data_6XVP # _model_server_result.job_id 8NeACoek1KTmdz-K6xjXIQ _model_server_result.datetime_utc '2024-11-13 10:09:16' _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 6xvp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":804}' # _entry.id 6XVP # _exptl.entry_id 6XVP _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 6XVP _cell.length_a 108.089 _cell.length_b 108.089 _cell.length_c 112.826 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XVP _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,I,J,K _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 29 A CYS 79 1_555 A SG CYS 684 A CYS 734 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 37 A CYS 87 1_555 A SG CYS 644 A CYS 694 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf6 A SG CYS 570 A CYS 620 1_555 A SG CYS 696 A CYS 746 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 94 A ASN 144 1_555 D C1 NAG . A NAG 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 234 A ASN 284 1_555 E C1 NAG . A NAG 804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 A ND2 ASN 274 A ASN 324 1_555 F C1 NAG . A NAG 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale4 A ND2 ASN 577 A ASN 627 1_555 G C1 NAG . A NAG 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? metalc ? metalc1 A NE2 HIS 533 A HIS 583 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc2 A NE2 HIS 537 A HIS 587 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc3 A OE1 GLU 596 A GLU 646 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc4 A OE2 GLU 596 A GLU 646 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc5 B ZN ZN . A ZN 801 1_555 C O39 D0Z . A D0Z 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? # _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 327 n n C1 O1 NAG sing 328 n n C1 O5 NAG sing 329 n n C1 H1 NAG sing 330 n n C2 C3 NAG sing 331 n n C2 N2 NAG sing 332 n n C2 H2 NAG sing 333 n n C3 C4 NAG sing 334 n n C3 O3 NAG sing 335 n n C3 H3 NAG sing 336 n n C4 C5 NAG sing 337 n n C4 O4 NAG sing 338 n n C4 H4 NAG sing 339 n n C5 C6 NAG sing 340 n n C5 O5 NAG sing 341 n n C5 H5 NAG sing 342 n n C6 O6 NAG sing 343 n n C6 H61 NAG sing 344 n n C6 H62 NAG sing 345 n n C7 C8 NAG sing 346 n n C7 N2 NAG sing 347 n n C7 O7 NAG doub 348 n n C8 H81 NAG sing 349 n n C8 H82 NAG sing 350 n n C8 H83 NAG sing 351 n n N2 HN2 NAG sing 352 n n O1 HO1 NAG sing 353 n n O3 HO3 NAG sing 354 n n O4 HO4 NAG sing 355 n n O6 HO6 NAG sing 356 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 6XVP _atom_sites.fract_transf_matrix[1][1] 0.009252 _atom_sites.fract_transf_matrix[1][2] 0.005341 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010683 _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] 0.008863 _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 1 801 805 ZN ZN . C 3 D0Z A 1 802 901 D0Z SP4 . 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 EDO A 1 807 1001 EDO EDO . I 5 EDO A 1 808 1101 EDO EDO . J 5 EDO A 1 809 1201 EDO EDO . K 6 HOH A 1 901 17 HOH HOH . K 6 HOH A 2 902 28 HOH HOH . K 6 HOH A 3 903 4 HOH HOH . K 6 HOH A 4 904 1 HOH HOH . K 6 HOH A 5 905 2 HOH HOH . K 6 HOH A 6 906 20 HOH HOH . K 6 HOH A 7 907 12 HOH HOH . K 6 HOH A 8 908 27 HOH HOH . K 6 HOH A 9 909 3 HOH HOH . K 6 HOH A 10 910 7 HOH HOH . K 6 HOH A 11 911 34 HOH HOH . K 6 HOH A 12 912 5 HOH HOH . K 6 HOH A 13 913 35 HOH HOH . K 6 HOH A 14 914 26 HOH HOH . K 6 HOH A 15 915 8 HOH HOH . K 6 HOH A 16 916 21 HOH HOH . K 6 HOH A 17 917 14 HOH HOH . K 6 HOH A 18 918 37 HOH HOH . K 6 HOH A 19 919 30 HOH HOH . K 6 HOH A 20 920 6 HOH HOH . K 6 HOH A 21 921 32 HOH HOH . K 6 HOH A 22 922 11 HOH HOH . K 6 HOH A 23 923 24 HOH HOH . K 6 HOH A 24 924 18 HOH HOH . K 6 HOH A 25 925 29 HOH HOH . K 6 HOH A 26 926 31 HOH HOH . K 6 HOH A 27 927 10 HOH HOH . K 6 HOH A 28 928 16 HOH HOH . K 6 HOH A 29 929 19 HOH HOH . K 6 HOH A 30 930 9 HOH HOH . K 6 HOH A 31 931 15 HOH HOH . K 6 HOH A 32 932 22 HOH HOH . K 6 HOH A 33 933 13 HOH HOH . K 6 HOH A 34 934 39 HOH HOH . K 6 HOH A 35 935 36 HOH HOH . K 6 HOH A 36 936 23 HOH HOH . K 6 HOH A 37 937 25 HOH HOH . K 6 HOH A 38 938 33 HOH HOH . K 6 HOH A 39 939 38 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 4 5.146 33.625 4.853 1 69.82 ? C1 NAG 804 A 1 HETATM 2 C C2 NAG . . . E 4 6.528 32.969 4.897 1 81.4 ? C2 NAG 804 A 1 HETATM 3 C C3 NAG . . . E 4 7.502 33.727 4 1 84.24 ? C3 NAG 804 A 1 HETATM 4 C C4 NAG . . . E 4 6.941 33.836 2.59 1 86.62 ? C4 NAG 804 A 1 HETATM 5 C C5 NAG . . . E 4 5.551 34.466 2.628 1 87.55 ? C5 NAG 804 A 1 HETATM 6 C C6 NAG . . . E 4 4.884 34.502 1.274 1 92.76 ? C6 NAG 804 A 1 HETATM 7 C C7 NAG . . . E 4 7.38 31.756 6.854 1 76.41 ? C7 NAG 804 A 1 HETATM 8 C C8 NAG . . . E 4 7.884 31.872 8.262 1 75.94 ? C8 NAG 804 A 1 HETATM 9 N N2 NAG . . . E 4 7.034 32.902 6.259 1 78.39 ? N2 NAG 804 A 1 HETATM 10 O O3 NAG . . . E 4 8.75 33.045 3.972 1 84.88 ? O3 NAG 804 A 1 HETATM 11 O O4 NAG . . . E 4 7.8 34.634 1.783 1 88.02 ? O4 NAG 804 A 1 HETATM 12 O O5 NAG . . . E 4 4.692 33.706 3.491 1 80.76 ? O5 NAG 804 A 1 HETATM 13 O O6 NAG . . . E 4 4.87 33.217 0.667 1 94.76 ? O6 NAG 804 A 1 HETATM 14 O O7 NAG . . . E 4 7.289 30.673 6.282 1 75.63 ? O7 NAG 804 A 1 HETATM 15 H H2 NAG . . . E 4 6.445 32.06 4.552 1 97.68 ? H2 NAG 804 A 1 HETATM 16 H H3 NAG . . . E 4 7.637 34.623 4.363 1 101.09 ? H3 NAG 804 A 1 HETATM 17 H H4 NAG . . . E 4 6.878 32.945 2.198 1 103.94 ? H4 NAG 804 A 1 HETATM 18 H H5 NAG . . . E 4 5.625 35.375 2.976 1 105.06 ? H5 NAG 804 A 1 HETATM 19 H H61 NAG . . . E 4 5.368 35.122 0.696 1 111.31 ? H61 NAG 804 A 1 HETATM 20 H H62 NAG . . . E 4 3.965 34.815 1.379 1 111.31 ? H62 NAG 804 A 1 HETATM 21 H H81 NAG . . . E 4 8.057 30.98 8.62 1 91.13 ? H81 NAG 804 A 1 HETATM 22 H H82 NAG . . . E 4 7.214 32.32 8.812 1 91.13 ? H82 NAG 804 A 1 HETATM 23 H H83 NAG . . . E 4 8.711 32.391 8.269 1 91.13 ? H83 NAG 804 A 1 HETATM 24 H HN2 NAG . . . E 4 7.12 33.679 6.73 1 94.07 ? HN2 NAG 804 A 1 HETATM 25 H HO3 NAG . . . E 4 8.856 32.654 3.181 1 101.86 ? HO3 NAG 804 A 1 HETATM 26 H HO4 NAG . . . E 4 7.667 34.439 0.927 1 105.62 ? HO4 NAG 804 A 1 HETATM 27 H HO6 NAG . . . E 4 4.647 32.606 1.272 1 113.71 ? HO6 NAG 804 A 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #