data_6WBF
#
_model_server_result.job_id            9k_eMyKwNpmfja2BC1l3Zw 
_model_server_result.datetime_utc      '2024-12-22 08:06:41' 
_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          6wbf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"DB","auth_seq_id":407}' 
#
_entry.id    6WBF 
#
_exptl.entry_id    6WBF 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          6 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    7 
_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            6WBF 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6WBF 
_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    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_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 
_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
? 6 N N N 
? 6 U N N 
? 6 BA N N 
? 6 IA N N 
? 6 PA N N 
? 6 WA N N 
? 6 DB 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 66 A CYS 66 1_555 A SG CYS 265 A CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 A SG CYS 84 A CYS 84 1_555 A SG CYS 246 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf3 B SG CYS 66 B CYS 66 1_555 B SG CYS 265 B CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 B SG CYS 84 B CYS 84 1_555 B SG CYS 246 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf5 C SG CYS 66 C CYS 66 1_555 C SG CYS 265 C CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf6 C SG CYS 84 C CYS 84 1_555 C SG CYS 246 C CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf7 D SG CYS 66 D CYS 66 1_555 D SG CYS 265 D CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf8 D SG CYS 84 D CYS 84 1_555 D SG CYS 246 D CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf9 E SG CYS 66 E CYS 66 1_555 E SG CYS 265 E CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf10 E SG CYS 84 E CYS 84 1_555 E SG CYS 246 E CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf11 F SG CYS 66 F CYS 66 1_555 F SG CYS 265 F CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf12 F SG CYS 84 F CYS 84 1_555 F SG CYS 246 F CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf13 G SG CYS 66 G CYS 66 1_555 G SG CYS 265 G CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf14 G SG CYS 84 G CYS 84 1_555 G SG CYS 246 G CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
covale ? covale1 A ND2 ASN 255 A ASN 255 1_555 N C1 NAG . A NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale2 B ND2 ASN 255 B ASN 255 1_555 U C1 NAG . B NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale3 C ND2 ASN 255 C ASN 255 1_555 BA C1 NAG . C NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale4 D ND2 ASN 255 D ASN 255 1_555 IA C1 NAG . D NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale5 E ND2 ASN 255 E ASN 255 1_555 PA C1 NAG . E NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale6 F ND2 ASN 255 F ASN 255 1_555 WA C1 NAG . F NAG 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale7 G ND2 ASN 255 G ASN 255 1_555 DB C1 NAG . G NAG 407 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 563 n n 
C1 O1 NAG sing 564 n n 
C1 O5 NAG sing 565 n n 
C1 H1 NAG sing 566 n n 
C2 C3 NAG sing 567 n n 
C2 N2 NAG sing 568 n n 
C2 H2 NAG sing 569 n n 
C3 C4 NAG sing 570 n n 
C3 O3 NAG sing 571 n n 
C3 H3 NAG sing 572 n n 
C4 C5 NAG sing 573 n n 
C4 O4 NAG sing 574 n n 
C4 H4 NAG sing 575 n n 
C5 C6 NAG sing 576 n n 
C5 O5 NAG sing 577 n n 
C5 H5 NAG sing 578 n n 
C6 O6 NAG sing 579 n n 
C6 H61 NAG sing 580 n n 
C6 H62 NAG sing 581 n n 
C7 C8 NAG sing 582 n n 
C7 N2 NAG sing 583 n n 
C7 O7 NAG doub 584 n n 
C8 H81 NAG sing 585 n n 
C8 H82 NAG sing 586 n n 
C8 H83 NAG sing 587 n n 
N2 HN2 NAG sing 588 n n 
O1 HO1 NAG sing 589 n n 
O3 HO3 NAG sing 590 n n 
O4 HO4 NAG sing 591 n n 
O6 HO6 NAG sing 592 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                     6WBF 
_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
H 2 PTY A 1 401 401 PTY PTY . 
I 2 PTY A 1 402 402 PTY PTY . 
J 3 3PE A 1 403 403 3PE PEH . 
K 4 DGA A 1 404 404 DGA DGA . 
L 5 CLR A 1 405 405 CLR CLR . 
M 5 CLR A 1 406 406 CLR CLR . 
N 6 NAG A 1 407 501 NAG NAG . 
O 2 PTY B 1 401 401 PTY PTY . 
P 2 PTY B 1 402 402 PTY PTY . 
Q 3 3PE B 1 403 403 3PE PEH . 
R 4 DGA B 1 404 404 DGA DGA . 
S 5 CLR B 1 405 405 CLR CLR . 
T 5 CLR B 1 406 406 CLR CLR . 
U 6 NAG B 1 407 501 NAG NAG . 
V 2 PTY C 1 401 401 PTY PTY . 
W 2 PTY C 1 402 402 PTY PTY . 
X 3 3PE C 1 403 403 3PE PEH . 
Y 4 DGA C 1 404 404 DGA DGA . 
Z 5 CLR C 1 405 405 CLR CLR . 
AA 5 CLR C 1 406 406 CLR CLR . 
BA 6 NAG C 1 407 501 NAG NAG . 
CA 2 PTY D 1 401 401 PTY PTY . 
DA 2 PTY D 1 402 402 PTY PTY . 
EA 3 3PE D 1 403 403 3PE PEH . 
FA 4 DGA D 1 404 404 DGA DGA . 
GA 5 CLR D 1 405 405 CLR CLR . 
HA 5 CLR D 1 406 406 CLR CLR . 
IA 6 NAG D 1 407 501 NAG NAG . 
JA 2 PTY E 1 401 401 PTY PTY . 
KA 2 PTY E 1 402 402 PTY PTY . 
LA 3 3PE E 1 403 403 3PE PEH . 
MA 4 DGA E 1 404 404 DGA DGA . 
NA 5 CLR E 1 405 405 CLR CLR . 
OA 5 CLR E 1 406 406 CLR CLR . 
PA 6 NAG E 1 407 501 NAG NAG . 
QA 2 PTY F 1 401 401 PTY PTY . 
RA 2 PTY F 1 402 402 PTY PTY . 
SA 3 3PE F 1 403 403 3PE PEH . 
TA 4 DGA F 1 404 404 DGA DGA . 
UA 5 CLR F 1 405 405 CLR CLR . 
VA 5 CLR F 1 406 406 CLR CLR . 
WA 6 NAG F 1 407 501 NAG NAG . 
XA 2 PTY G 1 401 401 PTY PTY . 
YA 2 PTY G 1 402 402 PTY PTY . 
ZA 3 3PE G 1 403 403 3PE PEH . 
AB 4 DGA G 1 404 404 DGA DGA . 
BB 5 CLR G 1 405 405 CLR CLR . 
CB 5 CLR G 1 406 406 CLR CLR . 
DB 6 NAG G 1 407 501 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 . . . DB 6 100.201 144.543 72.91 1 116.74 ? C1 NAG 407 G 1 
HETATM 2 C C2 NAG . . . DB 6 99.869 145.905 73.51 1 116.74 ? C2 NAG 407 G 1 
HETATM 3 C C3 NAG . . . DB 6 98.36 146.118 73.502 1 116.74 ? C3 NAG 407 G 1 
HETATM 4 C C4 NAG . . . DB 6 97.817 145.929 72.09 1 116.74 ? C4 NAG 407 G 1 
HETATM 5 C C5 NAG . . . DB 6 98.286 144.599 71.511 1 116.74 ? C5 NAG 407 G 1 
HETATM 6 C C6 NAG . . . DB 6 97.825 144.434 70.069 1 116.74 ? C6 NAG 407 G 1 
HETATM 7 C C7 NAG . . . DB 6 101.603 146.522 75.083 1 116.74 ? C7 NAG 407 G 1 
HETATM 8 C C8 NAG . . . DB 6 102.163 146.287 76.454 1 116.74 ? C8 NAG 407 G 1 
HETATM 9 N N2 NAG . . . DB 6 100.393 146.017 74.857 1 116.74 ? N2 NAG 407 G 1 
HETATM 10 O O3 NAG . . . DB 6 98.056 147.44 73.958 1 116.74 ? O3 NAG 407 G 1 
HETATM 11 O O4 NAG . . . DB 6 96.387 145.954 72.124 1 116.74 ? O4 NAG 407 G 1 
HETATM 12 O O5 NAG . . . DB 6 99.711 144.51 71.566 1 116.74 ? O5 NAG 407 G 1 
HETATM 13 O O6 NAG . . . DB 6 96.394 144.407 70.026 1 116.74 ? O6 NAG 407 G 1 
HETATM 14 O O7 NAG . . . DB 6 102.219 147.133 74.224 1 116.74 ? O7 NAG 407 G 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    38 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           14 
#