data_5XOO # _model_server_result.job_id rsDtSWq4pOJsyGwyh99Zrg _model_server_result.datetime_utc '2024-11-15 01:41:06' _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 5xoo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":502}' # _entry.id 5XOO # _exptl.entry_id 5XOO _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 4 _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 90 _cell.entry_id 5XOO _cell.length_a 80.601 _cell.length_b 123.58 _cell.length_c 143.936 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XOO _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 H N N ? 3 I 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 GAL _pdbx_entity_branch_link.comp_id_2 XYP _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 C XYP 1 C 1 XYP A 501 XYP 2 n C GAL 2 C 2 GAL A 502 GAL # 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 185 A CYS 207 1_555 A SG CYS 200 A CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 190 A CYS 212 1_555 A SG CYS 193 A CYS 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 245 A CYS 267 1_555 A SG CYS 318 A CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 319 A CYS 341 1_555 A SG CYS 378 A CYS 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 B SG CYS 185 B CYS 207 1_555 B SG CYS 200 B CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 B SG CYS 190 B CYS 212 1_555 B SG CYS 193 B CYS 215 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 245 B CYS 267 1_555 B SG CYS 318 B CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 B SG CYS 319 B CYS 341 1_555 B SG CYS 378 B CYS 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 203 A ASN 225 1_555 D C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale2 A ND2 ASN 288 A ASN 310 1_555 E C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale3 F C MBN . A MBN 503 1_555 C O1 XYP . C XYP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale4 B ND2 ASN 203 B ASN 225 1_555 H C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? covale ? covale5 B ND2 ASN 288 B ASN 310 1_555 I C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale6 C O4 XYP . C XYP 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 sing # _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 308 n n C1 O1 NAG sing 309 n n C1 O5 NAG sing 310 n n C1 H1 NAG sing 311 n n C2 C3 NAG sing 312 n n C2 N2 NAG sing 313 n n C2 H2 NAG sing 314 n n C3 C4 NAG sing 315 n n C3 O3 NAG sing 316 n n C3 H3 NAG sing 317 n n C4 C5 NAG sing 318 n n C4 O4 NAG sing 319 n n C4 H4 NAG sing 320 n n C5 C6 NAG sing 321 n n C5 O5 NAG sing 322 n n C5 H5 NAG sing 323 n n C6 O6 NAG sing 324 n n C6 H61 NAG sing 325 n n C6 H62 NAG sing 326 n n C7 C8 NAG sing 327 n n C7 N2 NAG sing 328 n n C7 O7 NAG doub 329 n n C8 H81 NAG sing 330 n n C8 H82 NAG sing 331 n n C8 H83 NAG sing 332 n n N2 HN2 NAG sing 333 n n O1 HO1 NAG sing 334 n n O3 HO3 NAG sing 335 n n O4 HO4 NAG sing 336 n n O6 HO6 NAG sing 337 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 5XOO _atom_sites.fract_transf_matrix[1][1] 0.012407 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008092 _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] 0.006948 _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 3 NAG A 1 501 451 NAG NAG . E 3 NAG A 1 502 453 NAG NAG . F 4 MBN A 1 503 500 MBN MBN . G 5 ADN A 1 506 601 ADN ADN . H 3 NAG B 1 501 451 NAG NAG . I 3 NAG B 1 502 453 NAG NAG . J 5 ADN B 1 503 601 ADN ADN . # 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 3 80.4 151.23 161.639 1 109.96 ? C1 NAG 502 B 1 HETATM 2 C C2 NAG . . . I 3 79.969 150.37 162.838 1 102.59 ? C2 NAG 502 B 1 HETATM 3 C C3 NAG . . . I 3 79.825 151.228 164.101 1 100.41 ? C3 NAG 502 B 1 HETATM 4 C C4 NAG . . . I 3 81.057 152.097 164.32 1 105.25 ? C4 NAG 502 B 1 HETATM 5 C C5 NAG . . . I 3 81.359 152.886 163.053 1 115.09 ? C5 NAG 502 B 1 HETATM 6 C C6 NAG . . . I 3 82.592 153.755 163.157 1 118.99 ? C6 NAG 502 B 1 HETATM 7 C C7 NAG . . . I 3 78.22 148.69 163.274 1 107.57 ? C7 NAG 502 B 1 HETATM 8 C C8 NAG . . . I 3 76.913 148.124 162.81 1 106.35 ? C8 NAG 502 B 1 HETATM 9 N N2 NAG . . . I 3 78.716 149.693 162.541 1 111.61 ? N2 NAG 502 B 1 HETATM 10 O O3 NAG . . . I 3 79.624 150.383 165.23 1 107.05 ? O3 NAG 502 B 1 HETATM 11 O O4 NAG . . . I 3 80.821 153.001 165.394 1 114.79 ? O4 NAG 502 B 1 HETATM 12 O O5 NAG . . . I 3 81.573 151.97 161.972 1 118.7 ? O5 NAG 502 B 1 HETATM 13 O O6 NAG . . . I 3 83.755 153.093 162.681 1 117.88 ? O6 NAG 502 B 1 HETATM 14 O O7 NAG . . . I 3 78.798 148.259 164.269 1 109.02 ? O7 NAG 502 B 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #