data_8WDR # _model_server_result.job_id p3uO2YdzjuT7GXlwuQNC1w _model_server_result.datetime_utc '2024-11-08 14:59:39' _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 8wdr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":902}' # _entry.id 8WDR # _exptl.entry_id 8WDR _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 8WDR _cell.length_a 123.583 _cell.length_b 135.407 _cell.length_c 154.48 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8WDR _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_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,I,J,K,L,M 1 1 C,D,F,G,H,N,O,P,Q 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 J N N ? 6 K N N ? 6 L N N ? 6 M N N ? 6 O N N ? 6 P N N ? 6 Q 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 3 n G NAG 1 G 1 NAG C 819 NAG 3 n G NAG 2 G 2 NAG C 822 NAG 3 n H NAG 1 H 1 NAG C 820 NAG 3 n H NAG 2 H 2 NAG C 823 NAG # 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 344 A CYS 344 1_555 A SG CYS 361 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 530 A CYS 530 1_555 A SG CYS 542 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf4 B SG CYS 36 B CYS 336 1_555 B SG CYS 61 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 79 B CYS 379 1_555 B SG CYS 132 B CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 91 B CYS 391 1_555 B SG CYS 225 B CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 B SG CYS 180 B CYS 480 1_555 B SG CYS 188 B CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 C SG CYS 133 C CYS 133 1_555 C SG CYS 141 C CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 C SG CYS 344 C CYS 344 1_555 C SG CYS 361 C CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 C SG CYS 530 C CYS 530 1_555 C SG CYS 542 C CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf11 D SG CYS 36 D CYS 336 1_555 D SG CYS 61 D CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf12 D SG CYS 79 D CYS 379 1_555 D SG CYS 132 D CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf13 D SG CYS 91 D CYS 391 1_555 D SG CYS 225 D CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf14 D SG CYS 180 D CYS 480 1_555 D SG CYS 188 D CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 53 A ASN 53 1_555 K C1 NAG . A NAG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 A ND2 ASN 90 A ASN 90 1_555 J C1 NAG . A NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 103 A ASN 103 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 A ND2 ASN 322 A ASN 322 1_555 L C1 NAG . A NAG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B ND2 ASN 43 B ASN 343 1_555 M C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale6 C ND2 ASN 53 C ASN 53 1_555 O C1 NAG . C NAG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 C ND2 ASN 90 C ASN 90 1_555 P C1 NAG . C NAG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 C ND2 ASN 103 C ASN 103 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 C ND2 ASN 322 C ASN 322 1_555 Q C1 NAG . C NAG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 C ND2 ASN 432 C ASN 432 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale11 C ND2 ASN 546 C ASN 546 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale13 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale14 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale15 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale16 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 A NE2 HIS 374 A HIS 374 1_555 I ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc2 A NE2 HIS 378 A HIS 378 1_555 I ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc3 A OE1 GLU 402 A GLU 402 1_555 I ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc4 A OE2 GLU 402 A GLU 402 1_555 I ZN ZN . A ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc5 C NE2 HIS 374 C HIS 374 1_555 N ZN ZN . C ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc6 C NE2 HIS 378 C HIS 378 1_555 N ZN ZN . C ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc7 C OE2 GLU 402 C GLU 402 1_555 N ZN ZN . C ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? # _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 8WDR _atom_sites.fract_transf_matrix[1][1] 0.008092 _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] 0.007385 _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] 0.006473 _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 I 5 ZN A 1 901 701 ZN ZN . J 6 NAG A 1 902 815 NAG NAG . K 6 NAG A 1 903 816 NAG NAG . L 6 NAG A 1 904 819 NAG NAG . M 6 NAG B 1 601 528 NAG NAG . N 5 ZN C 1 901 701 ZN ZN . O 6 NAG C 1 902 814 NAG NAG . P 6 NAG C 1 903 815 NAG NAG . Q 6 NAG C 1 904 821 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 . . . O 6 2.254 -27.891 37.07 1 178.13 ? C1 NAG 902 C 1 HETATM 2 C C2 NAG . . . O 6 1.88 -26.521 36.454 1 172.86 ? C2 NAG 902 C 1 HETATM 3 C C3 NAG . . . O 6 2.219 -26.478 34.955 1 174.5 ? C3 NAG 902 C 1 HETATM 4 C C4 NAG . . . O 6 3.629 -26.979 34.68 1 186.41 ? C4 NAG 902 C 1 HETATM 5 C C5 NAG . . . O 6 3.808 -28.351 35.304 1 182.39 ? C5 NAG 902 C 1 HETATM 6 C C6 NAG . . . O 6 5.195 -28.917 35.111 1 169.6 ? C6 NAG 902 C 1 HETATM 7 C C7 NAG . . . O 6 -0.138 -25.107 36.306 1 185.28 ? C7 NAG 902 C 1 HETATM 8 C C8 NAG . . . O 6 -1.61 -25.036 36.569 1 177.32 ? C8 NAG 902 C 1 HETATM 9 N N2 NAG . . . O 6 0.463 -26.252 36.652 1 183.79 ? N2 NAG 902 C 1 HETATM 10 O O3 NAG . . . O 6 2.104 -25.14 34.483 1 177.35 ? O3 NAG 902 C 1 HETATM 11 O O4 NAG . . . O 6 3.846 -27.068 33.276 1 189.11 ? O4 NAG 902 C 1 HETATM 12 O O5 NAG . . . O 6 3.597 -28.235 36.714 1 175.29 ? O5 NAG 902 C 1 HETATM 13 O O6 NAG . . . O 6 6.165 -28.193 35.854 1 153.98 ? O6 NAG 902 C 1 HETATM 14 O O7 NAG . . . O 6 0.477 -24.169 35.807 1 180.55 ? O7 NAG 902 C 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #