data_5MYB # _model_server_result.job_id kztruGZAJHWZMuzKcekpDA _model_server_result.datetime_utc '2024-10-19 17:38:08' _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 5myb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":802}' # _entry.id 5MYB # _exptl.entry_id 5MYB _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 111.09 _cell.angle_gamma 90 _cell.entry_id 5MYB _cell.length_a 78.46 _cell.length_b 48.49 _cell.length_c 80.67 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MYB _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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 ? 4 E N N ? 4 F N N ? 4 G N N ? 4 H N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O3 HO3 . sing 3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . 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 NAG 1 C 1 NAG A 801 NAG 2 n C NAG 2 C 2 NAG A 802 NAG 2 n C BMA 3 C 3 BMA A 803 BMA 3 n D NAG 1 D 1 NAG B 803 NAG 3 n D NAG 2 D 2 NAG B 804 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 covale ? covale1 A ND2 ASN 141 A ASN 560 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale2 A ND2 ASN 177 A ASN 596 1_555 E C1 NAG . A NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 230 A ASN 649 1_555 F C1 NAG . A NAG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.501 ? covale ? covale4 B ND2 ASN 141 B ASN 560 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 B ND2 ASN 177 B ASN 596 1_555 G C1 NAG . B NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 B ND2 ASN 230 B ASN 649 1_555 H C1 NAG . B NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale8 C O3 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 5MYB _atom_sites.fract_transf_matrix[1][1] 0.012745 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004916 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020623 _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] 0.013286 _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 E 4 NAG A 1 804 804 NAG NAG . F 4 NAG A 1 805 805 NAG NAG . G 4 NAG B 1 801 801 NAG NAG . H 4 NAG B 1 802 802 NAG NAG . I 5 HOH A 1 901 901 HOH HOH . I 5 HOH A 2 902 902 HOH HOH . I 5 HOH A 3 903 904 HOH HOH . I 5 HOH A 4 904 905 HOH HOH . I 5 HOH A 5 905 906 HOH HOH . I 5 HOH A 6 906 907 HOH HOH . I 5 HOH A 7 907 908 HOH HOH . I 5 HOH A 8 908 909 HOH HOH . I 5 HOH A 9 909 910 HOH HOH . I 5 HOH A 10 910 911 HOH HOH . I 5 HOH A 11 911 912 HOH HOH . I 5 HOH A 12 912 903 HOH HOH . I 5 HOH A 13 913 913 HOH HOH . I 5 HOH A 14 914 914 HOH HOH . I 5 HOH A 15 915 915 HOH HOH . I 5 HOH A 16 916 916 HOH HOH . I 5 HOH A 17 917 917 HOH HOH . I 5 HOH A 18 918 918 HOH HOH . I 5 HOH A 19 919 920 HOH HOH . I 5 HOH A 20 920 919 HOH HOH . I 5 HOH A 21 921 921 HOH HOH . J 5 HOH B 1 901 901 HOH HOH . J 5 HOH B 2 902 902 HOH HOH . J 5 HOH B 3 903 903 HOH HOH . J 5 HOH B 4 904 904 HOH HOH . J 5 HOH B 5 905 905 HOH HOH . J 5 HOH B 6 906 906 HOH HOH . J 5 HOH B 7 907 907 HOH HOH . J 5 HOH B 8 908 908 HOH HOH . J 5 HOH B 9 909 909 HOH HOH . J 5 HOH B 10 910 910 HOH HOH . J 5 HOH B 11 911 911 HOH HOH . J 5 HOH B 12 912 912 HOH HOH . J 5 HOH B 13 913 913 HOH HOH . J 5 HOH B 14 914 914 HOH HOH . J 5 HOH B 15 915 915 HOH HOH . J 5 HOH B 16 916 916 HOH HOH . J 5 HOH B 17 917 917 HOH HOH . J 5 HOH B 18 918 918 HOH HOH . J 5 HOH B 19 919 919 HOH HOH . J 5 HOH B 20 920 920 HOH HOH . J 5 HOH B 21 921 921 HOH HOH . J 5 HOH B 22 922 922 HOH HOH . J 5 HOH B 23 923 923 HOH HOH . J 5 HOH B 24 924 924 HOH HOH . J 5 HOH B 25 925 925 HOH HOH . J 5 HOH B 26 926 926 HOH HOH . J 5 HOH B 27 927 927 HOH HOH . J 5 HOH B 28 928 928 HOH HOH . J 5 HOH B 29 929 929 HOH HOH . J 5 HOH B 30 930 930 HOH HOH . J 5 HOH B 31 931 931 HOH HOH . J 5 HOH B 32 932 932 HOH HOH . J 5 HOH B 33 933 933 HOH HOH . J 5 HOH B 34 934 934 HOH HOH . J 5 HOH B 35 935 935 HOH HOH . J 5 HOH B 36 936 936 HOH HOH . J 5 HOH B 37 937 937 HOH HOH . J 5 HOH B 38 938 938 HOH HOH . J 5 HOH B 39 939 939 HOH HOH . J 5 HOH B 40 940 940 HOH HOH . J 5 HOH B 41 941 941 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 . . . H 4 32.53 27.883 20.94 1 135.12 ? C1 NAG 802 B 1 HETATM 2 C C2 NAG . . . H 4 33.741 27.38 20.148 1 150.15 ? C2 NAG 802 B 1 HETATM 3 C C3 NAG . . . H 4 33.777 27.947 18.728 1 160.7 ? C3 NAG 802 B 1 HETATM 4 C C4 NAG . . . H 4 32.419 27.881 18.028 1 163.32 ? C4 NAG 802 B 1 HETATM 5 C C5 NAG . . . H 4 31.309 28.418 18.938 1 158.99 ? C5 NAG 802 B 1 HETATM 6 C C6 NAG . . . H 4 29.921 28.332 18.292 1 159.82 ? C6 NAG 802 B 1 HETATM 7 C C7 NAG . . . H 4 35.851 26.9 21.359 1 159.76 ? C7 NAG 802 B 1 HETATM 8 C C8 NAG . . . H 4 37.053 27.528 22.007 1 158.07 ? C8 NAG 802 B 1 HETATM 9 N N2 NAG . . . H 4 34.975 27.76 20.825 1 154.94 ? N2 NAG 802 B 1 HETATM 10 O O3 NAG . . . H 4 34.746 27.229 17.954 1 159.89 ? O3 NAG 802 B 1 HETATM 11 O O4 NAG . . . H 4 32.499 28.635 16.81 1 155.79 ? O4 NAG 802 B 1 HETATM 12 O O5 NAG . . . H 4 31.329 27.698 20.18 1 150.07 ? O5 NAG 802 B 1 HETATM 13 O O6 NAG . . . H 4 29.263 27.101 18.622 1 160.12 ? O6 NAG 802 B 1 HETATM 14 O O7 NAG . . . H 4 35.714 25.686 21.338 1 162.74 ? O7 NAG 802 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #