data_1JPY # _model_server_result.job_id 0ety8_E0gaBPLf126JhKBA _model_server_result.datetime_utc '2024-11-26 00:21:49' _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 1jpy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":241}' # _entry.id 1JPY # _exptl.entry_id 1JPY _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 2 _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 120 _cell.entry_id 1JPY _cell.length_a 126.438 _cell.length_b 126.438 _cell.length_c 89.914 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JPY _symmetry.cell_setting hexagonal _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65' # 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,G,J,K 1 1 C,D,F,H,I,L,M 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 ? 4 G N N ? 4 I N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NDG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 NAG 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 2 n E NAG 1 C 1 NAG B 241 NAG 2 n E NDG 2 C 2 NDG B 242 NAG 3 n F NAG 1 D 1 NAG X 241 NAG 3 n F NAG 2 D 2 NAG X 242 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 21 A CYS 17 1_555 B SG CYS 111 B CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 76 A CYS 72 1_555 A SG CYS 126 A CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 81 A CYS 77 1_555 A SG CYS 128 A CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 111 A CYS 107 1_555 B SG CYS 21 B CYS 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf5 B SG CYS 76 B CYS 72 1_555 B SG CYS 126 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 B SG CYS 81 B CYS 77 1_555 B SG CYS 128 B CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf7 C SG CYS 21 X CYS 17 1_555 D SG CYS 111 Y CYS 107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 C SG CYS 76 X CYS 72 1_555 C SG CYS 126 X CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf9 C SG CYS 81 X CYS 77 1_555 C SG CYS 128 X CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf10 C SG CYS 111 X CYS 107 1_555 D SG CYS 21 Y CYS 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf11 D SG CYS 76 Y CYS 72 1_555 D SG CYS 126 Y CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 D SG CYS 81 Y CYS 77 1_555 D SG CYS 128 Y CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 57 A ASN 53 1_555 G C1 NAG . A NAG 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale2 B ND2 ASN 57 B ASN 53 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale3 C ND2 ASN 57 X ASN 53 1_555 F C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale4 D ND2 ASN 57 Y ASN 53 1_555 I C1 NAG . Y NAG 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale5 E O4 NAG . C NAG 1 1_555 E C1 NDG . C NDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale6 F O4 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? # _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 1JPY _atom_sites.fract_transf_matrix[1][1] 0.007909 _atom_sites.fract_transf_matrix[1][2] 0.004566 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009133 _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] 0.011122 _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 4 NAG A 1 241 241 NAG NAG . H 5 SO4 X 1 243 101 SO4 SO4 . I 4 NAG Y 1 241 241 NAG NAG . J 6 HOH A 1 242 2 HOH HOH . J 6 HOH A 2 243 3 HOH HOH . J 6 HOH A 3 244 12 HOH HOH . J 6 HOH A 4 245 19 HOH HOH . J 6 HOH A 5 246 21 HOH HOH . J 6 HOH A 6 247 23 HOH HOH . J 6 HOH A 7 248 27 HOH HOH . K 6 HOH B 1 243 1 HOH HOH . K 6 HOH B 2 244 4 HOH HOH . K 6 HOH B 3 245 5 HOH HOH . K 6 HOH B 4 246 6 HOH HOH . K 6 HOH B 5 247 7 HOH HOH . K 6 HOH B 6 248 8 HOH HOH . K 6 HOH B 7 249 13 HOH HOH . K 6 HOH B 8 250 14 HOH HOH . K 6 HOH B 9 251 17 HOH HOH . K 6 HOH B 10 252 18 HOH HOH . K 6 HOH B 11 253 25 HOH HOH . K 6 HOH B 12 254 26 HOH HOH . L 6 HOH X 1 244 11 HOH HOH . L 6 HOH X 2 245 15 HOH HOH . L 6 HOH X 3 246 20 HOH HOH . M 6 HOH Y 1 242 9 HOH HOH . M 6 HOH Y 2 243 10 HOH HOH . M 6 HOH Y 3 244 16 HOH HOH . M 6 HOH Y 4 245 22 HOH HOH . M 6 HOH Y 5 246 24 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 . . . I 4 18.877 34.852 65.233 1 55.93 ? C1 NAG 241 Y 1 HETATM 2 C C2 NAG . . . I 4 18.567 36.066 66.105 1 47.54 ? C2 NAG 241 Y 1 HETATM 3 C C3 NAG . . . I 4 18.798 35.669 67.575 1 42.46 ? C3 NAG 241 Y 1 HETATM 4 C C4 NAG . . . I 4 17.73 34.627 67.905 1 43.08 ? C4 NAG 241 Y 1 HETATM 5 C C5 NAG . . . I 4 17.837 33.408 66.927 1 44.11 ? C5 NAG 241 Y 1 HETATM 6 C C6 NAG . . . I 4 16.629 32.471 67.053 1 41.97 ? C6 NAG 241 Y 1 HETATM 7 C C7 NAG . . . I 4 20.389 37.702 66.236 1 41.52 ? C7 NAG 241 Y 1 HETATM 8 C C8 NAG . . . I 4 20.94 39.03 65.742 1 39.08 ? C8 NAG 241 Y 1 HETATM 9 N N2 NAG . . . I 4 19.242 37.295 65.69 1 43.61 ? N2 NAG 241 Y 1 HETATM 10 O O3 NAG . . . I 4 18.659 36.793 68.439 1 40.86 ? O3 NAG 241 Y 1 HETATM 11 O O4 NAG . . . I 4 17.849 34.207 69.273 1 40.43 ? O4 NAG 241 Y 1 HETATM 12 O O5 NAG . . . I 4 17.892 33.825 65.52 1 49 ? O5 NAG 241 Y 1 HETATM 13 O O6 NAG . . . I 4 15.547 33.073 67.768 1 41.42 ? O6 NAG 241 Y 1 HETATM 14 O O7 NAG . . . I 4 21.026 37.043 67.065 1 42.02 ? O7 NAG 241 Y 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #