data_3CDZ # _model_server_result.job_id VjCKl-Sv3NpJwSHQJTQP6g _model_server_result.datetime_utc '2025-01-02 17:19:51' _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 3cdz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":2333}' # _entry.id 3CDZ # _exptl.entry_id 3CDZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _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 3CDZ _cell.length_a 134.113 _cell.length_b 134.113 _cell.length_c 349.76 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CDZ _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 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 # _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 ? 7 G N N ? 7 H 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 ? 4 2 1 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 MAN MAN C1 O1 . O3 HO3 . sing 4 ? 4 4 2 MAN MAN 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 3 n C NAG 1 C 1 NAG A 755 NAG 3 n C NAG 2 C 2 NAG A 756 NAG 4 n D NAG 1 D 1 NAG B 2335 NAG 4 n D MAN 2 D 2 MAN B 2336 MAN 4 n D MAN 3 D 3 MAN B 2337 MAN 4 n D MAN 4 D 4 MAN B 2338 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 153 A CYS 153 1_555 A SG CYS 179 A CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf2 A SG CYS 248 A CYS 248 1_555 A SG CYS 329 A CYS 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf3 A SG CYS 528 A CYS 528 1_555 A SG CYS 554 A CYS 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 A SG CYS 630 A CYS 630 1_555 A SG CYS 711 A CYS 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 B SG CYS 184 B CYS 1832 1_555 B SG CYS 210 B CYS 1858 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 B SG CYS 251 B CYS 1899 1_555 B SG CYS 255 B CYS 1903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf7 B SG CYS 373 B CYS 2021 1_555 B SG CYS 521 B CYS 2169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf8 B SG CYS 526 B CYS 2174 1_555 B SG CYS 678 B CYS 2326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 A ND2 ASN 239 A ASN 239 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 B ND2 ASN 162 B ASN 1810 1_555 G C1 NAG . B NAG 2333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.537 ? covale ? covale3 B ND2 ASN 470 B ASN 2118 1_555 H C1 NAG . B NAG 2334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.25 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 MAN . D MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale6 D O3 MAN . D MAN 2 1_555 D C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale7 D O6 MAN . D MAN 2 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? metalc ? metalc1 A O LYS 107 A LYS 107 1_555 F CA CA . A CA 758 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc2 A O GLU 122 A GLU 122 1_555 F CA CA . A CA 758 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? metalc ? metalc3 A OD1 ASP 125 A ASP 125 1_555 F CA CA . A CA 758 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? metalc ? metalc4 A OD1 ASP 126 A ASP 126 1_555 F CA CA . A CA 758 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? metalc ? metalc5 A OD2 ASP 126 A ASP 126 1_555 F CA CA . A CA 758 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? metalc ? metalc6 A ND1 HIS 267 A HIS 267 1_555 E CU CU . A CU 757 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc7 I CU CU . B CU 1 1_555 B ND1 HIS 306 B HIS 1954 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc8 I CU CU . B CU 1 1_555 B ND1 HIS 357 B HIS 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 3CDZ _atom_sites.fract_transf_matrix[1][1] 0.007456 _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] 0.007456 _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] 0.002859 _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 CU A 1 757 757 CU CU . F 6 CA A 1 758 758 CA CA . G 7 NAG B 1 2333 2333 NAG NAG . H 7 NAG B 1 2334 2334 NAG NAG . I 5 CU B 1 1 1 CU CU . # 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 . . . G 7 2.726 -34.155 80.541 1 210.9 ? C1 NAG 2333 B 1 HETATM 2 C C2 NAG . . . G 7 3.257 -32.784 80.958 1 213.08 ? C2 NAG 2333 B 1 HETATM 3 C C3 NAG . . . G 7 3.122 -32.649 82.482 1 213.3 ? C3 NAG 2333 B 1 HETATM 4 C C4 NAG . . . G 7 1.774 -33.154 83.046 1 213.28 ? C4 NAG 2333 B 1 HETATM 5 C C5 NAG . . . G 7 0.81 -33.91 82.081 1 213.01 ? C5 NAG 2333 B 1 HETATM 6 C C6 NAG . . . G 7 -0.509 -33.116 81.857 1 213.18 ? C6 NAG 2333 B 1 HETATM 7 C C7 NAG . . . G 7 5.189 -31.487 80.006 1 214.04 ? C7 NAG 2333 B 1 HETATM 8 C C8 NAG . . . G 7 4.389 -30.615 79.063 1 213.82 ? C8 NAG 2333 B 1 HETATM 9 N N2 NAG . . . G 7 4.634 -32.62 80.483 1 213.6 ? N2 NAG 2333 B 1 HETATM 10 O O3 NAG . . . G 7 3.282 -31.292 82.858 1 213.71 ? O3 NAG 2333 B 1 HETATM 11 O O4 NAG . . . G 7 2.025 -33.955 84.198 1 212.99 ? O4 NAG 2333 B 1 HETATM 12 O O5 NAG . . . G 7 1.324 -34.237 80.773 1 212.04 ? O5 NAG 2333 B 1 HETATM 13 O O6 NAG . . . G 7 -1.061 -32.66 83.111 1 213.25 ? O6 NAG 2333 B 1 HETATM 14 O O7 NAG . . . G 7 6.341 -31.152 80.308 1 214.5 ? O7 NAG 2333 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 34 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #