data_6DG5
#
_model_server_result.job_id            kUUyqBulg7lMwB-J1mRJww 
_model_server_result.datetime_utc      '2024-11-09 02:39:59' 
_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          6dg5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":301}' 
#
_entry.id    6DG5 
#
_exptl.entry_id    6DG5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          6 
_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         90 
_cell.entry_id            6DG5 
_cell.length_a            65.125 
_cell.length_b            67.914 
_cell.length_c            172.084 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DG5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 2 21' 
#
_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,I 
_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 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
4 oligosaccharide 
5 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
3 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
4 ? 5 4 3 MAN BMA C1 O1 . O6 HO6 . sing 
5 ? 5 5 4 MAN MAN C1 O1 . O6 HO6 . sing 
6 ? 5 6 3 MAN BMA C1 O1 . O3 HO3 . sing 
7 ? 5 7 1 FUC NAG 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
4 n D NAG 1 D 1 NAG B 238 NAG 
4 n D NAG 2 D 2 NAG B 239 NAG 
5 n E NAG 1 E 1 NAG B 243 NAG 
5 n E NAG 2 E 2 NAG B 244 NAG 
5 n E BMA 3 E 3 BMA B 249 BMA 
5 n E MAN 4 E 4 MAN B 251 MAN 
5 n E MAN 5 E 5 MAN B 252 MAN 
5 n E MAN 6 E 6 MAN B 250 MAN 
5 n E FUC 7 E 7 FUC B 248 FUC 
#
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 5 B CYS 31 1_555 B SG CYS 97 B CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf2 B SG CYS 10 B CYS 36 1_555 B SG CYS 20 B CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 B SG CYS 33 B CYS 59 1_555 B SG CYS 85 B CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf4 B SG CYS 48 B CYS 74 1_555 B SG CYS 60 B CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf5 C SG CYS 7 C CYS 62 1_555 C SG CYS 17 C CYS 72 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf6 C SG CYS 47 C CYS 102 1_555 C SG CYS 60 C CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf7 C SG CYS 128 C CYS 183 1_555 C SG CYS 177 C CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
covale ? covale1 B ND2 ASN 17 B ASN 43 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale2 B ND2 ASN 124 B ASN 150 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
covale ? covale3 C ND2 ASN 16 C ASN 71 1_555 G C1 NAG . C NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? 
covale ? covale4 C ND2 ASN 29 C ASN 84 1_555 F C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale6 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale7 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale8 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale9 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale10 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale11 E O6 MAN . E MAN 4 1_555 E C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
#
_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                     6DG5 
_atom_sites.fract_transf_matrix[1][1]    0.015355 
_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]    0.014725 
_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]    0.005811 
_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 6 NAG C 1 301 249 NAG NAG . 
G 6 NAG C 1 302 250 NAG NAG . 
H 7 HOH B 1 401 4 HOH HOH . 
H 7 HOH B 2 402 1 HOH HOH . 
H 7 HOH B 3 403 6 HOH HOH . 
H 7 HOH B 4 404 8 HOH HOH . 
H 7 HOH B 5 405 7 HOH HOH . 
H 7 HOH B 6 406 2 HOH HOH . 
H 7 HOH B 7 407 3 HOH HOH . 
H 7 HOH B 8 408 5 HOH HOH . 
I 7 HOH C 1 401 14 HOH HOH . 
I 7 HOH C 2 402 13 HOH HOH . 
I 7 HOH C 3 403 10 HOH HOH . 
I 7 HOH C 4 404 12 HOH HOH . 
I 7 HOH C 5 405 11 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 -2.46 1.13 -26.607 1 58.22 ? C1 NAG 301 C 1 
HETATM 2 C C2 NAG . . . F 6 -3.607 1.515 -25.678 1 61.62 ? C2 NAG 301 C 1 
HETATM 3 C C3 NAG . . . F 6 -4.887 0.812 -26.114 1 62.79 ? C3 NAG 301 C 1 
HETATM 4 C C4 NAG . . . F 6 -5.174 1.097 -27.583 1 57.45 ? C4 NAG 301 C 1 
HETATM 5 C C5 NAG . . . F 6 -3.96 0.758 -28.443 1 49.26 ? C5 NAG 301 C 1 
HETATM 6 C C6 NAG . . . F 6 -4.13 1.174 -29.884 1 45.09 ? C6 NAG 301 C 1 
HETATM 7 C C7 NAG . . . F 6 -3.147 2.131 -23.349 1 68.44 ? C7 NAG 301 C 1 
HETATM 8 C C8 NAG . . . F 6 -2.827 1.631 -21.972 1 77.2 ? C8 NAG 301 C 1 
HETATM 9 N N2 NAG . . . F 6 -3.295 1.197 -24.293 1 66.85 ? N2 NAG 301 C 1 
HETATM 10 O O3 NAG . . . F 6 -5.97 1.249 -25.302 1 66.28 ? O3 NAG 301 C 1 
HETATM 11 O O4 NAG . . . F 6 -6.282 0.317 -28.018 1 58.16 ? O4 NAG 301 C 1 
HETATM 12 O O5 NAG . . . F 6 -2.806 1.455 -27.955 1 56.07 ? O5 NAG 301 C 1 
HETATM 13 O O6 NAG . . . F 6 -5.128 0.397 -30.531 1 51.23 ? O6 NAG 301 C 1 
HETATM 14 O O7 NAG . . . F 6 -3.266 3.326 -23.595 1 60.69 ? O7 NAG 301 C 1 
#
_model_server_stats.io_time_ms              85 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#