data_5B5K # _model_server_result.job_id xV78zNEcnO7LQSJ8yB0nuw _model_server_result.datetime_utc '2025-01-18 10:43:12' _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 5b5k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5B5K # _exptl.entry_id 5B5K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _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 90 _cell.angle_gamma 90 _cell.entry_id 5B5K _cell.length_a 103.28 _cell.length_b 103.28 _cell.length_c 139.27 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5B5K _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 1 A CYS 22 1_555 A SG CYS 128 A CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 4 A CYS 25 1_555 A SG CYS 131 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 114 A CYS 135 1_555 A SG CYS 138 A CYS 159 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 118 A CYS 139 1_555 A SG CYS 144 A CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 A SG CYS 161 A CYS 182 1_555 A SG CYS 212 A CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? covale ? covale1 A ND2 ASN 183 A ASN 204 1_555 B C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? # _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 270 n n C1 O1 NAG sing 271 n n C1 O5 NAG sing 272 n n C1 H1 NAG sing 273 n n C2 C3 NAG sing 274 n n C2 N2 NAG sing 275 n n C2 H2 NAG sing 276 n n C3 C4 NAG sing 277 n n C3 O3 NAG sing 278 n n C3 H3 NAG sing 279 n n C4 C5 NAG sing 280 n n C4 O4 NAG sing 281 n n C4 H4 NAG sing 282 n n C5 C6 NAG sing 283 n n C5 O5 NAG sing 284 n n C5 H5 NAG sing 285 n n C6 O6 NAG sing 286 n n C6 H61 NAG sing 287 n n C6 H62 NAG sing 288 n n C7 C8 NAG sing 289 n n C7 N2 NAG sing 290 n n C7 O7 NAG doub 291 n n C8 H81 NAG sing 292 n n C8 H82 NAG sing 293 n n C8 H83 NAG sing 294 n n N2 HN2 NAG sing 295 n n O1 HO1 NAG sing 296 n n O3 HO3 NAG sing 297 n n O4 HO4 NAG sing 298 n n O6 HO6 NAG sing 299 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 5B5K _atom_sites.fract_transf_matrix[1][1] 0.009682 _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] 0.009682 _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] 0.00718 _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 B 2 NAG A 1 301 500 NAG NAG . C 3 EPE A 1 302 510 EPE EPE . D 4 HOH A 1 401 23 HOH HOH . D 4 HOH A 2 402 28 HOH HOH . D 4 HOH A 3 403 16 HOH HOH . D 4 HOH A 4 404 20 HOH HOH . D 4 HOH A 5 405 6 HOH HOH . D 4 HOH A 6 406 26 HOH HOH . D 4 HOH A 7 407 22 HOH HOH . D 4 HOH A 8 408 8 HOH HOH . D 4 HOH A 9 409 4 HOH HOH . D 4 HOH A 10 410 10 HOH HOH . D 4 HOH A 11 411 9 HOH HOH . D 4 HOH A 12 412 14 HOH HOH . D 4 HOH A 13 413 12 HOH HOH . D 4 HOH A 14 414 25 HOH HOH . D 4 HOH A 15 415 18 HOH HOH . D 4 HOH A 16 416 15 HOH HOH . D 4 HOH A 17 417 2 HOH HOH . D 4 HOH A 18 418 19 HOH HOH . D 4 HOH A 19 419 11 HOH HOH . D 4 HOH A 20 420 1 HOH HOH . D 4 HOH A 21 421 13 HOH HOH . D 4 HOH A 22 422 7 HOH HOH . D 4 HOH A 23 423 24 HOH HOH . D 4 HOH A 24 424 3 HOH HOH . D 4 HOH A 25 425 5 HOH HOH . D 4 HOH A 26 426 27 HOH HOH . D 4 HOH A 27 427 17 HOH HOH . D 4 HOH A 28 428 21 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 . . . B 2 -13.248 34.89 73.059 1 51.43 ? C1 NAG 301 A 1 HETATM 2 C C2 NAG . . . B 2 -14.206 34.857 71.812 1 55.05 ? C2 NAG 301 A 1 HETATM 3 C C3 NAG . . . B 2 -15.049 33.581 71.76 1 56.74 ? C3 NAG 301 A 1 HETATM 4 C C4 NAG . . . B 2 -14.179 32.348 71.904 1 56.64 ? C4 NAG 301 A 1 HETATM 5 C C5 NAG . . . B 2 -13.552 32.414 73.278 1 58.89 ? C5 NAG 301 A 1 HETATM 6 C C6 NAG . . . B 2 -12.685 31.219 73.595 1 59.93 ? C6 NAG 301 A 1 HETATM 7 C C7 NAG . . . B 2 -14.913 37.178 72.398 1 59.32 ? C7 NAG 301 A 1 HETATM 8 C C8 NAG . . . B 2 -15.998 38.198 72.201 1 54.19 ? C8 NAG 301 A 1 HETATM 9 N N2 NAG . . . B 2 -15.095 36.014 71.762 1 58.49 ? N2 NAG 301 A 1 HETATM 10 O O3 NAG . . . B 2 -15.743 33.543 70.518 1 59.06 ? O3 NAG 301 A 1 HETATM 11 O O4 NAG . . . B 2 -14.951 31.16 71.765 1 59.25 ? O4 NAG 301 A 1 HETATM 12 O O5 NAG . . . B 2 -12.695 33.559 73.316 1 52.46 ? O5 NAG 301 A 1 HETATM 13 O O6 NAG . . . B 2 -11.436 31.626 74.14 1 59.49 ? O6 NAG 301 A 1 HETATM 14 O O7 NAG . . . B 2 -13.93 37.404 73.094 1 60.39 ? O7 NAG 301 A 1 HETATM 15 H H1 NAG . . . B 2 -13.748 35.188 73.842 1 61.72 ? H1 NAG 301 A 1 HETATM 16 H H2 NAG . . . B 2 -13.649 34.871 71.011 1 66.07 ? H2 NAG 301 A 1 HETATM 17 H H3 NAG . . . B 2 -15.699 33.598 72.488 1 68.09 ? H3 NAG 301 A 1 HETATM 18 H H4 NAG . . . B 2 -13.478 32.363 71.225 1 67.97 ? H4 NAG 301 A 1 HETATM 19 H H5 NAG . . . B 2 -14.251 32.503 73.954 1 70.67 ? H5 NAG 301 A 1 HETATM 20 H H61 NAG . . . B 2 -13.146 30.65 74.24 1 71.91 ? H61 NAG 301 A 1 HETATM 21 H H62 NAG . . . B 2 -12.526 30.711 72.776 1 71.91 ? H62 NAG 301 A 1 HETATM 22 H H81 NAG . . . B 2 -16.846 37.837 72.523 1 65.03 ? H81 NAG 301 A 1 HETATM 23 H H82 NAG . . . B 2 -16.075 38.412 71.252 1 65.03 ? H82 NAG 301 A 1 HETATM 24 H H83 NAG . . . B 2 -15.779 39.007 72.701 1 65.03 ? H83 NAG 301 A 1 HETATM 25 H HN2 NAG . . . B 2 -15.86 35.926 71.273 1 70.19 ? HN2 NAG 301 A 1 HETATM 26 H HO3 NAG . . . B 2 -16.564 33.231 70.646 1 70.87 ? HO3 NAG 301 A 1 HETATM 27 H HO4 NAG . . . B 2 -14.782 30.788 70.977 1 71.1 ? HO4 NAG 301 A 1 HETATM 28 H HO6 NAG . . . B 2 -11.037 30.928 74.517 1 71.38 ? HO6 NAG 301 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 238 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #