data_3QEM # _model_server_result.job_id RPKWXyLkSBT8fPF_JtZ_6Q _model_server_result.datetime_utc '2024-11-05 10:32:23' _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 3qem # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":395}' # _entry.id 3QEM # _exptl.entry_id 3QEM _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 5 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 116.32 _cell.angle_gamma 90 _cell.entry_id 3QEM _cell.length_a 268.029 _cell.length_b 61.255 _cell.length_c 144.423 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3QEM _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 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 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,F,G,H,I,J 1 1 C,D,K,L,M,N 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 F N N ? 4 H N N ? 4 I N N ? 4 K N N ? 4 M N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . 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 E NAG 1 E 1 NAG E 1 NAG 3 n E NAG 2 E 2 NAG E 2 NAG 3 n E BMA 3 E 3 BMA E 3 BMA 3 n E MAN 4 E 4 MAN E 5 MAN 3 n E MAN 5 E 5 MAN E 4 MAN # 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 57 A CYS 79 1_555 A SG CYS 307 A CYS 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf2 B SG CYS 56 B CYS 86 1_555 B SG CYS 291 B CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 C SG CYS 57 C CYS 79 1_555 C SG CYS 307 C CYS 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf4 D SG CYS 56 D CYS 86 1_555 D SG CYS 291 D CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale1 A ND2 ASN 275 A ASN 297 1_555 F C1 NAG . A NAG 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 A ND2 ASN 367 A ASN 389 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 H C1 NAG . B NAG 1 1_555 B ND2 ASN 44 B ASN 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 B ND2 ASN 311 B ASN 341 1_555 I C1 NAG . B NAG 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 K C1 NAG . C NAG 1 1_555 C ND2 ASN 275 C ASN 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 M C1 NAG . D NAG 1 1_555 D ND2 ASN 44 D ASN 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? metalc ? metalc1 A O PHE 115 A PHE 137 1_555 G NA NA . A NA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc2 A O ASP 342 A ASP 364 1_555 G NA NA . A NA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc3 C O PHE 115 C PHE 137 1_555 L NA NA . C NA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc4 C O ASP 342 C ASP 364 1_555 L NA NA . C NA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 3QEM _atom_sites.fract_transf_matrix[1][1] 0.003731 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001846 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016325 _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] 0.007725 _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 4 NAG A 1 406 1 NAG NAG . G 5 NA A 1 407 1 NA NA . H 4 NAG B 1 1 1 NAG NAG . I 4 NAG B 1 395 1 NAG NAG . J 6 QEM B 1 396 1 QEM QEM . K 4 NAG C 1 1 1 NAG NAG . L 5 NA C 1 406 1 NA NA . M 4 NAG D 1 1 1 NAG NAG . N 6 QEM D 1 2 2 QEM QEM . # 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 58.565 22.275 -21.379 1 100.91 ? C1 NAG 395 B 1 HETATM 2 C C2 NAG . . . I 4 58.379 23.481 -22.307 1 103.63 ? C2 NAG 395 B 1 HETATM 3 C C3 NAG . . . I 4 57.514 24.646 -21.79 1 107.14 ? C3 NAG 395 B 1 HETATM 4 C C4 NAG . . . I 4 57.161 24.633 -20.297 1 108.54 ? C4 NAG 395 B 1 HETATM 5 C C5 NAG . . . I 4 57.798 23.478 -19.522 1 109.63 ? C5 NAG 395 B 1 HETATM 6 C C6 NAG . . . I 4 57.144 23.265 -18.154 1 106 ? C6 NAG 395 B 1 HETATM 7 C C7 NAG . . . I 4 60.037 24.202 -23.939 1 104.67 ? C7 NAG 395 B 1 HETATM 8 C C8 NAG . . . I 4 61.444 23.827 -24.327 1 92.77 ? C8 NAG 395 B 1 HETATM 9 N N2 NAG . . . I 4 59.689 23.996 -22.67 1 103.67 ? N2 NAG 395 B 1 HETATM 10 O O3 NAG . . . I 4 56.326 24.75 -22.562 1 105.72 ? O3 NAG 395 B 1 HETATM 11 O O4 NAG . . . I 4 57.561 25.873 -19.746 1 99.78 ? O4 NAG 395 B 1 HETATM 12 O O5 NAG . . . I 4 57.686 22.289 -20.276 1 108.99 ? O5 NAG 395 B 1 HETATM 13 O O6 NAG . . . I 4 55.897 22.61 -18.278 1 101.63 ? O6 NAG 395 B 1 HETATM 14 O O7 NAG . . . I 4 59.256 24.679 -24.766 1 108.85 ? O7 NAG 395 B 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 226 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #