data_1PC8 # _model_server_result.job_id KlCYJgkyCK8qQnVKHlui1w _model_server_result.datetime_utc '2024-10-14 08:25:32' _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 1pc8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1002}' # _entry.id 1PC8 # _exptl.entry_id 1PC8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _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 1PC8 _cell.length_a 109.182 _cell.length_b 109.182 _cell.length_c 309.44 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PC8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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 _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 C NAG 1 C 1 NAG C 239 NAG 3 n C NAG 2 C 2 NAG C 4 NAG 4 n D NAG 1 D 1 NAG D 1 NAG 4 n D NAG 2 D 2 NAG D 5 NAG 4 n D BMA 3 D 3 BMA D 7 MAN 3 n E NAG 1 E 1 NAG E 3 NAG 3 n E NAG 2 E 2 NAG E 6 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 240 A CYS 240 1_555 B SG CYS 1 B CYS 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf2 B SG CYS 60 B CYS 60 1_555 B SG CYS 77 B CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? disulf ? disulf3 B SG CYS 148 B CYS 148 1_555 B SG CYS 161 B CYS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? disulf ? disulf4 B SG CYS 186 B CYS 186 1_555 B SG CYS 202 B CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? covale ? covale1 A ND2 ASN 107 A ASN 107 1_555 F C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale2 B ND2 ASN 57 B ASN 57 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.556 ? covale ? covale3 B ND2 ASN 92 B ASN 92 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale4 B ND2 ASN 132 B ASN 132 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale7 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 1PC8 _atom_sites.fract_transf_matrix[1][1] 0.009159 _atom_sites.fract_transf_matrix[1][2] 0.005288 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010576 _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] 0.003232 _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 F 5 NAG A 1 1002 1002 NAG NAG . G 6 HOH A 1 1003 1 HOH HOH . G 6 HOH A 2 1004 2 HOH HOH . G 6 HOH A 3 1005 3 HOH HOH . G 6 HOH A 4 1006 4 HOH HOH . G 6 HOH A 5 1007 7 HOH HOH . G 6 HOH A 6 1008 8 HOH HOH . G 6 HOH A 7 1009 9 HOH HOH . G 6 HOH A 8 1010 12 HOH HOH . H 6 HOH B 1 263 5 HOH HOH . H 6 HOH B 2 264 6 HOH HOH . H 6 HOH B 3 265 10 HOH HOH . H 6 HOH B 4 266 11 HOH HOH . H 6 HOH B 5 267 13 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 . . . F 5 47.407 45.821 29.186 1 123.44 ? C1 NAG 1002 A 1 HETATM 2 C C2 NAG . . . F 5 48.717 45.193 28.667 1 129.02 ? C2 NAG 1002 A 1 HETATM 3 C C3 NAG . . . F 5 48.566 43.726 28.228 1 130.72 ? C3 NAG 1002 A 1 HETATM 4 C C4 NAG . . . F 5 48.024 42.872 29.368 1 130.53 ? C4 NAG 1002 A 1 HETATM 5 C C5 NAG . . . F 5 46.861 43.609 30.05 1 130.25 ? C5 NAG 1002 A 1 HETATM 6 C C6 NAG . . . F 5 47.205 43.943 31.494 1 131.8 ? C6 NAG 1002 A 1 HETATM 7 C C7 NAG . . . F 5 49.715 47.182 27.749 1 132.95 ? C7 NAG 1002 A 1 HETATM 8 C C8 NAG . . . F 5 50.143 47.968 26.545 1 134.25 ? C8 NAG 1002 A 1 HETATM 9 N N2 NAG . . . F 5 49.248 45.96 27.558 1 130.37 ? N2 NAG 1002 A 1 HETATM 10 O O3 NAG . . . F 5 49.8 43.169 27.782 1 132.13 ? O3 NAG 1002 A 1 HETATM 11 O O4 NAG . . . F 5 47.649 41.585 28.892 1 129.63 ? O4 NAG 1002 A 1 HETATM 12 O O5 NAG . . . F 5 46.449 44.783 29.357 1 126.23 ? O5 NAG 1002 A 1 HETATM 13 O O6 NAG . . . F 5 46.558 43.011 32.324 1 134.41 ? O6 NAG 1002 A 1 HETATM 14 O O7 NAG . . . F 5 49.802 47.668 28.87 1 134.75 ? O7 NAG 1002 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #