data_8VDD
#
_model_server_result.job_id            Q3sf2p91mSOPdsyONQLcmA 
_model_server_result.datetime_utc      '2024-11-16 18:31:02' 
_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          8vdd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":201}' 
#
_entry.id    8VDD 
#
_exptl.entry_id    8VDD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          109.518 
_cell.angle_gamma         90 
_cell.entry_id            8VDD 
_cell.length_a            158.833 
_cell.length_b            40.698 
_cell.length_c            92.604 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8VDD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 75 A CYS 73 1_555 C SG CYS 14 C CYS 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf2 A SG CYS 110 A CYS 108 1_555 A SG CYS 166 A CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf3 B SG CYS 15 B CYS 15 1_555 B SG CYS 79 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 B SG CYS 117 B CYS 117 1_555 B SG CYS 173 B CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
covale ? covale1 A ND2 ASN 121 A ASN 119 1_555 D C1 NAG . A NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
#
_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 250 n n 
C1 O1 NAG sing 251 n n 
C1 O5 NAG sing 252 n n 
C1 H1 NAG sing 253 n n 
C2 C3 NAG sing 254 n n 
C2 N2 NAG sing 255 n n 
C2 H2 NAG sing 256 n n 
C3 C4 NAG sing 257 n n 
C3 O3 NAG sing 258 n n 
C3 H3 NAG sing 259 n n 
C4 C5 NAG sing 260 n n 
C4 O4 NAG sing 261 n n 
C4 H4 NAG sing 262 n n 
C5 C6 NAG sing 263 n n 
C5 O5 NAG sing 264 n n 
C5 H5 NAG sing 265 n n 
C6 O6 NAG sing 266 n n 
C6 H61 NAG sing 267 n n 
C6 H62 NAG sing 268 n n 
C7 C8 NAG sing 269 n n 
C7 N2 NAG sing 270 n n 
C7 O7 NAG doub 271 n n 
C8 H81 NAG sing 272 n n 
C8 H82 NAG sing 273 n n 
C8 H83 NAG sing 274 n n 
N2 HN2 NAG sing 275 n n 
O1 HO1 NAG sing 276 n n 
O3 HO3 NAG sing 277 n n 
O4 HO4 NAG sing 278 n n 
O6 HO6 NAG sing 279 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                     8VDD 
_atom_sites.fract_transf_matrix[1][1]    0.006296 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002232 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.024571 
_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]    0.011457 
_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
D 4 NAG A 1 201 202 NAG NAG . 
E 5 GOL C 1 201 201 GOL GOL . 
F 6 HOH A 1 301 36 HOH HOH . 
F 6 HOH A 2 302 33 HOH HOH . 
F 6 HOH A 3 303 34 HOH HOH . 
F 6 HOH A 4 304 45 HOH HOH . 
F 6 HOH A 5 305 8 HOH HOH . 
F 6 HOH A 6 306 37 HOH HOH . 
F 6 HOH A 7 307 40 HOH HOH . 
F 6 HOH A 8 308 38 HOH HOH . 
F 6 HOH A 9 309 12 HOH HOH . 
F 6 HOH A 10 310 55 HOH HOH . 
F 6 HOH A 11 311 14 HOH HOH . 
F 6 HOH A 12 312 30 HOH HOH . 
F 6 HOH A 13 313 10 HOH HOH . 
F 6 HOH A 14 314 7 HOH HOH . 
F 6 HOH A 15 315 32 HOH HOH . 
F 6 HOH A 16 316 35 HOH HOH . 
F 6 HOH A 17 317 39 HOH HOH . 
F 6 HOH A 18 318 5 HOH HOH . 
F 6 HOH A 19 319 16 HOH HOH . 
F 6 HOH A 20 320 43 HOH HOH . 
F 6 HOH A 21 321 51 HOH HOH . 
F 6 HOH A 22 322 13 HOH HOH . 
F 6 HOH A 23 323 44 HOH HOH . 
G 6 HOH B 1 201 25 HOH HOH . 
G 6 HOH B 2 202 17 HOH HOH . 
G 6 HOH B 3 203 21 HOH HOH . 
G 6 HOH B 4 204 23 HOH HOH . 
G 6 HOH B 5 205 41 HOH HOH . 
G 6 HOH B 6 206 20 HOH HOH . 
G 6 HOH B 7 207 52 HOH HOH . 
G 6 HOH B 8 208 47 HOH HOH . 
G 6 HOH B 9 209 49 HOH HOH . 
G 6 HOH B 10 210 9 HOH HOH . 
G 6 HOH B 11 211 24 HOH HOH . 
G 6 HOH B 12 212 28 HOH HOH . 
G 6 HOH B 13 213 27 HOH HOH . 
G 6 HOH B 14 214 48 HOH HOH . 
G 6 HOH B 15 215 11 HOH HOH . 
G 6 HOH B 16 216 18 HOH HOH . 
G 6 HOH B 17 217 22 HOH HOH . 
G 6 HOH B 18 218 26 HOH HOH . 
G 6 HOH B 19 219 50 HOH HOH . 
G 6 HOH B 20 220 31 HOH HOH . 
G 6 HOH B 21 221 4 HOH HOH . 
G 6 HOH B 22 222 42 HOH HOH . 
G 6 HOH B 23 223 56 HOH HOH . 
G 6 HOH B 24 224 46 HOH HOH . 
G 6 HOH B 25 225 54 HOH HOH . 
G 6 HOH B 26 226 53 HOH HOH . 
H 6 HOH C 1 301 1 HOH HOH . 
H 6 HOH C 2 302 29 HOH HOH . 
H 6 HOH C 3 303 19 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 . . . D 4 2.719 -26.029 16.449 1 75.63 ? C1 NAG 201 A 1 
HETATM 2 C C2 NAG . . . D 4 1.562 -25.333 17.17 1 73.42 ? C2 NAG 201 A 1 
HETATM 3 C C3 NAG . . . D 4 0.982 -26.248 18.247 1 68.75 ? C3 NAG 201 A 1 
HETATM 4 C C4 NAG . . . D 4 0.601 -27.596 17.651 1 76.66 ? C4 NAG 201 A 1 
HETATM 5 C C5 NAG . . . D 4 1.8 -28.204 16.932 1 73.25 ? C5 NAG 201 A 1 
HETATM 6 C C6 NAG . . . D 4 1.475 -29.497 16.221 1 77.43 ? C6 NAG 201 A 1 
HETATM 7 C C7 NAG . . . D 4 1.368 -22.906 17.514 1 72.97 ? C7 NAG 201 A 1 
HETATM 8 C C8 NAG . . . D 4 0.18 -22.965 16.599 1 68.28 ? C8 NAG 201 A 1 
HETATM 9 N N2 NAG . . . D 4 1.987 -24.069 17.748 1 70.77 ? N2 NAG 201 A 1 
HETATM 10 O O3 NAG . . . D 4 -0.162 -25.632 18.828 1 63.3 ? O3 NAG 201 A 1 
HETATM 11 O O4 NAG . . . D 4 0.165 -28.481 18.676 1 94.14 ? O4 NAG 201 A 1 
HETATM 12 O O5 NAG . . . D 4 2.278 -27.294 15.931 1 63.26 ? O5 NAG 201 A 1 
HETATM 13 O O6 NAG . . . D 4 2.63 -30.055 15.61 1 83.77 ? O6 NAG 201 A 1 
HETATM 14 O O7 NAG . . . D 4 1.748 -21.854 18.018 1 69.98 ? O7 NAG 201 A 1 
#
_model_server_stats.io_time_ms              75 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           391 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           14 
#