data_7KYB
#
_model_server_result.job_id            iJ3gcRkbumiRKsg9OampAw 
_model_server_result.datetime_utc      '2024-12-26 20:29:15' 
_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          7kyb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":1001}' 
#
_entry.id    7KYB 
#
_exptl.entry_id    7KYB 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          9 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    2 
_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            7KYB 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7KYB 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 9 K N N 
? 9 L N N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
3 oligosaccharide 
4 oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing 
3 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
3 n C NAG 1 C 1 NAG B 1002 NAG 
3 n C NAG 2 C 2 NAG B 1003 NAG 
3 n C MAN 3 C 3 MAN B 1004 MAN 
4 n D NAG 1 D 1 NAG B 1006 NAG 
4 n D NAG 2 D 2 NAG B 1007 NAG 
4 n E NAG 1 E 1 NAG B 1008 NAG 
4 n E NAG 2 E 2 NAG B 1009 NAG 
#
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 B SG CYS 110 B CYS 110 1_555 B SG CYS 159 B CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf2 B SG CYS 216 B CYS 216 1_555 B SG CYS 231 B CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
covale ? covale1 B ND2 ASN 113 B ASN 113 1_555 L C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale2 B ND2 ASN 240 B ASN 240 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? 
covale ? covale3 B ND2 ASN 256 B ASN 256 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale4 B ND2 ASN 298 B ASN 298 1_555 K C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale5 B ND2 ASN 332 B ASN 332 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? 
covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 MAN . C MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
metalc ? metalc1 A O GLN 797 A GLN 797 1_555 J MG MG . A MG 1605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? 
metalc ? metalc2 A OE1 GLU 1151 A GLU 1151 1_555 J MG MG . A MG 1605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.983 ? 
metalc ? metalc3 G O3B ADP . A ADP 1602 1_555 I MG MG . A MG 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? 
metalc ? metalc4 G O2A ADP . A ADP 1602 1_555 I MG MG . A MG 1604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
#
_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 307 n n 
C1 O1 NAG sing 308 n n 
C1 O5 NAG sing 309 n n 
C1 H1 NAG sing 310 n n 
C2 C3 NAG sing 311 n n 
C2 N2 NAG sing 312 n n 
C2 H2 NAG sing 313 n n 
C3 C4 NAG sing 314 n n 
C3 O3 NAG sing 315 n n 
C3 H3 NAG sing 316 n n 
C4 C5 NAG sing 317 n n 
C4 O4 NAG sing 318 n n 
C4 H4 NAG sing 319 n n 
C5 C6 NAG sing 320 n n 
C5 O5 NAG sing 321 n n 
C5 H5 NAG sing 322 n n 
C6 O6 NAG sing 323 n n 
C6 H61 NAG sing 324 n n 
C6 H62 NAG sing 325 n n 
C7 C8 NAG sing 326 n n 
C7 N2 NAG sing 327 n n 
C7 O7 NAG doub 328 n n 
C8 H81 NAG sing 329 n n 
C8 H82 NAG sing 330 n n 
C8 H83 NAG sing 331 n n 
N2 HN2 NAG sing 332 n n 
O1 HO1 NAG sing 333 n n 
O3 HO3 NAG sing 334 n n 
O4 HO4 NAG sing 335 n n 
O6 HO6 NAG sing 336 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                     7KYB 
_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
F 5 POV A 1 1601 2010 POV POV . 
G 6 ADP A 1 1602 2201 ADP ADP . 
H 7 ALF A 1 1603 2202 ALF ALF . 
I 8 MG A 1 1604 2203 MG MG . 
J 8 MG A 1 1605 2204 MG MG . 
K 9 NAG B 1 1001 1001 NAG NAG . 
L 9 NAG B 1 1002 1005 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 9 99.031 120.574 66.302 1 49.32 ? C1 NAG 1001 B 1 
HETATM 2 C C2 NAG . . . K 9 98.056 120.22 65.181 1 49.32 ? C2 NAG 1001 B 1 
HETATM 3 C C3 NAG . . . K 9 97.245 118.983 65.553 1 49.32 ? C3 NAG 1001 B 1 
HETATM 4 C C4 NAG . . . K 9 98.173 117.839 65.933 1 49.32 ? C4 NAG 1001 B 1 
HETATM 5 C C5 NAG . . . K 9 99.111 118.284 67.042 1 49.32 ? C5 NAG 1001 B 1 
HETATM 6 C C6 NAG . . . K 9 100.126 117.228 67.413 1 49.32 ? C6 NAG 1001 B 1 
HETATM 7 C C7 NAG . . . K 9 97.104 121.932 63.696 1 49.32 ? C7 NAG 1001 B 1 
HETATM 8 C C8 NAG . . . K 9 96.142 123.075 63.587 1 49.32 ? C8 NAG 1001 B 1 
HETATM 9 N N2 NAG . . . K 9 97.176 121.34 64.893 1 49.32 ? N2 NAG 1001 B 1 
HETATM 10 O O3 NAG . . . K 9 96.445 118.6 64.442 1 49.32 ? O3 NAG 1001 B 1 
HETATM 11 O O4 NAG . . . K 9 97.422 116.719 66.386 1 49.32 ? O4 NAG 1001 B 1 
HETATM 12 O O5 NAG . . . K 9 99.847 119.436 66.608 1 49.32 ? O5 NAG 1001 B 1 
HETATM 13 O O6 NAG . . . K 9 99.963 116.817 68.763 1 49.32 ? O6 NAG 1001 B 1 
HETATM 14 O O7 NAG . . . K 9 97.782 121.561 62.745 1 49.32 ? O7 NAG 1001 B 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#