data_4P8Q # _model_server_result.job_id mmk3DeawfSDiEv2lRSnFtA _model_server_result.datetime_utc '2024-11-16 10:05:28' _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 4p8q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":1106}' # _entry.id 4P8Q # _exptl.entry_id 4P8Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 11 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 115.12 _cell.angle_gamma 90 _cell.entry_id 4P8Q _cell.length_a 68.323 _cell.length_b 256.051 _cell.length_c 71.132 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4P8Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _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,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 ? 4 I N N ? 4 J N N ? 4 K N N ? 4 L N N ? 4 M N N ? 4 N N N ? 4 Q N N ? 4 R N N ? 4 S N N ? 4 T N N ? 4 U N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 2 n C NAG 1 C 1 NAG A 1102 NAG 2 n C NAG 2 C 2 NAG A 1103 NAG 2 n D NAG 1 D 1 NAG A 1107 NAG 2 n D NAG 2 D 2 NAG A 1108 NAG 2 n E NAG 1 E 1 NAG B 1102 NAG 2 n E NAG 2 E 2 NAG B 1103 NAG 2 n F NAG 1 F 1 NAG B 1105 NAG 2 n F NAG 2 F 2 NAG B 1106 NAG 2 n G NAG 1 G 1 NAG B 1108 NAG 2 n G NAG 2 G 2 NAG B 1109 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 675 A CYS 828 1_555 A SG CYS 682 A CYS 835 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf2 B SG CYS 675 B CYS 828 1_555 B SG CYS 682 B CYS 835 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? covale ? covale1 A ND2 ASN 31 A ASN 184 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 A ND2 ASN 62 A ASN 215 1_555 I C1 NAG . A NAG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 103 A ASN 256 1_555 J C1 NAG . A NAG 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 A ND2 ASN 113 A ASN 266 1_555 K C1 NAG . A NAG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 A ND2 ASN 215 A ASN 368 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale6 A ND2 ASN 529 A ASN 682 1_555 L C1 NAG . A NAG 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale7 A ND2 ASN 607 A ASN 760 1_555 M C1 NAG . A NAG 1110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale8 A ND2 ASN 697 A ASN 850 1_555 N C1 NAG . A NAG 1111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale9 B ND2 ASN 31 B ASN 184 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale10 B ND2 ASN 62 B ASN 215 1_555 Q C1 NAG . B NAG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale11 B ND2 ASN 103 B ASN 256 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale12 B ND2 ASN 113 B ASN 266 1_555 R C1 NAG . B NAG 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale13 B ND2 ASN 215 B ASN 368 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale14 B ND2 ASN 529 B ASN 682 1_555 S C1 NAG . B NAG 1110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale15 B ND2 ASN 607 B ASN 760 1_555 T C1 NAG . B NAG 1111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale16 B ND2 ASN 697 B ASN 850 1_555 U C1 NAG . B NAG 1112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale17 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale18 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale19 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale20 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale21 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? metalc ? metalc1 A NE2 HIS 311 A HIS 464 1_555 H ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.923 ? metalc ? metalc2 A NE2 HIS 315 A HIS 468 1_555 H ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc3 A OE1 GLU 334 A GLU 487 1_555 H ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? metalc ? metalc4 A OE2 GLU 334 A GLU 487 1_555 H ZN ZN . A ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc5 H ZN ZN . A ZN 1101 1_555 O O UNL . A UNL 1112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc6 B NE2 HIS 311 B HIS 464 1_555 P ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc7 B NE2 HIS 315 B HIS 468 1_555 P ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc8 B OE1 GLU 334 B GLU 487 1_555 P ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? metalc ? metalc9 B OE2 GLU 334 B GLU 487 1_555 P ZN ZN . B ZN 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? metalc ? metalc10 P ZN ZN . B ZN 1101 1_555 V O UNL . B UNL 1113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 4P8Q _atom_sites.fract_transf_matrix[1][1] 0.014636 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006862 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003905 _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] 0.015527 _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 H 3 ZN A 1 1101 1101 ZN ZN . I 4 NAG A 1 1104 1104 NAG NAG . J 4 NAG A 1 1105 1105 NAG NAG . K 4 NAG A 1 1106 1106 NAG NAG . L 4 NAG A 1 1109 1109 NAG NAG . M 4 NAG A 1 1110 1110 NAG NAG . N 4 NAG A 1 1111 1111 NAG NAG . O 5 UNL A 1 1112 1112 UNL UNL . P 3 ZN B 1 1101 1101 ZN ZN . Q 4 NAG B 1 1104 1104 NAG NAG . R 4 NAG B 1 1107 1107 NAG NAG . S 4 NAG B 1 1110 1110 NAG NAG . T 4 NAG B 1 1111 1111 NAG NAG . U 4 NAG B 1 1112 1112 NAG NAG . V 5 UNL B 1 1113 1113 UNL UNL . W 6 HOH A 1 1201 1201 HOH HOH . W 6 HOH A 2 1202 1202 HOH HOH . W 6 HOH A 3 1203 1203 HOH HOH . W 6 HOH A 4 1204 1204 HOH HOH . W 6 HOH A 5 1205 1205 HOH HOH . W 6 HOH A 6 1206 1206 HOH HOH . W 6 HOH A 7 1207 1207 HOH HOH . W 6 HOH A 8 1208 1208 HOH HOH . W 6 HOH A 9 1209 1209 HOH HOH . W 6 HOH A 10 1210 1210 HOH HOH . W 6 HOH A 11 1211 1211 HOH HOH . W 6 HOH A 12 1212 1212 HOH HOH . W 6 HOH A 13 1213 1213 HOH HOH . W 6 HOH A 14 1214 1214 HOH HOH . W 6 HOH A 15 1215 1215 HOH HOH . W 6 HOH A 16 1216 1216 HOH HOH . W 6 HOH A 17 1217 1217 HOH HOH . W 6 HOH A 18 1218 1218 HOH HOH . W 6 HOH A 19 1219 1219 HOH HOH . W 6 HOH A 20 1220 1220 HOH HOH . W 6 HOH A 21 1221 1221 HOH HOH . W 6 HOH A 22 1222 1222 HOH HOH . W 6 HOH A 23 1223 1223 HOH HOH . W 6 HOH A 24 1224 1224 HOH HOH . W 6 HOH A 25 1225 1225 HOH HOH . W 6 HOH A 26 1226 1226 HOH HOH . W 6 HOH A 27 1227 1227 HOH HOH . W 6 HOH A 28 1228 1228 HOH HOH . W 6 HOH A 29 1229 1229 HOH HOH . W 6 HOH A 30 1230 1230 HOH HOH . W 6 HOH A 31 1231 1231 HOH HOH . W 6 HOH A 32 1232 1232 HOH HOH . W 6 HOH A 33 1233 1233 HOH HOH . W 6 HOH A 34 1234 1234 HOH HOH . W 6 HOH A 35 1235 1235 HOH HOH . W 6 HOH A 36 1236 1236 HOH HOH . W 6 HOH A 37 1237 1237 HOH HOH . W 6 HOH A 38 1238 1238 HOH HOH . W 6 HOH A 39 1239 1239 HOH HOH . W 6 HOH A 40 1240 1240 HOH HOH . W 6 HOH A 41 1241 1241 HOH HOH . W 6 HOH A 42 1242 1242 HOH HOH . W 6 HOH A 43 1243 1243 HOH HOH . W 6 HOH A 44 1244 1244 HOH HOH . W 6 HOH A 45 1245 1245 HOH HOH . X 6 HOH B 1 1201 1201 HOH HOH . X 6 HOH B 2 1202 1202 HOH HOH . X 6 HOH B 3 1203 1203 HOH HOH . X 6 HOH B 4 1204 1204 HOH HOH . X 6 HOH B 5 1205 1205 HOH HOH . X 6 HOH B 6 1206 1206 HOH HOH . X 6 HOH B 7 1207 1207 HOH HOH . X 6 HOH B 8 1208 1208 HOH HOH . X 6 HOH B 9 1209 1209 HOH HOH . X 6 HOH B 10 1210 1210 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 . . . K 4 63.801 4.152 36.198 1 110.44 ? C1 NAG 1106 A 1 HETATM 2 C C2 NAG . . . K 4 64.929 3.492 36.999 1 111.84 ? C2 NAG 1106 A 1 HETATM 3 C C3 NAG . . . K 4 64.436 3.228 38.423 1 112.42 ? C3 NAG 1106 A 1 HETATM 4 C C4 NAG . . . K 4 63.896 4.51 39.049 1 113.86 ? C4 NAG 1106 A 1 HETATM 5 C C5 NAG . . . K 4 62.762 5.068 38.19 1 114.2 ? C5 NAG 1106 A 1 HETATM 6 C C6 NAG . . . K 4 62.22 6.391 38.684 1 114.1 ? C6 NAG 1106 A 1 HETATM 7 C C7 NAG . . . K 4 66.56 1.745 36.381 1 111.9 ? C7 NAG 1106 A 1 HETATM 8 C C8 NAG . . . K 4 66.795 0.545 35.514 1 112.18 ? C8 NAG 1106 A 1 HETATM 9 N N2 NAG . . . K 4 65.317 2.249 36.352 1 111.97 ? N2 NAG 1106 A 1 HETATM 10 O O3 NAG . . . K 4 65.488 2.701 39.224 1 111.31 ? O3 NAG 1106 A 1 HETATM 11 O O4 NAG . . . K 4 63.435 4.25 40.372 1 115.16 ? O4 NAG 1106 A 1 HETATM 12 O O5 NAG . . . K 4 63.237 5.295 36.851 1 113.38 ? O5 NAG 1106 A 1 HETATM 13 O O6 NAG . . . K 4 61.162 6.859 37.856 1 113.22 ? O6 NAG 1106 A 1 HETATM 14 O O7 NAG . . . K 4 67.451 2.233 37.073 1 111.72 ? O7 NAG 1106 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 49 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #