data_5GR8 # _model_server_result.job_id 9wi_zwzfEVwhU4f0QmR5ig _model_server_result.datetime_utc '2024-10-28 02:23:50' _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 5gr8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":806}' # _entry.id 5GR8 # _exptl.entry_id 5GR8 _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 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 110.79 _cell.angle_gamma 90 _cell.entry_id 5GR8 _cell.length_a 99.49 _cell.length_b 96.967 _cell.length_c 106.013 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GR8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_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,H,I,J,K,L,P,R 1 1 B,D,F,G,M,N,O,Q,S 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 H N N ? 4 I N N ? 4 J N N ? 4 K N N ? 4 M N N ? 4 N N N ? 4 O N 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 E NAG 1 B 1 NAG C 1 NAG 3 n E NAG 2 B 2 NAG C 2 NAG 3 n F NAG 1 C 1 NAG M 1 NAG 3 n F NAG 2 C 2 NAG M 2 NAG 3 n G NAG 1 E 1 NAG F 1 NAG 3 n G NAG 2 E 2 NAG F 2 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 36 A CYS 64 1_555 A SG CYS 43 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 238 A CYS 266 1_555 A SG CYS 262 A CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf3 A SG CYS 428 A CYS 456 1_555 A SG CYS 454 A CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 B SG CYS 36 D CYS 64 1_555 B SG CYS 43 D CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf5 B SG CYS 238 D CYS 266 1_555 B SG CYS 262 D CYS 290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf6 B SG CYS 428 D CYS 456 1_555 B SG CYS 454 D CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 53 A ASN 81 1_555 K C1 NAG . A NAG 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 224 A ASN 252 1_555 E C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 A ND2 ASN 261 A ASN 289 1_555 J C1 NAG . A NAG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 A ND2 ASN 392 A ASN 420 1_555 H C1 NAG . A NAG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale5 A ND2 ASN 532 A ASN 560 1_555 I C1 NAG . A NAG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale6 B ND2 ASN 29 D ASN 57 1_555 O C1 NAG . D NAG 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 B ND2 ASN 224 D ASN 252 1_555 G C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale8 B ND2 ASN 392 D ASN 420 1_555 F C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale9 B ND2 ASN 503 D ASN 531 1_555 M C1 NAG . D NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 B ND2 ASN 532 D ASN 560 1_555 N C1 NAG . D NAG 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale11 E O4 NAG . B NAG 1 1_555 E C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale12 F O4 NAG . C NAG 1 1_555 F C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale13 G O4 NAG . E NAG 1 1_555 G C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 5GR8 _atom_sites.fract_transf_matrix[1][1] 0.010051 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003817 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010313 _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] 0.01009 _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 H 4 NAG A 1 801 1 NAG NAG . I 4 NAG A 1 802 1 NAG NAG . J 4 NAG A 1 805 1 NAG NAG . K 4 NAG A 1 806 1 NAG NAG . L 5 SO4 A 1 807 1 SO4 SO4 . M 4 NAG D 1 803 1 NAG NAG . N 4 NAG D 1 806 1 NAG NAG . O 4 NAG D 1 807 1 NAG NAG . P 6 HOH A 1 901 49 HOH HOH . P 6 HOH A 2 902 65 HOH HOH . P 6 HOH A 3 903 33 HOH HOH . P 6 HOH A 4 904 56 HOH HOH . P 6 HOH A 5 905 38 HOH HOH . P 6 HOH A 6 906 57 HOH HOH . P 6 HOH A 7 907 3 HOH HOH . P 6 HOH A 8 908 20 HOH HOH . P 6 HOH A 9 909 29 HOH HOH . P 6 HOH A 10 910 34 HOH HOH . P 6 HOH A 11 911 4 HOH HOH . P 6 HOH A 12 912 63 HOH HOH . P 6 HOH A 13 913 26 HOH HOH . P 6 HOH A 14 914 5 HOH HOH . P 6 HOH A 15 915 53 HOH HOH . P 6 HOH A 16 916 55 HOH HOH . P 6 HOH A 17 917 48 HOH HOH . P 6 HOH A 18 918 44 HOH HOH . P 6 HOH A 19 919 14 HOH HOH . P 6 HOH A 20 920 43 HOH HOH . P 6 HOH A 21 921 19 HOH HOH . P 6 HOH A 22 922 11 HOH HOH . P 6 HOH A 23 923 27 HOH HOH . P 6 HOH A 24 924 39 HOH HOH . P 6 HOH A 25 925 9 HOH HOH . P 6 HOH A 26 926 1 HOH HOH . P 6 HOH A 27 927 7 HOH HOH . P 6 HOH A 28 928 59 HOH HOH . P 6 HOH A 29 929 54 HOH HOH . P 6 HOH A 30 930 42 HOH HOH . P 6 HOH A 31 931 23 HOH HOH . P 6 HOH A 32 932 31 HOH HOH . P 6 HOH A 33 933 28 HOH HOH . P 6 HOH A 34 934 41 HOH HOH . P 6 HOH A 35 935 35 HOH HOH . P 6 HOH A 36 936 36 HOH HOH . P 6 HOH A 37 937 61 HOH HOH . P 6 HOH A 38 938 30 HOH HOH . P 6 HOH A 39 939 22 HOH HOH . P 6 HOH A 40 940 37 HOH HOH . P 6 HOH A 41 941 25 HOH HOH . P 6 HOH A 42 942 2 HOH HOH . P 6 HOH A 43 943 21 HOH HOH . P 6 HOH A 44 944 16 HOH HOH . P 6 HOH A 45 945 15 HOH HOH . P 6 HOH A 46 946 46 HOH HOH . P 6 HOH A 47 947 62 HOH HOH . Q 6 HOH D 1 901 50 HOH HOH . Q 6 HOH D 2 902 13 HOH HOH . Q 6 HOH D 3 903 58 HOH HOH . Q 6 HOH D 4 904 32 HOH HOH . Q 6 HOH D 5 905 8 HOH HOH . Q 6 HOH D 6 906 24 HOH HOH . Q 6 HOH D 7 907 47 HOH HOH . Q 6 HOH D 8 908 45 HOH HOH . Q 6 HOH D 9 909 10 HOH HOH . Q 6 HOH D 10 910 12 HOH HOH . Q 6 HOH D 11 911 67 HOH HOH . Q 6 HOH D 12 912 17 HOH HOH . Q 6 HOH D 13 913 18 HOH HOH . R 6 HOH J 1 101 64 HOH HOH . R 6 HOH J 2 102 6 HOH HOH . R 6 HOH J 3 103 52 HOH HOH . R 6 HOH J 4 104 51 HOH HOH . S 6 HOH P 1 101 66 HOH HOH . S 6 HOH P 2 102 40 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 . . . K 4 9.72 -13.366 45.909 1 28.08 ? C1 NAG 806 A 1 HETATM 2 C C2 NAG . . . K 4 8.463 -12.496 46.066 1 26.73 ? C2 NAG 806 A 1 HETATM 3 C C3 NAG . . . K 4 8.594 -11.133 45.384 1 30.13 ? C3 NAG 806 A 1 HETATM 4 C C4 NAG . . . K 4 9.877 -10.466 45.829 1 29.97 ? C4 NAG 806 A 1 HETATM 5 C C5 NAG . . . K 4 11.022 -11.411 45.477 1 33.18 ? C5 NAG 806 A 1 HETATM 6 C C6 NAG . . . K 4 12.372 -10.78 45.793 1 30.68 ? C6 NAG 806 A 1 HETATM 7 C C7 NAG . . . K 4 6.152 -13.163 46.296 1 27.37 ? C7 NAG 806 A 1 HETATM 8 C C8 NAG . . . K 4 4.93 -13.769 45.655 1 18.42 ? C8 NAG 806 A 1 HETATM 9 N N2 NAG . . . K 4 7.275 -13.162 45.571 1 22.79 ? N2 NAG 806 A 1 HETATM 10 O O3 NAG . . . K 4 7.518 -10.281 45.717 1 35.15 ? O3 NAG 806 A 1 HETATM 11 O O4 NAG . . . K 4 9.995 -9.179 45.244 1 32.88 ? O4 NAG 806 A 1 HETATM 12 O O5 NAG . . . K 4 10.88 -12.616 46.228 1 32.68 ? O5 NAG 806 A 1 HETATM 13 O O6 NAG . . . K 4 12.474 -10.674 47.198 1 34.48 ? O6 NAG 806 A 1 HETATM 14 O O7 NAG . . . K 4 6.088 -12.706 47.447 1 26.02 ? O7 NAG 806 A 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #