data_6ZDG
#
_model_server_result.job_id            Bg0SvDj9E6YfWuhXpgdC4g 
_model_server_result.datetime_utc      '2024-10-12 04:28:18' 
_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          6zdg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":601}' 
#
_entry.id    6ZDG 
#
_exptl.entry_id    6ZDG 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    3 
_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            6ZDG 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6ZDG 
_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    nonameric 
_pdbx_struct_assembly.oligomeric_count      9 
_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
? 4 J N N 
? 4 K N N 
? 4 L N 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 4 E CYS 336 1_555 A SG CYS 29 E CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 47 E CYS 379 1_555 A SG CYS 100 E CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf3 A SG CYS 59 E CYS 391 1_555 A SG CYS 193 E CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf4 A SG CYS 148 E CYS 480 1_555 A SG CYS 156 E CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf6 B SG CYS 148 H CYS 148 1_555 B SG CYS 204 H CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf7 B SG CYS 224 H CYS 224 1_555 C SG CYS 215 L CYS 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
disulf ? disulf8 C SG CYS 23 L CYS 23 1_555 C SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf9 C SG CYS 135 L CYS 135 1_555 C SG CYS 195 L CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf10 D SG CYS 4 A CYS 336 1_555 D SG CYS 29 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf11 D SG CYS 47 A CYS 379 1_555 D SG CYS 100 A CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf12 D SG CYS 59 A CYS 391 1_555 D SG CYS 193 A CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf13 D SG CYS 148 A CYS 480 1_555 D SG CYS 156 A CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf14 E SG CYS 22 B CYS 22 1_555 E SG CYS 96 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf15 E SG CYS 148 B CYS 148 1_555 E SG CYS 204 B CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf16 E SG CYS 224 B CYS 224 1_555 F SG CYS 215 C CYS 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf17 F SG CYS 23 C CYS 23 1_555 F SG CYS 88 C CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf18 F SG CYS 135 C CYS 135 1_555 F SG CYS 195 C CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf19 G SG CYS 4 D CYS 336 1_555 G SG CYS 29 D CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf20 G SG CYS 47 D CYS 379 1_555 G SG CYS 100 D CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf21 G SG CYS 59 D CYS 391 1_555 G SG CYS 193 D CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf22 G SG CYS 148 D CYS 480 1_555 G SG CYS 156 D CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf23 H SG CYS 22 F CYS 22 1_555 H SG CYS 96 F CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf24 H SG CYS 148 F CYS 148 1_555 H SG CYS 204 F CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf25 H SG CYS 224 F CYS 224 1_555 I SG CYS 215 G CYS 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf26 I SG CYS 23 G CYS 23 1_555 I SG CYS 88 G CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf27 I SG CYS 135 G CYS 135 1_555 I SG CYS 195 G CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
covale ? covale1 A ND2 ASN 11 E ASN 343 1_555 J C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale2 D ND2 ASN 11 A ASN 343 1_555 K C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale3 G ND2 ASN 11 D ASN 343 1_555 L C1 NAG . D NAG 601 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_
_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                     6ZDG 
_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
J 4 NAG E 1 601 601 NAG NAG . 
K 4 NAG A 1 601 601 NAG NAG . 
L 4 NAG D 1 601 601 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 . . . J 4 251.42 276.468 262.122 1 170.77 ? C1 NAG 601 E 1 
HETATM 2 C C2 NAG . . . J 4 252.341 277.575 261.614 1 170.77 ? C2 NAG 601 E 1 
HETATM 3 C C3 NAG . . . J 4 253.794 277.245 261.943 1 170.77 ? C3 NAG 601 E 1 
HETATM 4 C C4 NAG . . . J 4 253.951 276.949 263.428 1 170.77 ? C4 NAG 601 E 1 
HETATM 5 C C5 NAG . . . J 4 252.965 275.867 263.853 1 170.77 ? C5 NAG 601 E 1 
HETATM 6 C C6 NAG . . . J 4 252.986 275.598 265.339 1 170.77 ? C6 NAG 601 E 1 
HETATM 7 C C7 NAG . . . J 4 252.503 278.911 259.563 1 170.77 ? C7 NAG 601 E 1 
HETATM 8 C C8 NAG . . . J 4 252.269 278.941 258.084 1 170.77 ? C8 NAG 601 E 1 
HETATM 9 N N2 NAG . . . J 4 252.175 277.774 260.185 1 170.77 ? N2 NAG 601 E 1 
HETATM 10 O O3 NAG . . . J 4 254.623 278.342 261.576 1 170.77 ? O3 NAG 601 E 1 
HETATM 11 O O4 NAG . . . J 4 255.276 276.509 263.701 1 170.77 ? O4 NAG 601 E 1 
HETATM 12 O O5 NAG . . . J 4 251.628 276.272 263.524 1 170.77 ? O5 NAG 601 E 1 
HETATM 13 O O6 NAG . . . J 4 251.883 274.794 265.735 1 170.77 ? O6 NAG 601 E 1 
HETATM 14 O O7 NAG . . . J 4 252.969 279.871 260.169 1 170.77 ? O7 NAG 601 E 1 
HETATM 15 H H2 NAG . . . J 4 252.107 278.403 262.075 1 170.77 ? H2 NAG 601 E 1 
HETATM 16 H H3 NAG . . . J 4 254.063 276.459 261.431 1 170.77 ? H3 NAG 601 E 1 
HETATM 17 H H4 NAG . . . J 4 253.771 277.762 263.937 1 170.77 ? H4 NAG 601 E 1 
HETATM 18 H H5 NAG . . . J 4 253.173 275.041 263.376 1 170.77 ? H5 NAG 601 E 1 
HETATM 19 H H61 NAG . . . J 4 252.949 276.449 265.817 1 170.77 ? H61 NAG 601 E 1 
HETATM 20 H H62 NAG . . . J 4 253.816 275.139 265.568 1 170.77 ? H62 NAG 601 E 1 
HETATM 21 H H81 NAG . . . J 4 252.442 279.84 257.745 1 170.77 ? H81 NAG 601 E 1 
HETATM 22 H H82 NAG . . . J 4 251.344 278.693 257.897 1 170.77 ? H82 NAG 601 E 1 
HETATM 23 H H83 NAG . . . J 4 252.869 278.306 257.649 1 170.77 ? H83 NAG 601 E 1 
HETATM 24 H HN2 NAG . . . J 4 251.834 277.089 259.688 1 170.77 ? HN2 NAG 601 E 1 
HETATM 25 H HO3 NAG . . . J 4 255.47 278.145 261.757 1 170.77 ? HO3 NAG 601 E 1 
HETATM 26 H HO4 NAG . . . J 4 255.423 276.54 264.576 1 170.77 ? HO4 NAG 601 E 1 
HETATM 27 H HO6 NAG . . . J 4 251.259 274.821 265.104 1 170.77 ? HO6 NAG 601 E 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    48 
_model_server_stats.query_time_ms           300 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           27 
#