data_6O8D # _model_server_result.job_id cJYVer6mBg5QSGHHHkK83w _model_server_result.datetime_utc '2024-12-26 08:54:50' _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 6o8d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 6O8D # _exptl.entry_id 6O8D _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 104.04 _cell.angle_gamma 90 _cell.entry_id 6O8D _cell.length_a 153.14 _cell.length_b 60.139 _cell.length_c 152.558 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6O8D _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -37.010453 0 148.000573 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 4 n D NAG 1 A 1 NAG C 136 NAG 4 n D NAG 2 A 2 NAG C 137 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 22 C CYS 40 1_555 A SG CYS 94 C CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 48 C CYS 66 1_555 A SG CYS 68 C CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf3 B SG CYS 23 L CYS 23 1_555 B SG CYS 93 L CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 B SG CYS 142 L CYS 142 1_555 B SG CYS 207 L CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 B SG CYS 258 L CYS 258 1_555 B SG CYS 318 L CYS 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 B SG CYS 338 L CYS 338 1_555 C SG CYS 347 H CYS 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 C SG CYS 143 H CYS 143 1_555 C SG CYS 219 H CYS 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf9 C SG CYS 271 H CYS 271 1_555 C SG CYS 327 H CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 87 C ASN 105 1_555 E C1 NAG . C NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 A ND2 ASN 111 C ASN 129 1_555 D C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 D O4 NAG . A NAG 1 1_555 D C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 6O8D _atom_sites.fract_transf_matrix[1][1] 0.00653 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001633 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016628 _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] 0.006757 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id E _pdbx_nonpoly_scheme.entity_id 5 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id C _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 201 _pdbx_nonpoly_scheme.auth_seq_num 135 _pdbx_nonpoly_scheme.pdb_mon_id NAG _pdbx_nonpoly_scheme.auth_mon_id NAG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . E 5 -18.541 -14.702 62.589 1 156.78 ? C1 NAG 201 C 1 HETATM 2 C C2 NAG . . . E 5 -19.374 -15.779 61.884 1 165.24 ? C2 NAG 201 C 1 HETATM 3 C C3 NAG . . . E 5 -18.475 -16.902 61.369 1 166.87 ? C3 NAG 201 C 1 HETATM 4 C C4 NAG . . . E 5 -17.354 -16.334 60.51 1 168.38 ? C4 NAG 201 C 1 HETATM 5 C C5 NAG . . . E 5 -16.589 -15.272 61.29 1 166.9 ? C5 NAG 201 C 1 HETATM 6 C C6 NAG . . . E 5 -15.518 -14.594 60.467 1 168.79 ? C6 NAG 201 C 1 HETATM 7 C C7 NAG . . . E 5 -21.542 -16.846 62.334 1 171.36 ? C7 NAG 201 C 1 HETATM 8 C C8 NAG . . . E 5 -22.482 -17.339 63.392 1 167.81 ? C8 NAG 201 C 1 HETATM 9 N N2 NAG . . . E 5 -20.398 -16.309 62.772 1 169.77 ? N2 NAG 201 C 1 HETATM 10 O O3 NAG . . . E 5 -19.25 -17.812 60.596 1 165.45 ? O3 NAG 201 C 1 HETATM 11 O O4 NAG . . . E 5 -16.462 -17.366 60.108 1 168.72 ? O4 NAG 201 C 1 HETATM 12 O O5 NAG . . . E 5 -17.497 -14.246 61.714 1 161.35 ? O5 NAG 201 C 1 HETATM 13 O O6 NAG . . . E 5 -14.216 -14.963 60.899 1 168.93 ? O6 NAG 201 C 1 HETATM 14 O O7 NAG . . . E 5 -21.805 -16.933 61.139 1 175.5 ? O7 NAG 201 C 1 # _model_server_stats.io_time_ms 89 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #