data_3D5O # _model_server_result.job_id ZsHOC3nEg2nYs2tf6KVjog _model_server_result.datetime_utc '2024-11-14 17:31:18' _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 3d5o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":208}' # _entry.id 3D5O # _exptl.entry_id 3D5O _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 5 _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 3D5O _cell.length_a 64.197 _cell.length_b 143.477 _cell.length_c 161.588 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D5O _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression F,AA,BA,HA 1 1 D,S,T,U,V,FA 1 2 A,B,C,E,G,H,I,J,K,L,M,N,O,P,Q,R,W,X,Y,Z,CA,DA,EA,GA 1 3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'crystal symmetry operation' 1_455 x-1,y,z 1 0 0 0 1 0 0 0 1 -64.197 0 0 2 'crystal symmetry operation' 3_554 -x,y+1/2,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 71.7385 -80.794 3 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 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 N N N ? 4 R N N ? 4 V N N ? 4 Z 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 36 A CYS 36 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf2 B SG CYS 36 B CYS 36 1_555 B SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 C SG CYS 36 C CYS 36 1_555 C SG CYS 95 C CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf4 D SG CYS 36 D CYS 36 1_555 D SG CYS 95 D CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf5 E SG CYS 36 E CYS 36 1_555 E SG CYS 95 E CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf6 F SG CYS 26 F CYS 26 1_555 F SG CYS 68 F CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 F SG CYS 107 F CYS 107 1_555 F SG CYS 151 F CYS 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 32 A ASN 32 1_555 J C1 NAG . A NAG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 B ND2 ASN 32 B ASN 32 1_555 N C1 NAG . B NAG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale3 C ND2 ASN 32 C ASN 32 1_555 R C1 NAG . C NAG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale4 D ND2 ASN 32 D ASN 32 1_555 V C1 NAG . D NAG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale5 E ND2 ASN 32 E ASN 32 1_555 Z C1 NAG . E NAG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? # _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 250 n n C1 O1 NAG sing 251 n n C1 O5 NAG sing 252 n n C1 H1 NAG sing 253 n n C2 C3 NAG sing 254 n n C2 N2 NAG sing 255 n n C2 H2 NAG sing 256 n n C3 C4 NAG sing 257 n n C3 O3 NAG sing 258 n n C3 H3 NAG sing 259 n n C4 C5 NAG sing 260 n n C4 O4 NAG sing 261 n n C4 H4 NAG sing 262 n n C5 C6 NAG sing 263 n n C5 O5 NAG sing 264 n n C5 H5 NAG sing 265 n n C6 O6 NAG sing 266 n n C6 H61 NAG sing 267 n n C6 H62 NAG sing 268 n n C7 C8 NAG sing 269 n n C7 N2 NAG sing 270 n n C7 O7 NAG doub 271 n n C8 H81 NAG sing 272 n n C8 H82 NAG sing 273 n n C8 H83 NAG sing 274 n n N2 HN2 NAG sing 275 n n O1 HO1 NAG sing 276 n n O3 HO3 NAG sing 277 n n O4 HO4 NAG sing 278 n n O6 HO6 NAG sing 279 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 3D5O _atom_sites.fract_transf_matrix[1][1] 0.015577 _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] 0.00697 _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] 0.006189 _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 3 SO4 A 1 205 1 SO4 SO4 . H 3 SO4 A 1 206 2 SO4 SO4 . I 3 SO4 A 1 207 3 SO4 SO4 . J 4 NAG A 1 208 1 NAG NAG . K 3 SO4 B 1 205 4 SO4 SO4 . L 3 SO4 B 1 206 5 SO4 SO4 . M 3 SO4 B 1 207 6 SO4 SO4 . N 4 NAG B 1 208 2 NAG NAG . O 3 SO4 C 1 205 7 SO4 SO4 . P 3 SO4 C 1 206 8 SO4 SO4 . Q 3 SO4 C 1 207 9 SO4 SO4 . R 4 NAG C 1 208 3 NAG NAG . S 3 SO4 D 1 205 10 SO4 SO4 . T 3 SO4 D 1 206 11 SO4 SO4 . U 3 SO4 D 1 207 12 SO4 SO4 . V 4 NAG D 1 208 4 NAG NAG . W 3 SO4 E 1 205 13 SO4 SO4 . X 3 SO4 E 1 206 14 SO4 SO4 . Y 3 SO4 E 1 207 15 SO4 SO4 . Z 4 NAG E 1 208 5 NAG NAG . AA 3 SO4 F 1 178 16 SO4 SO4 . BA 5 GOL F 1 179 1 GOL GOL . CA 6 HOH A 1 209 6 HOH HOH . CA 6 HOH A 2 210 13 HOH HOH . CA 6 HOH A 3 211 35 HOH HOH . DA 6 HOH B 1 209 7 HOH HOH . DA 6 HOH B 2 210 8 HOH HOH . DA 6 HOH B 3 211 10 HOH HOH . DA 6 HOH B 4 212 15 HOH HOH . DA 6 HOH B 5 213 16 HOH HOH . DA 6 HOH B 6 214 17 HOH HOH . DA 6 HOH B 7 215 20 HOH HOH . DA 6 HOH B 8 216 21 HOH HOH . DA 6 HOH B 9 217 22 HOH HOH . DA 6 HOH B 10 218 24 HOH HOH . DA 6 HOH B 11 219 27 HOH HOH . DA 6 HOH B 12 220 28 HOH HOH . DA 6 HOH B 13 221 36 HOH HOH . EA 6 HOH C 1 209 9 HOH HOH . EA 6 HOH C 2 210 11 HOH HOH . EA 6 HOH C 3 211 19 HOH HOH . EA 6 HOH C 4 212 23 HOH HOH . EA 6 HOH C 5 213 25 HOH HOH . EA 6 HOH C 6 214 32 HOH HOH . FA 6 HOH D 1 209 30 HOH HOH . FA 6 HOH D 2 210 31 HOH HOH . FA 6 HOH D 3 211 33 HOH HOH . GA 6 HOH E 1 209 12 HOH HOH . HA 6 HOH F 1 180 14 HOH HOH . HA 6 HOH F 2 181 18 HOH HOH . HA 6 HOH F 3 182 26 HOH HOH . HA 6 HOH F 4 183 29 HOH HOH . HA 6 HOH F 5 184 34 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 . . . Z 4 27.49 30.099 -19.195 1 78.76 ? C1 NAG 208 E 1 HETATM 2 C C2 NAG . . . Z 4 29.004 30.356 -19.012 1 76.89 ? C2 NAG 208 E 1 HETATM 3 C C3 NAG . . . Z 4 29.555 31.387 -19.993 1 84.15 ? C3 NAG 208 E 1 HETATM 4 C C4 NAG . . . Z 4 29.182 30.977 -21.401 1 80.7 ? C4 NAG 208 E 1 HETATM 5 C C5 NAG . . . Z 4 27.66 30.92 -21.49 1 72.97 ? C5 NAG 208 E 1 HETATM 6 C C6 NAG . . . Z 4 27.216 30.553 -22.896 1 71.85 ? C6 NAG 208 E 1 HETATM 7 C C7 NAG . . . Z 4 30.253 30.221 -16.955 1 84.49 ? C7 NAG 208 E 1 HETATM 8 C C8 NAG . . . Z 4 31.678 30.365 -17.471 1 67.75 ? C8 NAG 208 E 1 HETATM 9 N N2 NAG . . . Z 4 29.284 30.801 -17.661 1 77.42 ? N2 NAG 208 E 1 HETATM 10 O O3 NAG . . . Z 4 30.97 31.451 -19.876 1 91.86 ? O3 NAG 208 E 1 HETATM 11 O O4 NAG . . . Z 4 29.706 31.913 -22.335 1 87.77 ? O4 NAG 208 E 1 HETATM 12 O O5 NAG . . . Z 4 27.15 29.898 -20.592 1 78.95 ? O5 NAG 208 E 1 HETATM 13 O O6 NAG . . . Z 4 25.802 30.557 -23.015 1 82.95 ? O6 NAG 208 E 1 HETATM 14 O O7 NAG . . . Z 4 30.039 29.593 -15.915 1 81.52 ? O7 NAG 208 E 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #