data_5OY9 # _model_server_result.job_id 0XSWHtn8iiqsRcUosSuXcQ _model_server_result.datetime_utc '2024-11-15 19:12:30' _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 5oy9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 5OY9 # _exptl.entry_id 5OY9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _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 5OY9 _cell.length_a 122.35 _cell.length_b 122.35 _cell.length_c 197.81 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OY9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 177 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 6 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,I _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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 3 n C NAG 1 B 1 NAG A 514 NAG 3 n C NAG 2 B 2 NAG A 515 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 24 A CYS 24 1_555 A SG CYS 284 A CYS 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 59 A CYS 59 1_555 A SG CYS 92 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 68 A CYS 68 1_555 A SG CYS 114 A CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 153 A CYS 153 1_555 A SG CYS 158 A CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 177 A CYS 177 1_555 A SG CYS 224 A CYS 224 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf6 A SG CYS 219 A CYS 219 1_555 A SG CYS 253 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf7 B SG CYS 2 D CYS 88 1_555 B SG CYS 14 D CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 B SG CYS 9 D CYS 95 1_555 B SG CYS 27 D CYS 113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 B SG CYS 21 D CYS 107 1_555 B SG CYS 36 D CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A C HIS 49 A HIS 49 1_555 A N MLZ 50 A MLZ 50 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C MLZ 50 A MLZ 50 1_555 A N ALA 51 A ALA 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 A ND2 ASN 163 A ASN 163 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 A ND2 ASN 320 A ASN 320 1_555 D C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale5 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? metalc ? metalc1 A O TRP 360 A TRP 360 1_555 F CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc2 B O PHE 19 D PHE 105 1_555 H CA CA . D CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc3 B OD1 ASP 22 D ASP 108 1_555 H CA CA . D CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc4 B O ASP 24 D ASP 110 1_555 H CA CA . D CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? metalc ? metalc5 B OD2 ASP 26 D ASP 112 1_555 H CA CA . D CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc6 B OD2 ASP 32 D ASP 118 1_555 H CA CA . D CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? metalc ? metalc7 B OE2 GLU 33 D GLU 119 1_555 H CA CA . D CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? # _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 263 n n C1 O1 NAG sing 264 n n C1 O5 NAG sing 265 n n C1 H1 NAG sing 266 n n C2 C3 NAG sing 267 n n C2 N2 NAG sing 268 n n C2 H2 NAG sing 269 n n C3 C4 NAG sing 270 n n C3 O3 NAG sing 271 n n C3 H3 NAG sing 272 n n C4 C5 NAG sing 273 n n C4 O4 NAG sing 274 n n C4 H4 NAG sing 275 n n C5 C6 NAG sing 276 n n C5 O5 NAG sing 277 n n C5 H5 NAG sing 278 n n C6 O6 NAG sing 279 n n C6 H61 NAG sing 280 n n C6 H62 NAG sing 281 n n C7 C8 NAG sing 282 n n C7 N2 NAG sing 283 n n C7 O7 NAG doub 284 n n C8 H81 NAG sing 285 n n C8 H82 NAG sing 286 n n C8 H83 NAG sing 287 n n N2 HN2 NAG sing 288 n n O1 HO1 NAG sing 289 n n O3 HO3 NAG sing 290 n n O4 HO4 NAG sing 291 n n O6 HO6 NAG sing 292 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 5OY9 _atom_sites.fract_transf_matrix[1][1] 0.008173 _atom_sites.fract_transf_matrix[1][2] 0.004719 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009438 _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] 0.005055 _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 D 4 NAG A 1 503 516 NAG NAG . E 5 CA A 1 504 517 CA CA . F 5 CA A 1 505 518 CA CA . G 5 CA A 1 506 519 CA CA . H 5 CA D 1 1001 1001 CA CA . I 6 HOH A 1 601 522 HOH HOH . I 6 HOH A 2 602 520 HOH HOH . I 6 HOH A 3 603 521 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 . . . D 4 3.159 43.877 44.927 1 174.98 ? C1 NAG 503 A 1 HETATM 2 C C2 NAG . . . D 4 3.711 43.895 43.482 1 180.04 ? C2 NAG 503 A 1 HETATM 3 C C3 NAG . . . D 4 3.395 42.584 42.768 1 180.18 ? C3 NAG 503 A 1 HETATM 4 C C4 NAG . . . D 4 3.589 41.416 43.722 1 181.94 ? C4 NAG 503 A 1 HETATM 5 C C5 NAG . . . D 4 2.506 41.464 44.795 1 182.34 ? C5 NAG 503 A 1 HETATM 6 C C6 NAG . . . D 4 2.942 40.861 46.114 1 175.03 ? C6 NAG 503 A 1 HETATM 7 C C7 NAG . . . D 4 3.879 46.156 42.528 1 176.86 ? C7 NAG 503 A 1 HETATM 8 C C8 NAG . . . D 4 3.185 47.213 41.718 1 168.41 ? C8 NAG 503 A 1 HETATM 9 N N2 NAG . . . D 4 3.19 45.026 42.728 1 179.23 ? N2 NAG 503 A 1 HETATM 10 O O3 NAG . . . D 4 4.24 42.428 41.633 1 178.79 ? O3 NAG 503 A 1 HETATM 11 O O4 NAG . . . D 4 3.524 40.185 43.01 1 180.94 ? O4 NAG 503 A 1 HETATM 12 O O5 NAG . . . D 4 2.114 42.826 45.057 1 179.87 ? O5 NAG 503 A 1 HETATM 13 O O6 NAG . . . D 4 1.836 40.466 46.915 1 164.91 ? O6 NAG 503 A 1 HETATM 14 O O7 NAG . . . D 4 5.01 46.32 42.983 1 169.97 ? O7 NAG 503 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #