SG CYS 525 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf32 C SG CYS 480 B CYS 480 1_555 C SG CYS 488 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
disulf ? disulf33 C SG CYS 538 B CYS 538 1_555 C SG CYS 590 B CYS 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf34 C SG CYS 617 B CYS 617 1_555 C SG CYS 649 B CYS 649 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf35 C SG CYS 662 B CYS 662 1_555 C SG CYS 671 B CYS 671 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf36 C SG CYS 738 B CYS 738 1_555 C SG CYS 760 B CYS 760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf37 C SG CYS 743 B CYS 743 1_555 C SG CYS 749 B CYS 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
disulf ? disulf38 C SG CYS 1032 B CYS 1032 1_555 C SG CYS 1043 B CYS 1043 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf39 C SG CYS 1082 B CYS 1082 1_555 C SG CYS 1126 B CYS 1126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf40 D SG CYS 22 H CYS 22 1_555 D SG CYS 97 H CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf41 E SG CYS 22 I CYS 22 1_555 E SG CYS 90 I CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf42 F SG CYS 22 K CYS 22 1_555 F SG CYS 97 K CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
disulf ? disulf43 G SG CYS 22 L CYS 22 1_555 G SG CYS 90 L CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf44 H SG CYS 22 N CYS 22 1_555 H SG CYS 97 N CYS 97 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf45 I SG CYS 22 O CYS 22 1_555 I SG CYS 90 O CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
#
_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                     7YVK 
_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
J 4 NAG A 1 1301 1303 NAG NAG . 
K 4 NAG A 1 1302 1308 NAG NAG . 
L 4 NAG A 1 1303 1312 NAG NAG . 
M 4 NAG A 1 1304 1307 NAG NAG . 
N 4 NAG A 1 1305 1301 NAG NAG . 
O 4 NAG A 1 1306 1304 NAG NAG . 
P 4 NAG A 1 1307 1305 NAG NAG . 
Q 4 NAG A 1 1308 1306 NAG NAG . 
R 4 NAG A 1 1309 1307 NAG NAG . 
S 4 NAG A 1 1310 1309 NAG NAG . 
T 4 NAG A 1 1311 1310 NAG NAG . 
U 4 NAG A 1 1312 1311 NAG NAG . 
V 4 NAG C 1 1301 1301 NAG NAG . 
W 4 NAG C 1 1302 1304 NAG NAG . 
X 4 NAG C 1 1303 1305 NAG NAG . 
Y 4 NAG C 1 1304 1306 NAG NAG . 
Z 4 NAG C 1 1305 1307 NAG NAG . 
AA 4 NAG C 1 1306 1309 NAG NAG . 
BA 4 NAG C 1 1307 1310 NAG NAG . 
CA 4 NAG C 1 1308 1311 NAG NAG . 
DA 4 NAG C 1 1309 1303 NAG NAG . 
EA 4 NAG C 1 1310 1308 NAG NAG . 
FA 4 NAG C 1 1311 1312 NAG NAG . 
GA 4 NAG B 1 1301 1306 NAG NAG . 
HA 4 NAG B 1 1302 1308 NAG NAG . 
IA 4 NAG B 1 1303 1303 NAG NAG . 
JA 4 NAG B 1 1304 1308 NAG NAG . 
KA 4 NAG B 1 1305 1312 NAG NAG . 
LA 4 NAG B 1 1306 1301 NAG NAG . 
MA 4 NAG B 1 1307 1304 NAG NAG . 
NA 4 NAG B 1 1308 1305 NAG NAG . 
OA 4 NAG B 1 1309 1306 NAG NAG . 
PA 4 NAG B 1 1310 1307 NAG NAG . 
QA 4 NAG B 1 1311 1309 NAG NAG . 
RA 4 NAG B 1 1312 1310 NAG NAG . 
SA 4 NAG B 1 1313 1311 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 . . . LA 4 260.361 208.942 221.685 1 105.34 ? C1 NAG 1306 B 1 
HETATM 2 C C2 NAG . . . LA 4 261.17 208.314 222.816 1 105.34 ? C2 NAG 1306 B 1 
HETATM 3 C C3 NAG . . . LA 4 262.481 209.067 223.013 1 105.34 ? C3 NAG 1306 B 1 
HETATM 4 C C4 NAG . . . LA 4 263.238 209.149 221.695 1 105.34 ? C4 NAG 1306 B 1 
HETATM 5 C C5 NAG . . . LA 4 262.343 209.739 220.61 1 105.34 ? C5 NAG 1306 B 1 
HETATM 6 C C6 NAG . . . LA 4 262.994 209.728 219.249 1 105.34 ? C6 NAG 1306 B 1 
HETATM 7 C C7 NAG . . . LA 4 260.26 207.13 224.758 1 105.34 ? C7 NAG 1306 B 1 
HETATM 8 C C8 NAG . . . LA 4 259.435 207.235 226.005 1 105.34 ? C8 NAG 1306 B 1 
HETATM 9 N N2 NAG . . . LA 4 260.407 208.256 224.053 1 105.34 ? N2 NAG 1306 B 1 
HETATM 10 O O3 NAG . . . LA 4 263.276 208.4 223.987 1 105.34 ? O3 NAG 1306 B 1 
HETATM 11 O O4 NAG . . . LA 4 264.399 209.957 221.843 1 105.34 ? O4 NAG 1306 B 1 
HETATM 12 O O5 NAG . . . LA 4 261.139 208.966 220.497 1 105.34 ? O5 NAG 1306 B 1 
HETATM 13 O O6 NAG . . . LA 4 264.212 208.997 219.268 1 105.34 ? O6 NAG 1306 B 1 
HETATM 14 O O7 NAG . . . LA 4 260.775 206.074 224.407 1 105.34 ? O7 NAG 1306 B 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    59 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           14 
#