data_5YDH
#
_model_server_result.job_id            QFlBmCEq-YnlASwX_r2-Ng 
_model_server_result.datetime_utc      '2025-02-20 02:39:20' 
_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          5ydh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"KA","auth_seq_id":817}' 
#
_entry.id    5YDH 
#
_exptl.entry_id    5YDH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          5 
_entity.src_method                  man 
_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         120 
_cell.entry_id            5YDH 
_cell.length_a            148.659 
_cell.length_b            148.659 
_cell.length_c            226.021 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YDH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
B,D,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,PA 1 1 
A,C,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,OA 1 2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 6_445 x-y-1,x-1,z+1/6 0.5 -0.866025 0 0.866025 0.5 0 0 0 1 -74.3295 -128.742471 37.670167 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 O N N 
? 5 KA N N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
2 oligosaccharide 
3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 
4 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
5 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
6 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 
7 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . 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
2 n C NAG 1 C 1 NAG A 812 NAG 
2 n C NAG 2 C 2 NAG A 813 NAG 
2 n C BMA 3 C 3 BMA A 814 BMA 
2 n C MAN 4 C 4 MAN A 815 MAN 
3 n D NAG 1 D 1 NAG B 818 NAG 
3 n D NAG 2 D 2 NAG B 819 NAG 
3 n D BMA 3 D 3 BMA B 820 BMA 
3 n D MAN 4 D 4 MAN B 822 MAN 
3 n D MAN 5 D 5 MAN B 821 MAN 
#
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 67 A CYS 228 1_555 A SG CYS 94 A CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf2 A SG CYS 253 A CYS 414 1_555 A SG CYS 266 A CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf3 A SG CYS 401 A CYS 562 1_555 A SG CYS 522 A CYS 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf4 B SG CYS 67 B CYS 228 1_555 B SG CYS 94 B CYS 255 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf5 B SG CYS 253 B CYS 414 1_555 B SG CYS 266 B CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf6 B SG CYS 401 B CYS 562 1_555 B SG CYS 522 B CYS 683 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
covale ? covale1 A ND2 ASN 59 A ASN 220 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale2 A ND2 ASN 509 A ASN 670 1_555 O C1 NAG . A NAG 811 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale3 B ND2 ASN 59 B ASN 220 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale4 B ND2 ASN 509 B ASN 670 1_555 KA C1 NAG . B NAG 817 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
covale ? covale9 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale10 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale11 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
metalc ? metalc1 A NE2 HIS 255 A HIS 416 1_555 T CO CO . A CO 816 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc2 B NE2 HIS 255 B HIS 416 1_555 NA CO CO . B CO 820 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? 
#
_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 331 n n 
C1 O1 NAG sing 332 n n 
C1 O5 NAG sing 333 n n 
C1 H1 NAG sing 334 n n 
C2 C3 NAG sing 335 n n 
C2 N2 NAG sing 336 n n 
C2 H2 NAG sing 337 n n 
C3 C4 NAG sing 338 n n 
C3 O3 NAG sing 339 n n 
C3 H3 NAG sing 340 n n 
C4 C5 NAG sing 341 n n 
C4 O4 NAG sing 342 n n 
C4 H4 NAG sing 343 n n 
C5 C6 NAG sing 344 n n 
C5 O5 NAG sing 345 n n 
C5 H5 NAG sing 346 n n 
C6 O6 NAG sing 347 n n 
C6 H61 NAG sing 348 n n 
C6 H62 NAG sing 349 n n 
C7 C8 NAG sing 350 n n 
C7 N2 NAG sing 351 n n 
C7 O7 NAG doub 352 n n 
C8 H81 NAG sing 353 n n 
C8 H82 NAG sing 354 n n 
C8 H83 NAG sing 355 n n 
N2 HN2 NAG sing 356 n n 
O1 HO1 NAG sing 357 n n 
O3 HO3 NAG sing 358 n n 
O4 HO4 NAG sing 359 n n 
O6 HO6 NAG sing 360 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                     5YDH 
_atom_sites.fract_transf_matrix[1][1]    0.006727 
_atom_sites.fract_transf_matrix[1][2]    0.003884 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007767 
_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]    0.004424 
_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 4 SO4 A 1 801 801 SO4 SO4 . 
F 4 SO4 A 1 802 802 SO4 SO4 . 
G 4 SO4 A 1 803 803 SO4 SO4 . 
H 4 SO4 A 1 804 804 SO4 SO4 . 
I 4 SO4 A 1 805 805 SO4 SO4 . 
J 4 SO4 A 1 806 806 SO4 SO4 . 
K 4 SO4 A 1 807 807 SO4 SO4 . 
L 4 SO4 A 1 808 808 SO4 SO4 . 
M 4 SO4 A 1 809 809 SO4 SO4 . 
N 4 SO4 A 1 810 810 SO4 SO4 . 
O 5 NAG A 1 811 811 NAG NAG . 
P 6 EPE A 1 812 816 EPE EPE . 
Q 6 EPE A 1 813 817 EPE EPE . 
R 7 GOL A 1 814 818 GOL GOL . 
S 7 GOL A 1 815 819 GOL GOL . 
T 8 CO A 1 816 820 CO CO . 
U 4 SO4 B 1 801 801 SO4 SO4 . 
V 4 SO4 B 1 802 802 SO4 SO4 . 
W 4 SO4 B 1 803 803 SO4 SO4 . 
X 4 SO4 B 1 804 804 SO4 SO4 . 
Y 4 SO4 B 1 805 805 SO4 SO4 . 
Z 4 SO4 B 1 806 806 SO4 SO4 . 
AA 4 SO4 B 1 807 807 SO4 SO4 . 
BA 4 SO4 B 1 808 808 SO4 SO4 . 
CA 4 SO4 B 1 809 809 SO4 SO4 . 
DA 4 SO4 B 1 810 810 SO4 SO4 . 
EA 4 SO4 B 1 811 811 SO4 SO4 . 
FA 4 SO4 B 1 812 812 SO4 SO4 . 
GA 4 SO4 B 1 813 813 SO4 SO4 . 
HA 4 SO4 B 1 814 814 SO4 SO4 . 
IA 4 SO4 B 1 815 815 SO4 SO4 . 
JA 4 SO4 B 1 816 816 SO4 SO4 . 
KA 5 NAG B 1 817 817 NAG NAG . 
LA 6 EPE B 1 818 823 EPE EPE . 
MA 7 GOL B 1 819 824 GOL GOL . 
NA 8 CO B 1 820 825 CO CO . 
OA 9 HOH A 1 901 901 HOH HOH . 
OA 9 HOH A 2 902 903 HOH HOH . 
OA 9 HOH A 3 903 907 HOH HOH . 
OA 9 HOH A 4 904 904 HOH HOH . 
OA 9 HOH A 5 905 905 HOH HOH . 
OA 9 HOH A 6 906 906 HOH HOH . 
OA 9 HOH A 7 907 902 HOH HOH . 
PA 9 HOH B 1 901 901 HOH HOH . 
PA 9 HOH B 2 902 902 HOH HOH . 
PA 9 HOH B 3 903 903 HOH HOH . 
PA 9 HOH B 4 904 905 HOH HOH . 
PA 9 HOH B 5 905 904 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 . . . KA 5 -19.022 -76.512 8.532 1 142.36 ? C1 NAG 817 B 1 
HETATM 2 C C2 NAG . . . KA 5 -20.354 -76.178 7.856 1 148.34 ? C2 NAG 817 B 1 
HETATM 3 C C3 NAG . . . KA 5 -21.439 -77.233 8.074 1 150.75 ? C3 NAG 817 B 1 
HETATM 4 C C4 NAG . . . KA 5 -21.363 -77.848 9.472 1 151.28 ? C4 NAG 817 B 1 
HETATM 5 C C5 NAG . . . KA 5 -19.939 -78.195 9.919 1 149.12 ? C5 NAG 817 B 1 
HETATM 6 C C6 NAG . . . KA 5 -19.834 -79.674 10.274 1 147.64 ? C6 NAG 817 B 1 
HETATM 7 C C7 NAG . . . KA 5 -21.222 -73.943 7.479 1 150.6 ? C7 NAG 817 B 1 
HETATM 8 C C8 NAG . . . KA 5 -21.218 -72.544 8.021 1 148.36 ? C8 NAG 817 B 1 
HETATM 9 N N2 NAG . . . KA 5 -20.828 -74.89 8.326 1 148.88 ? N2 NAG 817 B 1 
HETATM 10 O O3 NAG . . . KA 5 -21.302 -78.266 7.092 1 152.92 ? O3 NAG 817 B 1 
HETATM 11 O O4 NAG . . . KA 5 -21.942 -76.939 10.415 1 151.88 ? O4 NAG 817 B 1 
HETATM 12 O O5 NAG . . . KA 5 -18.96 -77.883 8.924 1 146.1 ? O5 NAG 817 B 1 
HETATM 13 O O6 NAG . . . KA 5 -19.927 -79.832 11.695 1 148.89 ? O6 NAG 817 B 1 
HETATM 14 O O7 NAG . . . KA 5 -21.564 -74.196 6.336 1 153.03 ? O7 NAG 817 B 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           486 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           14 
#