data_6P9U # _model_server_result.job_id HTpx0LtphfmARxTlpsqA2w _model_server_result.datetime_utc '2024-11-07 04:33:49' _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 6p9u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":402}' # _entry.id 6P9U # _exptl.entry_id 6P9U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.04 _cell.angle_gamma 90 _cell.entry_id 6P9U _cell.length_a 136.32 _cell.length_b 44.232 _cell.length_c 136.187 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6P9U _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 2 1' # 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 PISA tetrameric 4 author_and_software_defined_assembly 3 PISA tetrameric 4 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J,T 1 1,2 C,D,K,L,M,N,U 2 1,3 E,F,O,P,Q,V,W 3 1,4 G,H,R,S,X 4 1,5 # 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 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_756 -x+2,y,-z+1 -1 0 0 0 1 0 0 0 -1 272.544924 0 136.186967 3 'crystal symmetry operation' 2_855 -x+3,y,-z -1 0 0 0 1 0 0 0 -1 408.96 0 0 4 'crystal symmetry operation' 2_856 -x+3,y,-z+1 -1 0 0 0 1 0 0 0 -1 408.864924 0 136.186967 5 'crystal symmetry operation' 2_755 -x+2,y,-z -1 0 0 0 1 0 0 0 -1 272.64 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 Q N N ? 4 S 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 4 A CYS 1 1_555 B SG CYS 119 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 B SG CYS 28 B CYS 42 1_555 B SG CYS 44 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf3 B SG CYS 173 B CYS 168 1_555 B SG CYS 187 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf4 B SG CYS 201 B CYS 191 1_555 B SG CYS 231 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf5 C SG CYS 4 C CYS 1 1_555 D SG CYS 119 D CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf6 D SG CYS 28 D CYS 42 1_555 D SG CYS 44 D CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf7 D SG CYS 173 D CYS 168 1_555 D SG CYS 187 D CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf8 D SG CYS 201 D CYS 191 1_555 D SG CYS 231 D CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? disulf ? disulf9 E SG CYS 4 E CYS 1 1_555 F SG CYS 119 F CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf10 F SG CYS 28 F CYS 42 1_555 F SG CYS 44 F CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf11 F SG CYS 173 F CYS 168 1_555 F SG CYS 187 F CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? disulf ? disulf12 F SG CYS 201 F CYS 191 1_555 F SG CYS 231 F CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf13 G SG CYS 4 G CYS 1 1_555 H SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf14 H SG CYS 28 H CYS 42 1_555 H SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf15 H SG CYS 173 H CYS 168 1_555 H SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? disulf ? disulf16 H SG CYS 201 H CYS 191 1_555 H SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? covale ? covale1 B ND2 ASN 53 B ASN 60 1_555 J C1 NAG . B NAG 402 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale2 D ND2 ASN 53 D ASN 60 1_555 N C1 NAG . D NAG 403 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 F ND2 ASN 53 F ASN 60 1_555 Q C1 NAG . F NAG 302 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 H ND2 ASN 53 H ASN 60 1_555 S C1 NAG . H NAG 701 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.456 ? metalc ? metalc1 A OD2 ASP 3 A ASP 1 1_555 I ZN ZN . B ZN 401 1_555 A ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc2 A OE1 GLU 25 A GLU 14 1_555 P ZN ZN . F ZN 301 1_555 H ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc3 B NE2 HIS 116 B HIS 119 1_555 I ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc4 B OE2 GLU 259 B GLU 247 1_555 I ZN ZN . B ZN 401 2_756 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc5 I ZN ZN . B ZN 401 1_555 T O HOH . B HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc6 C OD2 ASP 3 C ASP 1 1_555 L ZN ZN . D ZN 401 1_555 A ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc7 C OE1 GLU 25 C GLU 14 1_555 K ZN ZN . C ZN 101 1_555 H ? ? ? ? ? ? ? ? ? ? ? 1.991 ? metalc ? metalc8 C OE2 GLU 25 C GLU 14 1_555 K ZN ZN . C ZN 101 1_555 H ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc9 K ZN ZN . C ZN 101 1_555 H OE1 GLU 229 H GLU 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? metalc ? metalc10 K ZN ZN . C ZN 101 1_555 H OE2 GLU 229 H GLU 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc11 D NE2 HIS 116 D HIS 119 1_555 L ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc12 D OE1 GLU 229 D GLU 217 1_555 M ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc13 D OE2 GLU 229 D GLU 217 1_555 M ZN ZN . D ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc14 D OE1 GLU 259 D GLU 247 1_555 L ZN ZN . D ZN 401 2_855 ? ? ? ? ? ? ? ? ? ? ? ? 1.863 ? metalc ? metalc15 L ZN ZN . D ZN 401 1_555 U O HOH . D HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc16 M ZN ZN . D ZN 402 1_555 E OE1 GLU 25 E GLU 14 1_555 ? ? ? H ? ? ? ? ? ? ? ? 2.002 ? metalc ? metalc17 M ZN ZN . D ZN 402 1_555 E OE2 GLU 25 E GLU 14 1_555 ? ? ? H ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc18 E OD2 ASP 3 E ASP 1 1_555 O ZN ZN . E ZN 401 1_555 A ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc19 O ZN ZN . E ZN 401 1_555 F NE2 HIS 116 F HIS 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc20 O ZN ZN . E ZN 401 2_856 F OE1 GLU 259 F GLU 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.824 ? metalc ? metalc21 O ZN ZN . E ZN 401 1_555 W O HOH . F HOH 802 2_856 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc22 F OE1 GLU 229 F GLU 217 1_555 P ZN ZN . F ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc23 F OE2 GLU 229 F GLU 217 1_555 P ZN ZN . F ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc24 G OD2 ASP 3 G ASP 1 1_555 R ZN ZN . G ZN 401 1_555 A ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc25 R ZN ZN . G ZN 401 1_555 H NE2 HIS 116 H HIS 119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc26 R ZN ZN . G ZN 401 2_755 H OE1 GLU 259 H GLU 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc27 R ZN ZN . G ZN 401 2_755 H OE2 GLU 259 H GLU 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc28 R ZN ZN . G ZN 401 1_555 X O HOH . H HOH 802 2_755 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? # _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 6P9U _atom_sites.fract_transf_matrix[1][1] 0.007336 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000005 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.022608 _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] 0.007343 _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 3 ZN B 1 401 401 ZN ZN . J 4 NAG B 1 402 701 NAG NAG . K 3 ZN C 1 101 402 ZN ZN . L 3 ZN D 1 401 401 ZN ZN . M 3 ZN D 1 402 301 ZN ZN . N 4 NAG D 1 403 302 NAG NAG . O 3 ZN E 1 401 401 ZN ZN . P 3 ZN F 1 301 402 ZN ZN . Q 4 NAG F 1 302 701 NAG NAG . R 3 ZN G 1 401 401 ZN ZN . S 4 NAG H 1 701 701 NAG NAG . T 5 HOH B 1 801 801 HOH HOH . U 5 HOH D 1 501 401 HOH HOH . V 5 HOH E 1 501 501 HOH HOH . W 5 HOH F 1 801 801 HOH HOH . W 5 HOH F 2 802 802 HOH HOH . X 5 HOH H 1 801 801 HOH HOH . X 5 HOH H 2 802 802 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 . . . J 4 128.206 109.904 39.132 1 72.97 ? C1 NAG 402 B 1 HETATM 2 C C2 NAG . . . J 4 127.467 111.087 38.48 1 72.5 ? C2 NAG 402 B 1 HETATM 3 C C3 NAG . . . J 4 126.022 111.331 39.002 1 75.76 ? C3 NAG 402 B 1 HETATM 4 C C4 NAG . . . J 4 125.234 110.048 39.239 1 79.1 ? C4 NAG 402 B 1 HETATM 5 C C5 NAG . . . J 4 126.112 108.922 39.86 1 79.78 ? C5 NAG 402 B 1 HETATM 6 C C6 NAG . . . J 4 125.367 107.571 39.935 1 80.43 ? C6 NAG 402 B 1 HETATM 7 C C7 NAG . . . J 4 128.928 112.953 37.784 1 61.37 ? C7 NAG 402 B 1 HETATM 8 C C8 NAG . . . J 4 129.601 114.187 38.284 1 59.78 ? C8 NAG 402 B 1 HETATM 9 N N2 NAG . . . J 4 128.233 112.309 38.722 1 68.19 ? N2 NAG 402 B 1 HETATM 10 O O3 NAG . . . J 4 125.198 112.167 38.148 1 65.66 ? O3 NAG 402 B 1 HETATM 11 O O4 NAG . . . J 4 124.1 110.445 40.051 1 80.42 ? O4 NAG 402 B 1 HETATM 12 O O5 NAG . . . J 4 127.345 108.761 39.124 1 73.5 ? O5 NAG 402 B 1 HETATM 13 O O6 NAG . . . J 4 126.181 106.451 39.536 1 76.13 ? O6 NAG 402 B 1 HETATM 14 O O7 NAG . . . J 4 129.031 112.588 36.619 1 57.77 ? O7 NAG 402 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 14 #