data_5WB0 # _model_server_result.job_id DxUmIArxAC-nwo8oXxwYoQ _model_server_result.datetime_utc '2024-10-18 04:31:13' _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 5wb0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 5WB0 # _exptl.entry_id 5WB0 _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 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 5WB0 _cell.length_a 177.7 _cell.length_b 177.7 _cell.length_c 177.7 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WB0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . 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 B NAG 1 A 1 NAG F 672 NAG 2 n B NAG 2 A 2 NAG F 673 NAG 3 n C NAG 1 B 1 NAG F 853 NAG 3 n C NAG 2 B 2 NAG F 854 NAG 3 n C BMA 3 B 3 BMA F 855 BMA 3 n C MAN 4 B 4 MAN F 856 MAN # 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 28 F CYS 28 1_555 A SG CYS 407 F CYS 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 60 F CYS 60 1_555 A SG CYS 182 F CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 283 F CYS 283 1_555 A SG CYS 311 F CYS 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf4 A SG CYS 292 F CYS 292 1_555 A SG CYS 301 F CYS 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf5 A SG CYS 326 F CYS 326 1_555 A SG CYS 335 F CYS 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 A SG CYS 350 F CYS 350 1_555 A SG CYS 361 F CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 A SG CYS 384 F CYS 384 1_555 A SG CYS 390 F CYS 390 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 A ND2 ASN 57 F ASN 57 1_555 D C1 NAG . F NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale2 A ND2 ASN 172 F ASN 172 1_555 B C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 A ND2 ASN 353 F ASN 353 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 B O4 NAG . A NAG 1 1_555 B C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 C O4 NAG . B NAG 2 1_555 C C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 C O3 BMA . B BMA 3 1_555 C C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _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 285 n n C1 O1 NAG sing 286 n n C1 O5 NAG sing 287 n n C1 H1 NAG sing 288 n n C2 C3 NAG sing 289 n n C2 N2 NAG sing 290 n n C2 H2 NAG sing 291 n n C3 C4 NAG sing 292 n n C3 O3 NAG sing 293 n n C3 H3 NAG sing 294 n n C4 C5 NAG sing 295 n n C4 O4 NAG sing 296 n n C4 H4 NAG sing 297 n n C5 C6 NAG sing 298 n n C5 O5 NAG sing 299 n n C5 H5 NAG sing 300 n n C6 O6 NAG sing 301 n n C6 H61 NAG sing 302 n n C6 H62 NAG sing 303 n n C7 C8 NAG sing 304 n n C7 N2 NAG sing 305 n n C7 O7 NAG doub 306 n n C8 H81 NAG sing 307 n n C8 H82 NAG sing 308 n n C8 H83 NAG sing 309 n n N2 HN2 NAG sing 310 n n O1 HO1 NAG sing 311 n n O3 HO3 NAG sing 312 n n O4 HO4 NAG sing 313 n n O6 HO6 NAG sing 314 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 5WB0 _atom_sites.fract_transf_matrix[1][1] 0.005627 _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] 0.005627 _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] 0.005627 _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 D 4 NAG F 1 601 557 NAG NAG . E 5 SO4 F 1 608 1 SO4 SO4 . F 5 SO4 F 1 609 2 SO4 SO4 . G 5 SO4 F 1 610 3 SO4 SO4 . H 5 SO4 F 1 611 4 SO4 SO4 . I 6 HOH F 1 701 46 HOH HOH . I 6 HOH F 2 702 85 HOH HOH . I 6 HOH F 3 703 71 HOH HOH . I 6 HOH F 4 704 33 HOH HOH . I 6 HOH F 5 705 14 HOH HOH . I 6 HOH F 6 706 40 HOH HOH . I 6 HOH F 7 707 141 HOH HOH . I 6 HOH F 8 708 91 HOH HOH . I 6 HOH F 9 709 72 HOH HOH . I 6 HOH F 10 710 3 HOH HOH . I 6 HOH F 11 711 29 HOH HOH . I 6 HOH F 12 712 137 HOH HOH . I 6 HOH F 13 713 106 HOH HOH . I 6 HOH F 14 714 6 HOH HOH . I 6 HOH F 15 715 8 HOH HOH . I 6 HOH F 16 716 70 HOH HOH . I 6 HOH F 17 717 56 HOH HOH . I 6 HOH F 18 718 17 HOH HOH . I 6 HOH F 19 719 96 HOH HOH . I 6 HOH F 20 720 75 HOH HOH . I 6 HOH F 21 721 125 HOH HOH . I 6 HOH F 22 722 2 HOH HOH . I 6 HOH F 23 723 20 HOH HOH . I 6 HOH F 24 724 43 HOH HOH . I 6 HOH F 25 725 25 HOH HOH . I 6 HOH F 26 726 22 HOH HOH . I 6 HOH F 27 727 28 HOH HOH . I 6 HOH F 28 728 10 HOH HOH . I 6 HOH F 29 729 26 HOH HOH . I 6 HOH F 30 730 38 HOH HOH . I 6 HOH F 31 731 58 HOH HOH . I 6 HOH F 32 732 31 HOH HOH . I 6 HOH F 33 733 7 HOH HOH . I 6 HOH F 34 734 21 HOH HOH . I 6 HOH F 35 735 133 HOH HOH . I 6 HOH F 36 736 34 HOH HOH . I 6 HOH F 37 737 5 HOH HOH . I 6 HOH F 38 738 15 HOH HOH . I 6 HOH F 39 739 12 HOH HOH . I 6 HOH F 40 740 119 HOH HOH . I 6 HOH F 41 741 127 HOH HOH . I 6 HOH F 42 742 89 HOH HOH . I 6 HOH F 43 743 105 HOH HOH . I 6 HOH F 44 744 36 HOH HOH . I 6 HOH F 45 745 24 HOH HOH . I 6 HOH F 46 746 88 HOH HOH . I 6 HOH F 47 747 81 HOH HOH . I 6 HOH F 48 748 142 HOH HOH . I 6 HOH F 49 749 11 HOH HOH . I 6 HOH F 50 750 18 HOH HOH . I 6 HOH F 51 751 60 HOH HOH . I 6 HOH F 52 752 44 HOH HOH . I 6 HOH F 53 753 41 HOH HOH . I 6 HOH F 54 754 13 HOH HOH . I 6 HOH F 55 755 54 HOH HOH . I 6 HOH F 56 756 102 HOH HOH . I 6 HOH F 57 757 1 HOH HOH . I 6 HOH F 58 758 76 HOH HOH . I 6 HOH F 59 759 118 HOH HOH . I 6 HOH F 60 760 16 HOH HOH . I 6 HOH F 61 761 53 HOH HOH . I 6 HOH F 62 762 50 HOH HOH . I 6 HOH F 63 763 107 HOH HOH . I 6 HOH F 64 764 92 HOH HOH . I 6 HOH F 65 765 61 HOH HOH . I 6 HOH F 66 766 23 HOH HOH . I 6 HOH F 67 767 42 HOH HOH . I 6 HOH F 68 768 4 HOH HOH . I 6 HOH F 69 769 27 HOH HOH . I 6 HOH F 70 770 66 HOH HOH . I 6 HOH F 71 771 49 HOH HOH . I 6 HOH F 72 772 19 HOH HOH . I 6 HOH F 73 773 55 HOH HOH . I 6 HOH F 74 774 51 HOH HOH . I 6 HOH F 75 775 84 HOH HOH . I 6 HOH F 76 776 100 HOH HOH . I 6 HOH F 77 777 47 HOH HOH . I 6 HOH F 78 778 37 HOH HOH . I 6 HOH F 79 779 132 HOH HOH . I 6 HOH F 80 780 120 HOH HOH . I 6 HOH F 81 781 129 HOH HOH . I 6 HOH F 82 782 87 HOH HOH . I 6 HOH F 83 783 98 HOH HOH . I 6 HOH F 84 784 93 HOH HOH . I 6 HOH F 85 785 99 HOH HOH . I 6 HOH F 86 786 57 HOH HOH . I 6 HOH F 87 787 35 HOH HOH . I 6 HOH F 88 788 59 HOH HOH . I 6 HOH F 89 789 68 HOH HOH . I 6 HOH F 90 790 111 HOH HOH . I 6 HOH F 91 791 64 HOH HOH . I 6 HOH F 92 792 116 HOH HOH . I 6 HOH F 93 793 110 HOH HOH . I 6 HOH F 94 794 39 HOH HOH . I 6 HOH F 95 795 139 HOH HOH . I 6 HOH F 96 796 124 HOH HOH . I 6 HOH F 97 797 9 HOH HOH . I 6 HOH F 98 798 135 HOH HOH . I 6 HOH F 99 799 65 HOH HOH . I 6 HOH F 100 800 112 HOH HOH . I 6 HOH F 101 801 69 HOH HOH . I 6 HOH F 102 802 78 HOH HOH . I 6 HOH F 103 803 115 HOH HOH . I 6 HOH F 104 804 97 HOH HOH . I 6 HOH F 105 805 117 HOH HOH . I 6 HOH F 106 806 113 HOH HOH . I 6 HOH F 107 807 114 HOH HOH . I 6 HOH F 108 808 82 HOH HOH . I 6 HOH F 109 809 79 HOH HOH . I 6 HOH F 110 810 101 HOH HOH . I 6 HOH F 111 811 48 HOH HOH . I 6 HOH F 112 812 138 HOH HOH . I 6 HOH F 113 813 104 HOH HOH . I 6 HOH F 114 814 136 HOH HOH . I 6 HOH F 115 815 86 HOH HOH . I 6 HOH F 116 816 128 HOH HOH . I 6 HOH F 117 817 95 HOH HOH . I 6 HOH F 118 818 130 HOH HOH . I 6 HOH F 119 819 122 HOH HOH . I 6 HOH F 120 820 134 HOH HOH . I 6 HOH F 121 821 45 HOH HOH . I 6 HOH F 122 822 131 HOH HOH . I 6 HOH F 123 823 123 HOH HOH . I 6 HOH F 124 824 74 HOH HOH . I 6 HOH F 125 825 90 HOH HOH . I 6 HOH F 126 826 32 HOH HOH . I 6 HOH F 127 827 140 HOH HOH . I 6 HOH F 128 828 143 HOH HOH . I 6 HOH F 129 829 121 HOH HOH . I 6 HOH F 130 830 83 HOH HOH . I 6 HOH F 131 831 103 HOH HOH . I 6 HOH F 132 832 67 HOH HOH . I 6 HOH F 133 833 63 HOH HOH . I 6 HOH F 134 834 77 HOH HOH . I 6 HOH F 135 835 126 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 . . . D 4 22.345 -8.132 -15.915 1 108.66 ? C1 NAG 601 F 1 HETATM 2 C C2 NAG . . . D 4 21.631 -7.741 -17.22 1 117.2 ? C2 NAG 601 F 1 HETATM 3 C C3 NAG . . . D 4 22.329 -8.375 -18.424 1 119.92 ? C3 NAG 601 F 1 HETATM 4 C C4 NAG . . . D 4 23.812 -8.028 -18.425 1 118.42 ? C4 NAG 601 F 1 HETATM 5 C C5 NAG . . . D 4 24.44 -8.456 -17.103 1 119.05 ? C5 NAG 601 F 1 HETATM 6 C C6 NAG . . . D 4 25.9 -8.08 -16.99 1 111.68 ? C6 NAG 601 F 1 HETATM 7 C C7 NAG . . . D 4 19.248 -7.359 -17.683 1 107.67 ? C7 NAG 601 F 1 HETATM 8 C C8 NAG . . . D 4 17.859 -7.91 -17.563 1 95.5 ? C8 NAG 601 F 1 HETATM 9 N N2 NAG . . . D 4 20.228 -8.123 -17.186 1 115.9 ? N2 NAG 601 F 1 HETATM 10 O O3 NAG . . . D 4 21.721 -7.913 -19.625 1 119.39 ? O3 NAG 601 F 1 HETATM 11 O O4 NAG . . . D 4 24.474 -8.68 -19.503 1 110.16 ? O4 NAG 601 F 1 HETATM 12 O O5 NAG . . . D 4 23.757 -7.815 -16.014 1 119.97 ? O5 NAG 601 F 1 HETATM 13 O O6 NAG . . . D 4 26.073 -6.678 -16.83 1 107.11 ? O6 NAG 601 F 1 HETATM 14 O O7 NAG . . . D 4 19.473 -6.271 -18.205 1 110 ? O7 NAG 601 F 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #