data_6YJR # _model_server_result.job_id 6jdEzkj2lCe5Vt4a34raFQ _model_server_result.datetime_utc '2024-11-20 03:21:06' _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 6yjr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":803}' # _entry.id 6YJR # _exptl.entry_id 6YJR _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 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 6YJR _cell.length_a 59.809 _cell.length_b 100.415 _cell.length_c 207.981 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YJR _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,J 1 1 B,D,H,I,K 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 FUC _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 O6 _pdbx_entity_branch_link.leaving_atom_id_2 HO6 _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 NAG 1 A 1 NAG AaA 742 NAG 2 n C FUC 2 A 2 FUC AeA 903 FUC 2 n D NAG 1 B 1 NAG BaB 742 NAG 2 n D FUC 2 B 2 FUC BcB 802 FUC # 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 159 AAA CYS 372 1_555 A SG CYS 413 AAA CYS 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? disulf ? disulf2 A SG CYS 436 AAA CYS 649 1_555 A SG CYS 511 AAA CYS 724 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf3 A SG CYS 440 AAA CYS 653 1_555 A SG CYS 513 AAA CYS 726 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf4 A SG CYS 447 AAA CYS 660 1_555 A SG CYS 500 AAA CYS 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? disulf ? disulf5 A SG CYS 468 AAA CYS 681 1_555 A SG CYS 489 AAA CYS 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 A SG CYS 524 AAA CYS 737 1_555 A SG CYS 527 AAA CYS 740 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? disulf ? disulf7 B SG CYS 159 BBB CYS 372 1_555 B SG CYS 413 BBB CYS 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? disulf ? disulf8 B SG CYS 436 BBB CYS 649 1_555 B SG CYS 511 BBB CYS 724 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf9 B SG CYS 440 BBB CYS 653 1_555 B SG CYS 513 BBB CYS 726 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf10 B SG CYS 447 BBB CYS 660 1_555 B SG CYS 500 BBB CYS 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? disulf ? disulf11 B SG CYS 468 BBB CYS 681 1_555 B SG CYS 489 BBB CYS 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf12 B SG CYS 524 BBB CYS 737 1_555 B SG CYS 527 BBB CYS 740 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? covale ? covale1 A ND2 ASN 220 AAA ASN 433 1_555 E C1 NAG . AAA NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale2 A ND2 ASN 234 AAA ASN 447 1_555 C C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 B ND2 ASN 234 BBB ASN 447 1_555 D C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.481 ? covale ? covale4 C O6 NAG . A NAG 1 1_555 C C1 FUC . A FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale5 D O6 NAG . B NAG 1 1_555 D C1 FUC . B FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? # _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 269 n n C1 O1 NAG sing 270 n n C1 O5 NAG sing 271 n n C1 H1 NAG sing 272 n n C2 C3 NAG sing 273 n n C2 N2 NAG sing 274 n n C2 H2 NAG sing 275 n n C3 C4 NAG sing 276 n n C3 O3 NAG sing 277 n n C3 H3 NAG sing 278 n n C4 C5 NAG sing 279 n n C4 O4 NAG sing 280 n n C4 H4 NAG sing 281 n n C5 C6 NAG sing 282 n n C5 O5 NAG sing 283 n n C5 H5 NAG sing 284 n n C6 O6 NAG sing 285 n n C6 H61 NAG sing 286 n n C6 H62 NAG sing 287 n n C7 C8 NAG sing 288 n n C7 N2 NAG sing 289 n n C7 O7 NAG doub 290 n n C8 H81 NAG sing 291 n n C8 H82 NAG sing 292 n n C8 H83 NAG sing 293 n n N2 HN2 NAG sing 294 n n O1 HO1 NAG sing 295 n n O3 HO3 NAG sing 296 n n O4 HO4 NAG sing 297 n n O6 HO6 NAG sing 298 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 6YJR _atom_sites.fract_transf_matrix[1][1] 0.01672 _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] 0.009959 _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] 0.004808 _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 3 NAG AAA 1 803 744 NAG NAG . F 4 EDO AAA 1 804 801 EDO EDO . G 4 EDO AAA 1 805 901 EDO EDO . H 4 EDO BBB 1 803 801 EDO EDO . I 4 EDO BBB 1 804 901 EDO EDO . J 5 HOH AAA 1 901 34 HOH HOH . J 5 HOH AAA 2 902 135 HOH HOH . J 5 HOH AAA 3 903 142 HOH HOH . J 5 HOH AAA 4 904 120 HOH HOH . J 5 HOH AAA 5 905 65 HOH HOH . J 5 HOH AAA 6 906 143 HOH HOH . J 5 HOH AAA 7 907 137 HOH HOH . J 5 HOH AAA 8 908 1 HOH HOH . J 5 HOH AAA 9 909 33 HOH HOH . J 5 HOH AAA 10 910 2 HOH HOH . J 5 HOH AAA 11 911 127 HOH HOH . J 5 HOH AAA 12 912 117 HOH HOH . J 5 HOH AAA 13 913 168 HOH HOH . J 5 HOH AAA 14 914 21 HOH HOH . J 5 HOH AAA 15 915 138 HOH HOH . J 5 HOH AAA 16 916 45 HOH HOH . J 5 HOH AAA 17 917 133 HOH HOH . J 5 HOH AAA 18 918 83 HOH HOH . J 5 HOH AAA 19 919 39 HOH HOH . J 5 HOH AAA 20 920 3 HOH HOH . J 5 HOH AAA 21 921 51 HOH HOH . J 5 HOH AAA 22 922 119 HOH HOH . J 5 HOH AAA 23 923 30 HOH HOH . J 5 HOH AAA 24 924 169 HOH HOH . J 5 HOH AAA 25 925 165 HOH HOH . J 5 HOH AAA 26 926 147 HOH HOH . J 5 HOH AAA 27 927 170 HOH HOH . J 5 HOH AAA 28 928 56 HOH HOH . J 5 HOH AAA 29 929 50 HOH HOH . J 5 HOH AAA 30 930 81 HOH HOH . J 5 HOH AAA 31 931 27 HOH HOH . J 5 HOH AAA 32 932 31 HOH HOH . J 5 HOH AAA 33 933 28 HOH HOH . J 5 HOH AAA 34 934 46 HOH HOH . J 5 HOH AAA 35 935 47 HOH HOH . J 5 HOH AAA 36 936 37 HOH HOH . J 5 HOH AAA 37 937 167 HOH HOH . J 5 HOH AAA 38 938 124 HOH HOH . J 5 HOH AAA 39 939 52 HOH HOH . J 5 HOH AAA 40 940 49 HOH HOH . J 5 HOH AAA 41 941 35 HOH HOH . J 5 HOH AAA 42 942 22 HOH HOH . J 5 HOH AAA 43 943 36 HOH HOH . J 5 HOH AAA 44 944 48 HOH HOH . J 5 HOH AAA 45 945 43 HOH HOH . J 5 HOH AAA 46 946 121 HOH HOH . J 5 HOH AAA 47 947 125 HOH HOH . J 5 HOH AAA 48 948 41 HOH HOH . J 5 HOH AAA 49 949 32 HOH HOH . J 5 HOH AAA 50 950 116 HOH HOH . J 5 HOH AAA 51 951 40 HOH HOH . J 5 HOH AAA 52 952 123 HOH HOH . J 5 HOH AAA 53 953 166 HOH HOH . J 5 HOH AAA 54 954 42 HOH HOH . J 5 HOH AAA 55 955 126 HOH HOH . K 5 HOH BBB 1 901 155 HOH HOH . K 5 HOH BBB 2 902 136 HOH HOH . K 5 HOH BBB 3 903 175 HOH HOH . K 5 HOH BBB 4 904 159 HOH HOH . K 5 HOH BBB 5 905 158 HOH HOH . K 5 HOH BBB 6 906 156 HOH HOH . K 5 HOH BBB 7 907 9 HOH HOH . K 5 HOH BBB 8 908 5 HOH HOH . K 5 HOH BBB 9 909 103 HOH HOH . K 5 HOH BBB 10 910 19 HOH HOH . K 5 HOH BBB 11 911 132 HOH HOH . K 5 HOH BBB 12 912 62 HOH HOH . K 5 HOH BBB 13 913 13 HOH HOH . K 5 HOH BBB 14 914 164 HOH HOH . K 5 HOH BBB 15 915 12 HOH HOH . K 5 HOH BBB 16 916 173 HOH HOH . K 5 HOH BBB 17 917 23 HOH HOH . K 5 HOH BBB 18 918 17 HOH HOH . K 5 HOH BBB 19 919 174 HOH HOH . K 5 HOH BBB 20 920 15 HOH HOH . K 5 HOH BBB 21 921 7 HOH HOH . K 5 HOH BBB 22 922 150 HOH HOH . K 5 HOH BBB 23 923 161 HOH HOH . K 5 HOH BBB 24 924 11 HOH HOH . K 5 HOH BBB 25 925 10 HOH HOH . K 5 HOH BBB 26 926 176 HOH HOH . K 5 HOH BBB 27 927 20 HOH HOH . K 5 HOH BBB 28 928 8 HOH HOH . K 5 HOH BBB 29 929 14 HOH HOH . K 5 HOH BBB 30 930 154 HOH HOH . K 5 HOH BBB 31 931 163 HOH HOH . K 5 HOH BBB 32 932 162 HOH HOH . K 5 HOH BBB 33 933 149 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 . . . E 3 -17.258 -21.549 16.285 1 112.16 ? C1 NAG 803 AAA 1 HETATM 2 C C2 NAG . . . E 3 -18.168 -21.589 15.043 1 112.8 ? C2 NAG 803 AAA 1 HETATM 3 C C3 NAG . . . E 3 -17.38 -21.48 13.733 1 114.15 ? C3 NAG 803 AAA 1 HETATM 4 C C4 NAG . . . E 3 -16.482 -20.234 13.767 1 115 ? C4 NAG 803 AAA 1 HETATM 5 C C5 NAG . . . E 3 -15.543 -20.379 14.975 1 113.34 ? C5 NAG 803 AAA 1 HETATM 6 C C6 NAG . . . E 3 -14.367 -19.367 15.057 1 112.4 ? C6 NAG 803 AAA 1 HETATM 7 C C7 NAG . . . E 3 -20.259 -22.728 15.669 1 123.83 ? C7 NAG 803 AAA 1 HETATM 8 C C8 NAG . . . E 3 -21.041 -24.002 15.784 1 123.42 ? C8 NAG 803 AAA 1 HETATM 9 N N2 NAG . . . E 3 -19.02 -22.771 15.116 1 113.87 ? N2 NAG 803 AAA 1 HETATM 10 O O3 NAG . . . E 3 -18.252 -21.423 12.598 1 116.74 ? O3 NAG 803 AAA 1 HETATM 11 O O4 NAG . . . E 3 -15.79 -20.085 12.517 1 115.24 ? O4 NAG 803 AAA 1 HETATM 12 O O5 NAG . . . E 3 -16.383 -20.398 16.166 1 112.42 ? O5 NAG 803 AAA 1 HETATM 13 O O6 NAG . . . E 3 -14.618 -18.079 14.464 1 113.8 ? O6 NAG 803 AAA 1 HETATM 14 O O7 NAG . . . E 3 -20.774 -21.708 16.107 1 131.68 ? O7 NAG 803 AAA 1 HETATM 15 H H1 NAG . . . E 3 -16.644 -22.46 16.283 1 111.8 ? H1 NAG 803 AAA 1 HETATM 16 H H2 NAG . . . E 3 -18.81 -20.699 15.09 1 113.51 ? H2 NAG 803 AAA 1 HETATM 17 H H3 NAG . . . E 3 -16.737 -22.367 13.646 1 114.29 ? H3 NAG 803 AAA 1 HETATM 18 H H4 NAG . . . E 3 -17.122 -19.356 13.935 1 114.78 ? H4 NAG 803 AAA 1 HETATM 19 H H5 NAG . . . E 3 -15.075 -21.37 14.887 1 113.11 ? H5 NAG 803 AAA 1 HETATM 20 H H61 NAG . . . E 3 -13.494 -19.809 14.57 1 112.72 ? H61 NAG 803 AAA 1 HETATM 21 H H62 NAG . . . E 3 -14.107 -19.22 16.107 1 111.66 ? H62 NAG 803 AAA 1 HETATM 22 H H81 NAG . . . E 3 -21.175 -24.238 16.808 1 122.87 ? H81 NAG 803 AAA 1 HETATM 23 H H82 NAG . . . E 3 -21.988 -23.875 15.328 1 124.65 ? H82 NAG 803 AAA 1 HETATM 24 H H83 NAG . . . E 3 -20.524 -24.791 15.305 1 123.86 ? H83 NAG 803 AAA 1 HETATM 25 H HN2 NAG . . . E 3 -18.651 -23.645 14.768 1 116.34 ? HN2 NAG 803 AAA 1 HETATM 26 H HO3 NAG . . . E 3 -17.381 -21.316 11.902 0 30 ? HO3 NAG 803 AAA 1 HETATM 27 H HO4 NAG . . . E 3 -14.793 -19.434 12.938 0 30 ? HO4 NAG 803 AAA 1 HETATM 28 H HO6 NAG . . . E 3 -14.463 -17.255 15.07 0 30 ? HO6 NAG 803 AAA 1 # _model_server_stats.io_time_ms 104 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #