data_6VXK
#
_model_server_result.job_id            1fsDCAusk1rEd1YRVumRKw 
_model_server_result.datetime_utc      '2024-11-25 23:14:26' 
_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          6vxk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":1606}' 
#
_entry.id    6VXK 
#
_exptl.entry_id    6VXK 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          3 
_entity.src_method                  man 
_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                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            6VXK 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VXK 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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
? 3 E N N 
? 3 F N N 
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N N 
? 3 M N N 
? 3 N N N 
? 3 O N N 
? 3 P N N 
? 3 Q N N 
? 3 R N N 
? 3 S N N 
? 3 T N N 
? 3 U N N 
? 3 V 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 65 A CYS 76 1_555 A SG CYS 74 A CYS 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf2 A SG CYS 106 A CYS 117 1_555 A SG CYS 128 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf3 A SG CYS 181 A CYS 192 1_555 A SG CYS 275 A CYS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf4 A SG CYS 206 A CYS 217 1_555 A SG CYS 244 A CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf5 B SG CYS 30 B CYS 64 1_555 B SG CYS 53 B CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf6 B SG CYS 122 B CYS 156 1_555 B SG CYS 160 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf7 B SG CYS 192 B CYS 226 1_555 B SG CYS 320 B CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf8 B SG CYS 249 B CYS 283 1_555 B SG CYS 295 B CYS 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf9 B SG CYS 378 B CYS 412 1_555 B SG CYS 669 B CYS 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf10 B SG CYS 421 B CYS 455 1_555 B SG CYS 438 B CYS 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf11 B SG CYS 427 B CYS 461 1_555 B SG CYS 472 B CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf12 B SG CYS 430 B CYS 464 1_555 B SG CYS 447 B CYS 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf13 B SG CYS 441 B CYS 475 1_555 B SG CYS 453 B CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf14 B SG CYS 700 B CYS 734 1_555 B SG CYS 708 B CYS 742 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf15 B SG CYS 722 B CYS 756 1_555 B SG CYS 801 B CYS 835 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf16 B SG CYS 767 B CYS 801 1_555 B SG CYS 772 B CYS 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf17 B SG CYS 857 B CYS 891 1_555 B SG CYS 873 B CYS 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf18 C SG CYS 65 C CYS 76 1_555 C SG CYS 74 C CYS 85 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf19 C SG CYS 106 C CYS 117 1_555 C SG CYS 128 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf20 C SG CYS 181 C CYS 192 1_555 C SG CYS 275 C CYS 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf21 C SG CYS 206 C CYS 217 1_555 C SG CYS 244 C CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf22 D SG CYS 30 D CYS 64 1_555 D SG CYS 53 D CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf23 D SG CYS 122 D CYS 156 1_555 D SG CYS 160 D CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf24 D SG CYS 192 D CYS 226 1_555 D SG CYS 320 D CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf25 D SG CYS 249 D CYS 283 1_555 D SG CYS 295 D CYS 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf26 D SG CYS 378 D CYS 412 1_555 D SG CYS 669 D CYS 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf27 D SG CYS 421 D CYS 455 1_555 D SG CYS 438 D CYS 472 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf28 D SG CYS 427 D CYS 461 1_555 D SG CYS 472 D CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf29 D SG CYS 430 D CYS 464 1_555 D SG CYS 447 D CYS 481 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf30 D SG CYS 441 D CYS 475 1_555 D SG CYS 453 D CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf31 D SG CYS 700 D CYS 734 1_555 D SG CYS 708 D CYS 742 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf32 D SG CYS 722 D CYS 756 1_555 D SG CYS 801 D CYS 835 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf33 D SG CYS 767 D CYS 801 1_555 D SG CYS 772 D CYS 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf34 D SG CYS 857 D CYS 891 1_555 D SG CYS 873 D CYS 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
covale ? covale1 A ND2 ASN 42 A ASN 53 1_555 E C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale2 B ND2 ASN 52 B ASN 86 1_555 J C1 NAG . B NAG 1605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale3 B ND2 ASN 107 B ASN 141 1_555 F C1 NAG . B NAG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale4 B ND2 ASN 115 B ASN 149 1_555 H C1 NAG . B NAG 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale5 B ND2 ASN 207 B ASN 241 1_555 G C1 NAG . B NAG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? 
covale ? covale6 B ND2 ASN 218 B ASN 252 1_555 I C1 NAG . B NAG 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale7 B ND2 ASN 681 B ASN 715 1_555 K C1 NAG . B NAG 1606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
covale ? covale8 B ND2 ASN 737 B ASN 771 1_555 L C1 NAG . B NAG 1607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale9 B ND2 ASN 837 B ASN 871 1_555 M C1 NAG . B NAG 1608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale10 C ND2 ASN 42 C ASN 53 1_555 N C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale11 D ND2 ASN 52 D ASN 86 1_555 S C1 NAG . D NAG 1605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
covale ? covale12 D ND2 ASN 107 D ASN 141 1_555 O C1 NAG . D NAG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale13 D ND2 ASN 115 D ASN 149 1_555 Q C1 NAG . D NAG 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale14 D ND2 ASN 207 D ASN 241 1_555 P C1 NAG . D NAG 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? 
covale ? covale15 D ND2 ASN 218 D ASN 252 1_555 R C1 NAG . D NAG 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale16 D ND2 ASN 681 D ASN 715 1_555 T C1 NAG . D NAG 1606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
covale ? covale17 D ND2 ASN 737 D ASN 771 1_555 U C1 NAG . D NAG 1607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale18 D ND2 ASN 837 D ASN 871 1_555 V C1 NAG . D NAG 1608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
#
_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                     6VXK 
_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
E 3 NAG A 1 501 392 NAG NAG . 
F 3 NAG B 1 1601 3729 NAG NAG . 
G 3 NAG B 1 1602 3730 NAG NAG . 
H 3 NAG B 1 1603 3732 NAG NAG . 
I 3 NAG B 1 1604 3733 NAG NAG . 
J 3 NAG B 1 1605 3734 NAG NAG . 
K 3 NAG B 1 1606 3735 NAG NAG . 
L 3 NAG B 1 1607 3736 NAG NAG . 
M 3 NAG B 1 1608 3737 NAG NAG . 
N 3 NAG C 1 501 392 NAG NAG . 
O 3 NAG D 1 1601 3729 NAG NAG . 
P 3 NAG D 1 1602 3730 NAG NAG . 
Q 3 NAG D 1 1603 3732 NAG NAG . 
R 3 NAG D 1 1604 3733 NAG NAG . 
S 3 NAG D 1 1605 3734 NAG NAG . 
T 3 NAG D 1 1606 3735 NAG NAG . 
U 3 NAG D 1 1607 3736 NAG NAG . 
V 3 NAG D 1 1608 3737 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 . . . K 3 94.493 123.041 110.641 1 155.24 ? C1 NAG 1606 B 1 
HETATM 2 C C2 NAG . . . K 3 95.913 122.464 110.661 1 155.24 ? C2 NAG 1606 B 1 
HETATM 3 C C3 NAG . . . K 3 96.954 123.579 110.615 1 155.24 ? C3 NAG 1606 B 1 
HETATM 4 C C4 NAG . . . K 3 96.684 124.508 109.442 1 155.24 ? C4 NAG 1606 B 1 
HETATM 5 C C5 NAG . . . K 3 95.262 125.036 109.549 1 155.24 ? C5 NAG 1606 B 1 
HETATM 6 C C6 NAG . . . K 3 94.868 125.929 108.398 1 155.24 ? C6 NAG 1606 B 1 
HETATM 7 C C7 NAG . . . K 3 95.761 120.344 111.885 1 155.24 ? C7 NAG 1606 B 1 
HETATM 8 C C8 NAG . . . K 3 96.042 119.636 113.174 1 155.24 ? C8 NAG 1606 B 1 
HETATM 9 N N2 NAG . . . K 3 96.114 121.632 111.836 1 155.24 ? N2 NAG 1606 B 1 
HETATM 10 O O3 NAG . . . K 3 98.25 123.007 110.487 1 155.24 ? O3 NAG 1606 B 1 
HETATM 11 O O4 NAG . . . K 3 97.606 125.591 109.452 1 155.24 ? O4 NAG 1606 B 1 
HETATM 12 O O5 NAG . . . K 3 94.35 123.932 109.543 1 155.24 ? O5 NAG 1606 B 1 
HETATM 13 O O6 NAG . . . K 3 93.468 126.173 108.406 1 155.24 ? O6 NAG 1606 B 1 
HETATM 14 O O7 NAG . . . K 3 95.238 119.777 110.932 1 155.24 ? O7 NAG 1606 B 1 
#
_model_server_stats.io_time_ms              0 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    36 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           14 
#