data_9JR4
#
_model_server_result.job_id            X3V0cZWhQtWXlAnz0PjBsg 
_model_server_result.datetime_utc      '2025-08-10 22:00:08' 
_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          9jr4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":702}' 
#
_entry.id    9JR4 
#
_exptl.entry_id    9JR4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    4 
_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            9JR4 
_cell.length_a            168.99 
_cell.length_b            168.99 
_cell.length_c            86.08 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 9JR4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_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    x,y,z 
_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 F N N 
? 6 G N N 
? 6 H N N 
? 6 J 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 BMA NAG C1 O1 . O4 HO4 . sing 
3 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 
4 ? 3 5 1 FUC NAG C1 O1 . O6 HO6 . sing 
5 ? 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 A 1 NAG A 1 NAG 
3 n C NAG 2 A 2 NAG A 2 NAG 
3 n C BMA 3 A 3 BMA A 3 BMA 
3 n C MAN 4 A 4 MAN A 4 MAN 
3 n C FUC 5 A 5 FUC A 5 FUC 
4 n D NAG 1 C 1 NAG C 1 NAG 
4 n D NAG 2 C 2 NAG C 2 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 A SG CYS 115 B CYS 133 1_555 A SG CYS 123 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 A SG CYS 326 B CYS 344 1_555 A SG CYS 343 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf3 A SG CYS 512 B CYS 533 1_555 A SG CYS 524 B CYS 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 B SG CYS 5 E CYS 336 1_555 B SG CYS 30 E CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf5 B SG CYS 48 E CYS 379 1_555 B SG CYS 101 E CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf6 B SG CYS 60 E CYS 391 1_555 B SG CYS 194 E CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf7 B SG CYS 149 E CYS 480 1_555 B SG CYS 157 E CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 A ND2 ASN 35 B ASN 53 1_555 G C1 NAG . B NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale2 A ND2 ASN 72 B ASN 90 1_555 H C1 NAG . B NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale3 A ND2 ASN 304 B ASN 322 1_555 C C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale4 A ND2 ASN 528 B ASN 549 1_555 F C1 NAG . B NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale5 B ND2 ASN 12 E ASN 343 1_555 J C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale6 B ND2 ASN 39 E ASN 370 1_555 D C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale7 C O4 NAG . A NAG 1 1_555 C C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale8 C O6 NAG . A NAG 1 1_555 C C1 FUC . A FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale9 C O4 NAG . A NAG 2 1_555 C C1 BMA . A BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? 
covale ? covale10 C O6 BMA . A BMA 3 1_555 C C1 MAN . A MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale11 D O4 NAG . C NAG 1 1_555 D C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? 
metalc ? metalc1 A NE2 HIS 356 B HIS 374 1_555 I ZN ZN . B ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? 
metalc ? metalc2 A OE1 GLU 357 B GLU 375 1_555 I ZN ZN . B ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? 
metalc ? metalc3 A OE1 GLU 384 B GLU 402 1_555 I ZN ZN . B ZN 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
#
_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 308 n n 
C1 O1 NAG sing 309 n n 
C1 O5 NAG sing 310 n n 
C1 H1 NAG sing 311 n n 
C2 C3 NAG sing 312 n n 
C2 N2 NAG sing 313 n n 
C2 H2 NAG sing 314 n n 
C3 C4 NAG sing 315 n n 
C3 O3 NAG sing 316 n n 
C3 H3 NAG sing 317 n n 
C4 C5 NAG sing 318 n n 
C4 O4 NAG sing 319 n n 
C4 H4 NAG sing 320 n n 
C5 C6 NAG sing 321 n n 
C5 O5 NAG sing 322 n n 
C5 H5 NAG sing 323 n n 
C6 O6 NAG sing 324 n n 
C6 H61 NAG sing 325 n n 
C6 H62 NAG sing 326 n n 
C7 C8 NAG sing 327 n n 
C7 N2 NAG sing 328 n n 
C7 O7 NAG doub 329 n n 
C8 H81 NAG sing 330 n n 
C8 H82 NAG sing 331 n n 
C8 H83 NAG sing 332 n n 
N2 HN2 NAG sing 333 n n 
O1 HO1 NAG sing 334 n n 
O3 HO3 NAG sing 335 n n 
O4 HO4 NAG sing 336 n n 
O6 HO6 NAG sing 337 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                     9JR4 
_atom_sites.fract_transf_matrix[1][1]    0.005918 
_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]    0.005918 
_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]    0.011617 
_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 5 CL B 1 701 1905 CL CL . 
F 6 NAG B 1 702 1912 NAG NAG . 
G 6 NAG B 1 703 1919 NAG NAG . 
H 6 NAG B 1 704 1920 NAG NAG . 
I 7 ZN B 1 705 1 ZN ZN . 
J 6 NAG E 1 601 539 NAG NAG . 
K 8 HOH B 1 801 1 HOH HOH . 
K 8 HOH B 2 802 3 HOH HOH . 
K 8 HOH B 3 803 12 HOH HOH . 
K 8 HOH B 4 804 19 HOH HOH . 
K 8 HOH B 5 805 9 HOH HOH . 
K 8 HOH B 6 806 7 HOH HOH . 
K 8 HOH B 7 807 11 HOH HOH . 
K 8 HOH B 8 808 10 HOH HOH . 
K 8 HOH B 9 809 18 HOH HOH . 
K 8 HOH B 10 810 2 HOH HOH . 
K 8 HOH B 11 811 8 HOH HOH . 
K 8 HOH B 12 812 4 HOH HOH . 
K 8 HOH B 13 813 14 HOH HOH . 
L 8 HOH E 1 701 13 HOH HOH . 
L 8 HOH E 2 702 16 HOH HOH . 
L 8 HOH E 3 703 17 HOH HOH . 
#
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 . . . F 6 -41.624 -15.917 -53.74 1 139.49 ? C1 NAG 702 B 1 
HETATM 2 C C2 NAG . . . F 6 -41.522 -14.829 -54.827 1 144.15 ? C2 NAG 702 B 1 
HETATM 3 C C3 NAG . . . F 6 -42.4 -15.18 -56.035 1 152.06 ? C3 NAG 702 B 1 
HETATM 4 C C4 NAG . . . F 6 -42.047 -16.562 -56.563 1 158.92 ? C4 NAG 702 B 1 
HETATM 5 C C5 NAG . . . F 6 -42.224 -17.586 -55.449 1 153.35 ? C5 NAG 702 B 1 
HETATM 6 C C6 NAG . . . F 6 -41.837 -18.983 -55.879 1 157.68 ? C6 NAG 702 B 1 
HETATM 7 C C7 NAG . . . F 6 -41.454 -12.37 -54.835 1 146.56 ? C7 NAG 702 B 1 
HETATM 8 C C8 NAG . . . F 6 -41.93 -11.116 -54.168 1 137 ? C8 NAG 702 B 1 
HETATM 9 N N2 NAG . . . F 6 -41.88 -13.521 -54.298 1 144.73 ? N2 NAG 702 B 1 
HETATM 10 O O3 NAG . . . F 6 -42.219 -14.225 -57.076 1 147.12 ? O3 NAG 702 B 1 
HETATM 11 O O4 NAG . . . F 6 -42.855 -16.895 -57.689 1 158.31 ? O4 NAG 702 B 1 
HETATM 12 O O5 NAG . . . F 6 -41.386 -17.238 -54.334 1 143.86 ? O5 NAG 702 B 1 
HETATM 13 O O6 NAG . . . F 6 -41.838 -19.105 -57.296 1 158.03 ? O6 NAG 702 B 1 
HETATM 14 O O7 NAG . . . F 6 -40.72 -12.342 -55.82 1 145.44 ? O7 NAG 702 B 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           30 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           330 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           14 
#