data_6SVY # _model_server_result.job_id p6pXc2LSrahHdtfdyBLW8g _model_server_result.datetime_utc '2024-11-14 04:08:55' _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 6svy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":806}' # _entry.id 6SVY # _exptl.entry_id 6SVY _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 90 _cell.angle_gamma 120 _cell.entry_id 6SVY _cell.length_a 108.164 _cell.length_b 108.164 _cell.length_c 112.955 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6SVY _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall 'P 32 2"' _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 D N N ? 4 E N N ? 4 F N N ? 4 G N 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 6 A CYS 56 1_555 A SG CYS 11 A CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 29 A CYS 79 1_555 A SG CYS 684 A CYS 734 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 37 A CYS 87 1_555 A SG CYS 644 A CYS 694 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 92 A CYS 142 1_555 A SG CYS 360 A CYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 183 A CYS 233 1_555 A SG CYS 191 A CYS 241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 A SG CYS 570 A CYS 620 1_555 A SG CYS 696 A CYS 746 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 94 A ASN 144 1_555 D C1 NAG . A NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A ND2 ASN 234 A ASN 284 1_555 E C1 NAG . A NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 274 A ASN 324 1_555 F C1 NAG . A NAG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 A ND2 ASN 577 A ASN 627 1_555 G C1 NAG . A NAG 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? metalc ? metalc1 A NE2 HIS 533 A HIS 583 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc2 A NE2 HIS 537 A HIS 587 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc3 A OE1 GLU 596 A GLU 646 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? metalc ? metalc4 B ZN ZN . A ZN 801 1_555 C O37 D0W . A D0W 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? # _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 309 n n C1 O1 NAG sing 310 n n C1 O5 NAG sing 311 n n C1 H1 NAG sing 312 n n C2 C3 NAG sing 313 n n C2 N2 NAG sing 314 n n C2 H2 NAG sing 315 n n C3 C4 NAG sing 316 n n C3 O3 NAG sing 317 n n C3 H3 NAG sing 318 n n C4 C5 NAG sing 319 n n C4 O4 NAG sing 320 n n C4 H4 NAG sing 321 n n C5 C6 NAG sing 322 n n C5 O5 NAG sing 323 n n C5 H5 NAG sing 324 n n C6 O6 NAG sing 325 n n C6 H61 NAG sing 326 n n C6 H62 NAG sing 327 n n C7 C8 NAG sing 328 n n C7 N2 NAG sing 329 n n C7 O7 NAG doub 330 n n C8 H81 NAG sing 331 n n C8 H82 NAG sing 332 n n C8 H83 NAG sing 333 n n N2 HN2 NAG sing 334 n n O1 HO1 NAG sing 335 n n O3 HO3 NAG sing 336 n n O4 HO4 NAG sing 337 n n O6 HO6 NAG sing 338 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 6SVY _atom_sites.fract_transf_matrix[1][1] 0.009245 _atom_sites.fract_transf_matrix[1][2] 0.005338 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010675 _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] 0.008853 _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 ZN A 1 801 806 ZN ZN . C 3 D0W A 1 802 901 D0W LIG . D 4 NAG A 1 803 902 NAG NAG . E 4 NAG A 1 804 903 NAG NAG . F 4 NAG A 1 805 904 NAG NAG . G 4 NAG A 1 806 905 NAG NAG . H 5 HOH A 1 901 24 HOH HOH . H 5 HOH A 2 902 1 HOH HOH . H 5 HOH A 3 903 57 HOH HOH . H 5 HOH A 4 904 11 HOH HOH . H 5 HOH A 5 905 23 HOH HOH . H 5 HOH A 6 906 25 HOH HOH . H 5 HOH A 7 907 5 HOH HOH . H 5 HOH A 8 908 51 HOH HOH . H 5 HOH A 9 909 9 HOH HOH . H 5 HOH A 10 910 17 HOH HOH . H 5 HOH A 11 911 46 HOH HOH . H 5 HOH A 12 912 27 HOH HOH . H 5 HOH A 13 913 3 HOH HOH . H 5 HOH A 14 914 6 HOH HOH . H 5 HOH A 15 915 4 HOH HOH . H 5 HOH A 16 916 53 HOH HOH . H 5 HOH A 17 917 7 HOH HOH . H 5 HOH A 18 918 58 HOH HOH . H 5 HOH A 19 919 8 HOH HOH . H 5 HOH A 20 920 2 HOH HOH . H 5 HOH A 21 921 38 HOH HOH . H 5 HOH A 22 922 52 HOH HOH . H 5 HOH A 23 923 20 HOH HOH . H 5 HOH A 24 924 18 HOH HOH . H 5 HOH A 25 925 33 HOH HOH . H 5 HOH A 26 926 21 HOH HOH . H 5 HOH A 27 927 37 HOH HOH . H 5 HOH A 28 928 39 HOH HOH . H 5 HOH A 29 929 14 HOH HOH . H 5 HOH A 30 930 22 HOH HOH . H 5 HOH A 31 931 43 HOH HOH . H 5 HOH A 32 932 34 HOH HOH . H 5 HOH A 33 933 45 HOH HOH . H 5 HOH A 34 934 47 HOH HOH . H 5 HOH A 35 935 32 HOH HOH . H 5 HOH A 36 936 19 HOH HOH . H 5 HOH A 37 937 15 HOH HOH . H 5 HOH A 38 938 13 HOH HOH . H 5 HOH A 39 939 42 HOH HOH . H 5 HOH A 40 940 54 HOH HOH . H 5 HOH A 41 941 28 HOH HOH . H 5 HOH A 42 942 16 HOH HOH . H 5 HOH A 43 943 12 HOH HOH . H 5 HOH A 44 944 56 HOH HOH . H 5 HOH A 45 945 59 HOH HOH . H 5 HOH A 46 946 36 HOH HOH . H 5 HOH A 47 947 48 HOH HOH . H 5 HOH A 48 948 35 HOH HOH . H 5 HOH A 49 949 44 HOH HOH . H 5 HOH A 50 950 30 HOH HOH . H 5 HOH A 51 951 31 HOH HOH . H 5 HOH A 52 952 10 HOH HOH . H 5 HOH A 53 953 50 HOH HOH . H 5 HOH A 54 954 26 HOH HOH . H 5 HOH A 55 955 40 HOH HOH . H 5 HOH A 56 956 55 HOH HOH . H 5 HOH A 57 957 41 HOH HOH . H 5 HOH A 58 958 49 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 . . . G 4 -0.819 59.633 11.871 1 64.02 ? C1 NAG 806 A 1 HETATM 2 C C2 NAG . . . G 4 -0.597 58.459 10.916 1 65.7 ? C2 NAG 806 A 1 HETATM 3 C C3 NAG . . . G 4 0.459 58.817 9.872 1 63.76 ? C3 NAG 806 A 1 HETATM 4 C C4 NAG . . . G 4 0.089 60.113 9.164 1 63.9 ? C4 NAG 806 A 1 HETATM 5 C C5 NAG . . . G 4 -0.148 61.22 10.187 1 66.4 ? C5 NAG 806 A 1 HETATM 6 C C6 NAG . . . G 4 -0.628 62.51 9.563 1 64.67 ? C6 NAG 806 A 1 HETATM 7 C C7 NAG . . . G 4 -0.841 56.091 11.515 1 60.02 ? C7 NAG 806 A 1 HETATM 8 C C8 NAG . . . G 4 -0.304 54.96 12.34 1 63.61 ? C8 NAG 806 A 1 HETATM 9 N N2 NAG . . . G 4 -0.208 57.261 11.643 1 64.73 ? N2 NAG 806 A 1 HETATM 10 O O3 NAG . . . G 4 0.566 57.759 8.926 1 62.62 ? O3 NAG 806 A 1 HETATM 11 O O4 NAG . . . G 4 1.136 60.502 8.283 1 66.94 ? O4 NAG 806 A 1 HETATM 12 O O5 NAG . . . G 4 -1.159 60.81 11.12 1 64.38 ? O5 NAG 806 A 1 HETATM 13 O O6 NAG . . . G 4 -1.469 62.263 8.444 1 65.86 ? O6 NAG 806 A 1 HETATM 14 O O7 NAG . . . G 4 -1.805 55.952 10.769 1 53.04 ? O7 NAG 806 A 1 HETATM 15 H H2 NAG . . . G 4 -1.435 58.283 10.448 1 78.84 ? H2 NAG 806 A 1 HETATM 16 H H3 NAG . . . G 4 1.319 58.934 10.318 1 76.51 ? H3 NAG 806 A 1 HETATM 17 H H4 NAG . . . G 4 -0.727 59.975 8.648 1 76.68 ? H4 NAG 806 A 1 HETATM 18 H H5 NAG . . . G 4 0.683 61.389 10.671 1 79.68 ? H5 NAG 806 A 1 HETATM 19 H H61 NAG . . . G 4 0.145 63.03 9.273 1 77.61 ? H61 NAG 806 A 1 HETATM 20 H H62 NAG . . . G 4 -1.126 63.02 10.229 1 77.61 ? H62 NAG 806 A 1 HETATM 21 H H81 NAG . . . G 4 -0.882 54.18 12.238 1 76.33 ? H81 NAG 806 A 1 HETATM 22 H H82 NAG . . . G 4 -0.277 55.225 13.278 1 76.33 ? H82 NAG 806 A 1 HETATM 23 H H83 NAG . . . G 4 0.598 54.737 12.039 1 76.33 ? H83 NAG 806 A 1 HETATM 24 H HN2 NAG . . . G 4 0.501 57.311 12.214 1 77.68 ? HN2 NAG 806 A 1 HETATM 25 H HO3 NAG . . . G 4 -0.03 57.878 8.279 1 75.14 ? HO3 NAG 806 A 1 HETATM 26 H HO4 NAG . . . G 4 0.842 61.137 7.736 1 80.32 ? HO4 NAG 806 A 1 HETATM 27 H HO6 NAG . . . G 4 -1.705 63.036 8.076 1 79.04 ? HO6 NAG 806 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #