data_8DNR
#
_model_server_result.job_id            LW9Uj8SwnxwwITOeHHGX1A 
_model_server_result.datetime_utc      '2024-11-09 02:04:55' 
_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          8dnr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":602}' 
#
_entry.id    8DNR 
#
_exptl.entry_id    8DNR 
_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    12 
_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 
_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 
#
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 46 A CYS 71 1_555 A SG CYS 167 A CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 A SG CYS 79 A CYS 104 1_555 A SG CYS 89 A CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 A SG CYS 306 A CYS 331 1_555 A SG CYS 315 A CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 A SG CYS 330 A CYS 355 1_555 A SG CYS 338 A CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf5 A SG CYS 362 A CYS 387 1_555 A SG CYS 367 A CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf6 A SG CYS 369 A CYS 394 1_555 A SG CYS 392 A CYS 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf7 B SG CYS 46 B CYS 71 1_555 B SG CYS 167 B CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf8 B SG CYS 79 B CYS 104 1_555 B SG CYS 89 B CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf9 B SG CYS 306 B CYS 331 1_555 B SG CYS 315 B CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf10 B SG CYS 330 B CYS 355 1_555 B SG CYS 338 B CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf11 B SG CYS 362 B CYS 387 1_555 B SG CYS 367 B CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf12 B SG CYS 369 B CYS 394 1_555 B SG CYS 392 B CYS 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf13 C SG CYS 46 E CYS 71 1_555 C SG CYS 167 E CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf14 C SG CYS 79 E CYS 104 1_555 C SG CYS 89 E CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf15 C SG CYS 306 E CYS 331 1_555 C SG CYS 315 E CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf16 C SG CYS 330 E CYS 355 1_555 C SG CYS 338 E CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf17 C SG CYS 362 E CYS 387 1_555 C SG CYS 367 E CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf18 C SG CYS 369 E CYS 394 1_555 C SG CYS 392 E CYS 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
covale ? covale1 A ND2 ASN 42 A ASN 67 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale2 A ND2 ASN 74 A ASN 99 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale3 A ND2 ASN 389 A ASN 414 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale4 A ND2 ASN 439 A ASN 464 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale5 B ND2 ASN 42 B ASN 67 1_555 I C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale6 B ND2 ASN 74 B ASN 99 1_555 H C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale7 B ND2 ASN 389 B ASN 414 1_555 J C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale8 B ND2 ASN 439 B ASN 464 1_555 K C1 NAG . B NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale9 C ND2 ASN 42 E ASN 67 1_555 M C1 NAG . E NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale10 C ND2 ASN 74 E ASN 99 1_555 L C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale11 C ND2 ASN 389 E ASN 414 1_555 O C1 NAG . E NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale12 C ND2 ASN 439 E ASN 464 1_555 N C1 NAG . E NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
#
_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                     8DNR 
_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 1 601 601 NAG NAG . 
E 2 NAG A 1 602 602 NAG NAG . 
F 2 NAG A 1 603 603 NAG NAG . 
G 2 NAG A 1 604 604 NAG NAG . 
H 2 NAG B 1 601 601 NAG NAG . 
I 2 NAG B 1 602 602 NAG NAG . 
J 2 NAG B 1 603 603 NAG NAG . 
K 2 NAG B 1 604 604 NAG NAG . 
L 2 NAG E 1 601 601 NAG NAG . 
M 2 NAG E 1 602 602 NAG NAG . 
N 2 NAG E 1 603 604 NAG NAG . 
O 2 NAG E 1 604 605 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 . . . E 2 136.206 125.811 170.953 1 96.58 ? C1 NAG 602 A 1 
HETATM 2 C C2 NAG . . . E 2 137.695 125.625 170.655 1 98.06 ? C2 NAG 602 A 1 
HETATM 3 C C3 NAG . . . E 2 138.284 124.542 171.556 1 97.38 ? C3 NAG 602 A 1 
HETATM 4 C C4 NAG . . . E 2 137.988 124.845 173.018 1 99.19 ? C4 NAG 602 A 1 
HETATM 5 C C5 NAG . . . E 2 136.49 125.048 173.217 1 97.84 ? C5 NAG 602 A 1 
HETATM 6 C C6 NAG . . . E 2 136.129 125.458 174.626 1 98.11 ? C6 NAG 602 A 1 
HETATM 7 C C7 NAG . . . E 2 138.931 125.782 168.54 1 98.72 ? C7 NAG 602 A 1 
HETATM 8 C C8 NAG . . . E 2 139.003 125.336 167.111 1 94.06 ? C8 NAG 602 A 1 
HETATM 9 N N2 NAG . . . E 2 137.911 125.296 169.255 1 98.7 ? N2 NAG 602 A 1 
HETATM 10 O O3 NAG . . . E 2 139.69 124.467 171.35 1 97.78 ? O3 NAG 602 A 1 
HETATM 11 O O4 NAG . . . E 2 138.43 123.77 173.84 1 98.85 ? O4 NAG 602 A 1 
HETATM 12 O O5 NAG . . . E 2 136.024 126.092 172.35 1 99.99 ? O5 NAG 602 A 1 
HETATM 13 O O6 NAG . . . E 2 136.568 126.779 174.913 1 98.14 ? O6 NAG 602 A 1 
HETATM 14 O O7 NAG . . . E 2 139.757 126.548 169.024 1 97.5 ? O7 NAG 602 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#