data_8WDS # _model_server_result.job_id EQS57ya-o28KsvMG2xqMDQ _model_server_result.datetime_utc '2024-11-04 20:50:55' _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 8wds # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":601}' # _entry.id 8WDS # _exptl.entry_id 8WDS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 7 _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 8WDS _cell.length_a 122.695 _cell.length_b 137.349 _cell.length_c 154.765 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WDS _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab (z,x,y)' _symmetry.space_group_name_H-M 'P 2 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,G,H,I,J 1 1 C,D,F,K,L,M,N,O 2 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 H N N ? 6 I N N ? 6 J N N ? 6 L N N ? 6 M N N ? 6 N N N ? 6 O 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 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . 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 E NAG 1 E 1 NAG A 817 NAG 3 n E NAG 2 E 2 NAG A 818 NAG 4 n F NAG 1 F 1 NAG C 816 NAG 4 n F NAG 2 F 2 NAG C 817 NAG 4 n F BMA 3 F 3 BMA C 818 BMA # 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 133 A CYS 133 1_555 A SG CYS 141 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 344 A CYS 344 1_555 A SG CYS 361 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 530 A CYS 530 1_555 A SG CYS 542 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 B SG CYS 36 B CYS 336 1_555 B SG CYS 61 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 B SG CYS 79 B CYS 379 1_555 B SG CYS 132 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 B SG CYS 91 B CYS 391 1_555 B SG CYS 225 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 B SG CYS 180 B CYS 480 1_555 B SG CYS 188 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 C SG CYS 133 C CYS 133 1_555 C SG CYS 141 C CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 C SG CYS 344 C CYS 344 1_555 C SG CYS 361 C CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf10 C SG CYS 530 C CYS 530 1_555 C SG CYS 542 C CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 D SG CYS 36 D CYS 336 1_555 D SG CYS 61 D CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 D SG CYS 79 D CYS 379 1_555 D SG CYS 132 D CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 D SG CYS 91 D CYS 391 1_555 D SG CYS 225 D CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf14 D SG CYS 180 D CYS 480 1_555 D SG CYS 188 D CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 53 A ASN 53 1_555 I C1 NAG . A NAG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale2 A ND2 ASN 90 A ASN 90 1_555 H C1 NAG . A NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 A ND2 ASN 103 A ASN 103 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale4 B ND2 ASN 43 B ASN 343 1_555 J C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 C ND2 ASN 53 C ASN 53 1_555 L C1 NAG . C NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 C ND2 ASN 90 C ASN 90 1_555 M C1 NAG . C NAG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale7 C ND2 ASN 103 C ASN 103 1_555 O C1 NAG . C NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale8 C ND2 ASN 432 C ASN 432 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale9 C ND2 ASN 546 C ASN 546 1_555 N C1 NAG . C NAG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale11 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale12 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? metalc ? metalc1 A NE2 HIS 374 A HIS 374 1_555 G ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc2 A NE2 HIS 378 A HIS 378 1_555 G ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc3 A OE2 GLU 402 A GLU 402 1_555 G ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc4 C NE2 HIS 374 C HIS 374 1_555 K ZN ZN . C ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc5 C NE2 HIS 378 C HIS 378 1_555 K ZN ZN . C ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc6 C OE1 GLU 402 C GLU 402 1_555 K ZN ZN . C ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc7 C OE2 GLU 402 C GLU 402 1_555 K ZN ZN . C ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? # _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 8WDS _atom_sites.fract_transf_matrix[1][1] 0.00815 _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] 0.007281 _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] 0.006461 _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 G 5 ZN A 1 901 701 ZN ZN . H 6 NAG A 1 902 815 NAG NAG . I 6 NAG A 1 903 816 NAG NAG . J 6 NAG B 1 601 528 NAG NAG . K 5 ZN C 1 901 701 ZN ZN . L 6 NAG C 1 902 814 NAG NAG . M 6 NAG C 1 903 815 NAG NAG . N 6 NAG C 1 904 819 NAG NAG . O 6 NAG C 1 905 820 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 6 -47.455 -2.554 44.446 1 150.06 ? C1 NAG 601 B 1 HETATM 2 C C2 NAG . . . J 6 -48.532 -2.11 45.438 1 153.42 ? C2 NAG 601 B 1 HETATM 3 C C3 NAG . . . J 6 -48.193 -2.603 46.844 1 152.21 ? C3 NAG 601 B 1 HETATM 4 C C4 NAG . . . J 6 -47.931 -4.104 46.838 1 153.48 ? C4 NAG 601 B 1 HETATM 5 C C5 NAG . . . J 6 -46.879 -4.454 45.791 1 149.93 ? C5 NAG 601 B 1 HETATM 6 C C6 NAG . . . J 6 -46.657 -5.942 45.653 1 143.57 ? C6 NAG 601 B 1 HETATM 7 C C7 NAG . . . J 6 -49.721 -0.037 44.862 1 155.32 ? C7 NAG 601 B 1 HETATM 8 C C8 NAG . . . J 6 -49.712 1.46 44.952 1 149.82 ? C8 NAG 601 B 1 HETATM 9 N N2 NAG . . . J 6 -48.684 -0.663 45.429 1 153.87 ? N2 NAG 601 B 1 HETATM 10 O O3 NAG . . . J 6 -49.274 -2.303 47.719 1 151.43 ? O3 NAG 601 B 1 HETATM 11 O O4 NAG . . . J 6 -47.478 -4.533 48.117 1 151.7 ? O4 NAG 601 B 1 HETATM 12 O O5 NAG . . . J 6 -47.302 -3.98 44.505 1 149.77 ? O5 NAG 601 B 1 HETATM 13 O O6 NAG . . . J 6 -47.69 -6.54 44.882 1 145.13 ? O6 NAG 601 B 1 HETATM 14 O O7 NAG . . . J 6 -50.626 -0.651 44.302 1 154.49 ? O7 NAG 601 B 1 # _model_server_stats.io_time_ms 37 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #