data_3WMB # _model_server_result.job_id j77E2_y9d7Xd_XoSZ9SwgA _model_server_result.datetime_utc '2024-10-15 06:12:32' _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 3wmb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":603}' # _entry.id 3WMB # _exptl.entry_id 3WMB _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 2 _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 3WMB _cell.length_a 107.773 _cell.length_b 107.773 _cell.length_c 175.346 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3WMB _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 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 ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 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,B,C,D,E 1 1 A,B,C,D,E 2 1,2 # 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 x-y,-y,-z+1/3 1 0 0 0 -1 0 0 0 -1 0 0 58.448667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 D 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 9 A CYS 31 1_555 A SG CYS 37 A CYS 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 A SG CYS 14 A CYS 36 1_555 A SG CYS 33 A CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? disulf ? disulf3 A SG CYS 294 A CYS 316 1_555 A SG CYS 351 A CYS 373 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 A SG CYS 304 A CYS 326 1_555 A SG CYS 309 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf5 A SG CYS 456 A CYS 478 1_555 A SG CYS 469 A CYS 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf6 A SG CYS 563 A CYS 585 1_555 A SG CYS 570 A CYS 592 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? covale ? covale1 A ND2 ASN 142 A ASN 164 1_555 C C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 A ND2 ASN 353 A ASN 375 1_555 D C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 3WMB _atom_sites.fract_transf_matrix[1][1] 0.009279 _atom_sites.fract_transf_matrix[1][2] 0.005357 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010714 _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] 0.005703 _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 NF1 A 1 601 1 NF1 DRG . C 3 NAG A 1 602 3 NAG NAG . D 3 NAG A 1 603 4 NAG NAG . E 4 HOH A 1 701 1 HOH HOH . E 4 HOH A 2 702 2 HOH HOH . E 4 HOH A 3 703 3 HOH HOH . E 4 HOH A 4 704 4 HOH HOH . E 4 HOH A 5 705 5 HOH HOH . E 4 HOH A 6 706 6 HOH HOH . E 4 HOH A 7 707 7 HOH HOH . E 4 HOH A 8 708 8 HOH HOH . E 4 HOH A 9 709 9 HOH HOH . E 4 HOH A 10 710 10 HOH HOH . E 4 HOH A 11 711 11 HOH HOH . E 4 HOH A 12 712 12 HOH HOH . E 4 HOH A 13 713 13 HOH HOH . E 4 HOH A 14 714 14 HOH HOH . E 4 HOH A 15 715 15 HOH HOH . E 4 HOH A 16 716 16 HOH HOH . E 4 HOH A 17 717 19 HOH HOH . E 4 HOH A 18 718 20 HOH HOH . E 4 HOH A 19 719 21 HOH HOH . E 4 HOH A 20 720 22 HOH HOH . E 4 HOH A 21 721 23 HOH HOH . E 4 HOH A 22 722 24 HOH HOH . E 4 HOH A 23 723 25 HOH HOH . E 4 HOH A 24 724 26 HOH HOH . E 4 HOH A 25 725 27 HOH HOH . E 4 HOH A 26 726 28 HOH HOH . E 4 HOH A 27 727 29 HOH HOH . E 4 HOH A 28 728 30 HOH HOH . E 4 HOH A 29 729 31 HOH HOH . E 4 HOH A 30 730 32 HOH HOH . E 4 HOH A 31 731 33 HOH HOH . E 4 HOH A 32 732 34 HOH HOH . E 4 HOH A 33 733 35 HOH HOH . E 4 HOH A 34 734 36 HOH HOH . E 4 HOH A 35 735 37 HOH HOH . E 4 HOH A 36 736 38 HOH HOH . E 4 HOH A 37 737 39 HOH HOH . E 4 HOH A 38 738 40 HOH HOH . E 4 HOH A 39 739 41 HOH HOH . E 4 HOH A 40 740 42 HOH HOH . E 4 HOH A 41 741 43 HOH HOH . E 4 HOH A 42 742 44 HOH HOH . E 4 HOH A 43 743 45 HOH HOH . E 4 HOH A 44 744 46 HOH HOH . E 4 HOH A 45 745 47 HOH HOH . E 4 HOH A 46 746 48 HOH HOH . E 4 HOH A 47 747 49 HOH HOH . E 4 HOH A 48 748 50 HOH HOH . E 4 HOH A 49 749 51 HOH HOH . E 4 HOH A 50 750 52 HOH HOH . E 4 HOH A 51 751 53 HOH HOH . E 4 HOH A 52 752 54 HOH HOH . E 4 HOH A 53 753 55 HOH HOH . E 4 HOH A 54 754 57 HOH HOH . E 4 HOH A 55 755 58 HOH HOH . E 4 HOH A 56 756 59 HOH HOH . E 4 HOH A 57 757 60 HOH HOH . E 4 HOH A 58 758 61 HOH HOH . E 4 HOH A 59 759 62 HOH HOH . E 4 HOH A 60 760 63 HOH HOH . E 4 HOH A 61 761 64 HOH HOH . E 4 HOH A 62 762 65 HOH HOH . E 4 HOH A 63 763 66 HOH HOH . E 4 HOH A 64 764 67 HOH HOH . E 4 HOH A 65 765 68 HOH HOH . E 4 HOH A 66 766 70 HOH HOH . E 4 HOH A 67 767 71 HOH HOH . E 4 HOH A 68 768 72 HOH HOH . E 4 HOH A 69 769 73 HOH HOH . E 4 HOH A 70 770 74 HOH HOH . E 4 HOH A 71 771 75 HOH HOH . E 4 HOH A 72 772 76 HOH HOH . E 4 HOH A 73 773 77 HOH HOH . E 4 HOH A 74 774 78 HOH HOH . E 4 HOH A 75 775 79 HOH HOH . E 4 HOH A 76 776 81 HOH HOH . E 4 HOH A 77 777 82 HOH HOH . E 4 HOH A 78 778 83 HOH HOH . E 4 HOH A 79 779 84 HOH HOH . E 4 HOH A 80 780 85 HOH HOH . E 4 HOH A 81 781 86 HOH HOH . E 4 HOH A 82 782 87 HOH HOH . E 4 HOH A 83 783 88 HOH HOH . E 4 HOH A 84 784 89 HOH HOH . E 4 HOH A 85 785 90 HOH HOH . E 4 HOH A 86 786 91 HOH HOH . E 4 HOH A 87 787 92 HOH HOH . E 4 HOH A 88 788 93 HOH HOH . E 4 HOH A 89 789 94 HOH HOH . E 4 HOH A 90 790 95 HOH HOH . E 4 HOH A 91 791 96 HOH HOH . E 4 HOH A 92 792 97 HOH HOH . E 4 HOH A 93 793 98 HOH HOH . E 4 HOH A 94 794 99 HOH HOH . E 4 HOH A 95 795 100 HOH HOH . E 4 HOH A 96 796 101 HOH HOH . E 4 HOH A 97 797 102 HOH HOH . E 4 HOH A 98 798 103 HOH HOH . E 4 HOH A 99 799 104 HOH HOH . E 4 HOH A 100 800 105 HOH HOH . E 4 HOH A 101 801 106 HOH HOH . E 4 HOH A 102 802 107 HOH HOH . E 4 HOH A 103 803 108 HOH HOH . E 4 HOH A 104 804 109 HOH HOH . E 4 HOH A 105 805 110 HOH HOH . E 4 HOH A 106 806 111 HOH HOH . E 4 HOH A 107 807 112 HOH HOH . E 4 HOH A 108 808 113 HOH HOH . E 4 HOH A 109 809 114 HOH HOH . E 4 HOH A 110 810 115 HOH HOH . E 4 HOH A 111 811 116 HOH HOH . E 4 HOH A 112 812 117 HOH HOH . E 4 HOH A 113 813 118 HOH HOH . E 4 HOH A 114 814 119 HOH HOH . E 4 HOH A 115 815 120 HOH HOH . E 4 HOH A 116 816 121 HOH HOH . E 4 HOH A 117 817 122 HOH HOH . E 4 HOH A 118 818 123 HOH HOH . E 4 HOH A 119 819 124 HOH HOH . E 4 HOH A 120 820 125 HOH HOH . E 4 HOH A 121 821 126 HOH HOH . E 4 HOH A 122 822 127 HOH HOH . E 4 HOH A 123 823 128 HOH HOH . E 4 HOH A 124 824 129 HOH HOH . E 4 HOH A 125 825 130 HOH HOH . E 4 HOH A 126 826 131 HOH HOH . E 4 HOH A 127 827 133 HOH HOH . E 4 HOH A 128 828 134 HOH HOH . E 4 HOH A 129 829 135 HOH HOH . E 4 HOH A 130 830 136 HOH HOH . E 4 HOH A 131 831 137 HOH HOH . E 4 HOH A 132 832 139 HOH HOH . E 4 HOH A 133 833 140 HOH HOH . E 4 HOH A 134 834 141 HOH HOH . E 4 HOH A 135 835 142 HOH HOH . E 4 HOH A 136 836 143 HOH HOH . E 4 HOH A 137 837 144 HOH HOH . E 4 HOH A 138 838 145 HOH HOH . E 4 HOH A 139 839 146 HOH HOH . E 4 HOH A 140 840 147 HOH HOH . E 4 HOH A 141 841 148 HOH HOH . E 4 HOH A 142 842 149 HOH HOH . E 4 HOH A 143 843 150 HOH HOH . E 4 HOH A 144 844 151 HOH HOH . E 4 HOH A 145 845 153 HOH HOH . E 4 HOH A 146 846 154 HOH HOH . E 4 HOH A 147 847 155 HOH HOH . E 4 HOH A 148 848 156 HOH HOH . E 4 HOH A 149 849 157 HOH HOH . E 4 HOH A 150 850 158 HOH HOH . E 4 HOH A 151 851 159 HOH HOH . E 4 HOH A 152 852 160 HOH HOH . E 4 HOH A 153 853 161 HOH HOH . E 4 HOH A 154 854 162 HOH HOH . E 4 HOH A 155 855 163 HOH HOH . E 4 HOH A 156 856 164 HOH HOH . E 4 HOH A 157 857 165 HOH HOH . E 4 HOH A 158 858 166 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 3 27.263 7.865 -7.726 1 68.64 ? C1 NAG 603 A 1 HETATM 2 C C2 NAG . . . D 3 26.063 7.262 -6.997 1 65.57 ? C2 NAG 603 A 1 HETATM 3 C C3 NAG . . . D 3 24.821 7.303 -7.887 1 68.66 ? C3 NAG 603 A 1 HETATM 4 C C4 NAG . . . D 3 24.587 8.704 -8.447 1 69.93 ? C4 NAG 603 A 1 HETATM 5 C C5 NAG . . . D 3 25.866 9.297 -9.037 1 66.78 ? C5 NAG 603 A 1 HETATM 6 C C6 NAG . . . D 3 25.669 10.772 -9.362 1 58.88 ? C6 NAG 603 A 1 HETATM 7 C C7 NAG . . . D 3 26.301 5.533 -5.278 1 50.83 ? C7 NAG 603 A 1 HETATM 8 C C8 NAG . . . D 3 26.51 4.074 -4.982 1 45.7 ? C8 NAG 603 A 1 HETATM 9 N N2 NAG . . . D 3 26.359 5.906 -6.558 1 58.91 ? N2 NAG 603 A 1 HETATM 10 O O3 NAG . . . D 3 23.689 6.91 -7.143 1 64.08 ? O3 NAG 603 A 1 HETATM 11 O O4 NAG . . . D 3 23.578 8.66 -9.437 1 68.59 ? O4 NAG 603 A 1 HETATM 12 O O5 NAG . . . D 3 26.959 9.183 -8.144 1 68.85 ? O5 NAG 603 A 1 HETATM 13 O O6 NAG . . . D 3 26.929 11.383 -9.527 1 58.38 ? O6 NAG 603 A 1 HETATM 14 O O7 NAG . . . D 3 26.085 6.324 -4.36 1 48.98 ? O7 NAG 603 A 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 24 _model_server_stats.element_count 14 #