data_3SQ9 # _model_server_result.job_id 07wPAw5WGexBVIUZlDFiKQ _model_server_result.datetime_utc '2024-11-28 16:05:32' _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 3sq9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":801}' # _entry.id 3SQ9 # _exptl.entry_id 3SQ9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 14 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.46 _cell.angle_gamma 90 _cell.entry_id 3SQ9 _cell.length_a 79.123 _cell.length_b 144.558 _cell.length_c 131.115 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SQ9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 pentameric 5 author_and_software_defined_assembly 1 PISA pentameric 5 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,C,D,E,K,N,O,P,Q,R,S,T,U 1 1 F,G,H,I,J,L,M,V,W,X,Y,Z,AA 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 ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q N N ? 3 R N N ? 3 S N N ? 3 T N N ? 3 U N N ? 3 V N N ? 3 W N N ? 3 X N N ? 3 Y N N ? 3 Z N N ? 3 AA N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 2 n K NAG 1 K 1 NAG B 801 NAG 2 n K NAG 2 K 2 NAG B 802 NAG 2 n L NAG 1 L 1 NAG H 901 NAG 2 n L NAG 2 L 2 NAG H 902 NAG 2 n M NAG 1 M 1 NAG I 901 NAG 2 n M NAG 2 M 2 NAG I 902 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 125 A CYS 125 1_555 A SG CYS 138 A CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 186 A CYS 186 1_555 A SG CYS 187 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf3 B SG CYS 125 B CYS 125 1_555 B SG CYS 138 B CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 B SG CYS 186 B CYS 186 1_555 B SG CYS 187 B CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf5 C SG CYS 125 C CYS 125 1_555 C SG CYS 138 C CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 C SG CYS 186 C CYS 186 1_555 C SG CYS 187 C CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf7 D SG CYS 125 D CYS 125 1_555 D SG CYS 138 D CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 D SG CYS 186 D CYS 186 1_555 D SG CYS 187 D CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf9 E SG CYS 125 E CYS 125 1_555 E SG CYS 138 E CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 E SG CYS 186 E CYS 186 1_555 E SG CYS 187 E CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf11 F SG CYS 125 F CYS 125 1_555 F SG CYS 138 F CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 F SG CYS 186 F CYS 186 1_555 F SG CYS 187 F CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf13 G SG CYS 125 G CYS 125 1_555 G SG CYS 138 G CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf14 G SG CYS 186 G CYS 186 1_555 G SG CYS 187 G CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf15 H SG CYS 125 H CYS 125 1_555 H SG CYS 138 H CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf16 H SG CYS 186 H CYS 186 1_555 H SG CYS 187 H CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf17 I SG CYS 125 I CYS 125 1_555 I SG CYS 138 I CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf18 I SG CYS 186 I CYS 186 1_555 I SG CYS 187 I CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf19 J SG CYS 125 J CYS 125 1_555 J SG CYS 138 J CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf20 J SG CYS 186 J CYS 186 1_555 J SG CYS 187 J CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? covale ? covale1 A ND2 ASN 66 A ASN 66 1_555 N C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale2 A ND2 ASN 108 A ASN 108 1_555 O C1 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale3 B ND2 ASN 66 B ASN 66 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale4 B ND2 ASN 108 B ASN 108 1_555 P C1 NAG . B NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale5 C ND2 ASN 66 C ASN 66 1_555 Q C1 NAG . C NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale6 C ND2 ASN 108 C ASN 108 1_555 R C1 NAG . C NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale7 D ND2 ASN 66 D ASN 66 1_555 S C1 NAG . D NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale8 E ND2 ASN 66 E ASN 66 1_555 T C1 NAG . E NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale9 E ND2 ASN 108 E ASN 108 1_555 U C1 NAG . E NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale10 F ND2 ASN 66 F ASN 66 1_555 V C1 NAG . F NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale11 G ND2 ASN 108 G ASN 108 1_555 W C1 NAG . G NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale12 H ND2 ASN 66 H ASN 66 1_555 X C1 NAG . H NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale13 H ND2 ASN 108 H ASN 108 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale14 I ND2 ASN 66 I ASN 66 1_555 Y C1 NAG . I NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale15 I ND2 ASN 108 I ASN 108 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale16 J ND2 ASN 66 J ASN 66 1_555 Z C1 NAG . J NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale17 J ND2 ASN 108 J ASN 108 1_555 AA C1 NAG . J NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale18 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale19 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? covale ? covale20 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? # _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 3SQ9 _atom_sites.fract_transf_matrix[1][1] 0.012639 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002793 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006918 _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] 0.007811 _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 N 3 NAG A 1 801 801 NAG NAG . O 3 NAG A 1 901 901 NAG NAG . P 3 NAG B 1 901 901 NAG NAG . Q 3 NAG C 1 801 801 NAG NAG . R 3 NAG C 1 901 901 NAG NAG . S 3 NAG D 1 801 801 NAG NAG . T 3 NAG E 1 801 801 NAG NAG . U 3 NAG E 1 901 901 NAG NAG . V 3 NAG F 1 801 801 NAG NAG . W 3 NAG G 1 901 901 NAG NAG . X 3 NAG H 1 801 801 NAG NAG . Y 3 NAG I 1 801 801 NAG NAG . Z 3 NAG J 1 801 801 NAG NAG . AA 3 NAG J 1 901 901 NAG NAG . # 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 . . . Y 3 12.924 5.908 24.724 1 152.17 ? C1 NAG 801 I 1 HETATM 2 C C2 NAG . . . Y 3 13.319 7.311 24.213 1 151.61 ? C2 NAG 801 I 1 HETATM 3 C C3 NAG . . . Y 3 14.757 7.336 23.647 1 154.13 ? C3 NAG 801 I 1 HETATM 4 C C4 NAG . . . Y 3 15.054 6.186 22.645 1 155.18 ? C4 NAG 801 I 1 HETATM 5 C C5 NAG . . . Y 3 14.21 4.939 22.954 1 155.19 ? C5 NAG 801 I 1 HETATM 6 C C6 NAG . . . Y 3 14.911 3.632 22.614 1 155 ? C6 NAG 801 I 1 HETATM 7 C C7 NAG . . . Y 3 11.885 9.006 23.243 1 141.03 ? C7 NAG 801 I 1 HETATM 8 C C8 NAG . . . Y 3 10.768 9.347 22.26 1 133.15 ? C8 NAG 801 I 1 HETATM 9 N N2 NAG . . . Y 3 12.373 7.767 23.205 1 145.93 ? N2 NAG 801 I 1 HETATM 10 O O3 NAG . . . Y 3 15.681 7.27 24.725 1 156.32 ? O3 NAG 801 I 1 HETATM 11 O O4 NAG . . . Y 3 14.828 6.613 21.304 1 149.06 ? O4 NAG 801 I 1 HETATM 12 O O5 NAG . . . Y 3 13.895 4.909 24.362 1 154.81 ? O5 NAG 801 I 1 HETATM 13 O O6 NAG . . . Y 3 14.075 2.517 22.886 1 151.4 ? O6 NAG 801 I 1 HETATM 14 O O7 NAG . . . Y 3 12.298 9.864 24.027 1 135.3 ? O7 NAG 801 I 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #