data_8EG3 # _model_server_result.job_id zrWKdTSdQCS2DD7OZKd6zA _model_server_result.datetime_utc '2024-11-26 15:43:10' _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 8eg3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 8EG3 # _exptl.entry_id 8EG3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method syn _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 8EG3 _cell.length_a 117.19 _cell.length_b 117.19 _cell.length_c 102.68 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8EG3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 2 1' # _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 _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' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 58.595 -101.489517 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 117.19 0 0 # 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 141 A CYS 141 1_555 A SG CYS 148 A CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 170 A CYS 170 1_555 A SG CYS 242 A CYS 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf3 A SG CYS 446 A CYS 446 1_555 A SG CYS 489 A CYS 489 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 481 A CYS 481 1_555 A SG CYS 487 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf5 A SG CYS 562 A CYS 562 1_555 A SG CYS 570 A CYS 570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 A SG CYS 563 A CYS 563 1_555 A SG CYS 572 A CYS 572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? covale ? covale1 A ND2 ASN 47 A ASN 47 1_555 C C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale2 A C LEU 74 A LEU 74 1_555 A N ALS 75 A ALS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 A C ALS 75 A ALS 75 1_555 A N THR 76 A THR 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale4 A ND2 ASN 333 A ASN 333 1_555 D C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? metalc ? metalc1 A OD2 ASP 35 A ASP 35 1_555 B CA CA . A CA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc2 A OD1 ASP 36 A ASP 36 1_555 B CA CA . A CA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc3 A OS1 ALS 75 A ALS 75 1_555 B CA CA . A CA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc4 A OS3 ALS 75 A ALS 75 1_555 B CA CA . A CA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc5 A OD1 ASP 342 A ASP 342 1_555 B CA CA . A CA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? metalc ? metalc6 A OD2 ASP 342 A ASP 342 1_555 B CA CA . A CA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc7 A OE1 GLN 343 A GLN 343 1_555 B CA CA . A CA 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? # _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 303 n n C1 O1 NAG sing 304 n n C1 O5 NAG sing 305 n n C1 H1 NAG sing 306 n n C2 C3 NAG sing 307 n n C2 N2 NAG sing 308 n n C2 H2 NAG sing 309 n n C3 C4 NAG sing 310 n n C3 O3 NAG sing 311 n n C3 H3 NAG sing 312 n n C4 C5 NAG sing 313 n n C4 O4 NAG sing 314 n n C4 H4 NAG sing 315 n n C5 C6 NAG sing 316 n n C5 O5 NAG sing 317 n n C5 H5 NAG sing 318 n n C6 O6 NAG sing 319 n n C6 H61 NAG sing 320 n n C6 H62 NAG sing 321 n n C7 C8 NAG sing 322 n n C7 N2 NAG sing 323 n n C7 O7 NAG doub 324 n n C8 H81 NAG sing 325 n n C8 H82 NAG sing 326 n n C8 H83 NAG sing 327 n n N2 HN2 NAG sing 328 n n O1 HO1 NAG sing 329 n n O3 HO3 NAG sing 330 n n O4 HO4 NAG sing 331 n n O6 HO6 NAG sing 332 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 8EG3 _atom_sites.fract_transf_matrix[1][1] 0.008533 _atom_sites.fract_transf_matrix[1][2] 0.004927 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009853 _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] 0.009739 _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 CA A 1 600 600 CA CA . C 3 NAG A 1 601 601 NAG NAG . D 3 NAG A 1 602 602 NAG NAG . E 4 PO4 A 1 603 603 PO4 PO4 . F 5 BOG A 1 604 604 BOG BOG . G 5 BOG A 1 605 605 BOG BOG . H 6 HOH A 1 701 41 HOH HOH . H 6 HOH A 2 702 131 HOH HOH . H 6 HOH A 3 703 116 HOH HOH . H 6 HOH A 4 704 80 HOH HOH . H 6 HOH A 5 705 43 HOH HOH . H 6 HOH A 6 706 100 HOH HOH . H 6 HOH A 7 707 62 HOH HOH . H 6 HOH A 8 708 61 HOH HOH . H 6 HOH A 9 709 57 HOH HOH . H 6 HOH A 10 710 74 HOH HOH . H 6 HOH A 11 711 118 HOH HOH . H 6 HOH A 12 712 54 HOH HOH . H 6 HOH A 13 713 64 HOH HOH . H 6 HOH A 14 714 125 HOH HOH . H 6 HOH A 15 715 101 HOH HOH . H 6 HOH A 16 716 98 HOH HOH . H 6 HOH A 17 717 70 HOH HOH . H 6 HOH A 18 718 24 HOH HOH . H 6 HOH A 19 719 20 HOH HOH . H 6 HOH A 20 720 16 HOH HOH . H 6 HOH A 21 721 60 HOH HOH . H 6 HOH A 22 722 23 HOH HOH . H 6 HOH A 23 723 12 HOH HOH . H 6 HOH A 24 724 56 HOH HOH . H 6 HOH A 25 725 53 HOH HOH . H 6 HOH A 26 726 10 HOH HOH . H 6 HOH A 27 727 163 HOH HOH . H 6 HOH A 28 728 17 HOH HOH . H 6 HOH A 29 729 8 HOH HOH . H 6 HOH A 30 730 110 HOH HOH . H 6 HOH A 31 731 34 HOH HOH . H 6 HOH A 32 732 6 HOH HOH . H 6 HOH A 33 733 99 HOH HOH . H 6 HOH A 34 734 18 HOH HOH . H 6 HOH A 35 735 35 HOH HOH . H 6 HOH A 36 736 36 HOH HOH . H 6 HOH A 37 737 121 HOH HOH . H 6 HOH A 38 738 58 HOH HOH . H 6 HOH A 39 739 37 HOH HOH . H 6 HOH A 40 740 11 HOH HOH . H 6 HOH A 41 741 90 HOH HOH . H 6 HOH A 42 742 77 HOH HOH . H 6 HOH A 43 743 59 HOH HOH . H 6 HOH A 44 744 51 HOH HOH . H 6 HOH A 45 745 49 HOH HOH . H 6 HOH A 46 746 103 HOH HOH . H 6 HOH A 47 747 47 HOH HOH . H 6 HOH A 48 748 78 HOH HOH . H 6 HOH A 49 749 9 HOH HOH . H 6 HOH A 50 750 108 HOH HOH . H 6 HOH A 51 751 114 HOH HOH . H 6 HOH A 52 752 22 HOH HOH . H 6 HOH A 53 753 2 HOH HOH . H 6 HOH A 54 754 29 HOH HOH . H 6 HOH A 55 755 25 HOH HOH . H 6 HOH A 56 756 162 HOH HOH . H 6 HOH A 57 757 3 HOH HOH . H 6 HOH A 58 758 106 HOH HOH . H 6 HOH A 59 759 112 HOH HOH . H 6 HOH A 60 760 44 HOH HOH . H 6 HOH A 61 761 19 HOH HOH . H 6 HOH A 62 762 39 HOH HOH . H 6 HOH A 63 763 89 HOH HOH . H 6 HOH A 64 764 15 HOH HOH . H 6 HOH A 65 765 145 HOH HOH . H 6 HOH A 66 766 5 HOH HOH . H 6 HOH A 67 767 38 HOH HOH . H 6 HOH A 68 768 63 HOH HOH . H 6 HOH A 69 769 115 HOH HOH . H 6 HOH A 70 770 97 HOH HOH . H 6 HOH A 71 771 66 HOH HOH . H 6 HOH A 72 772 155 HOH HOH . H 6 HOH A 73 773 21 HOH HOH . H 6 HOH A 74 774 109 HOH HOH . H 6 HOH A 75 775 7 HOH HOH . H 6 HOH A 76 776 147 HOH HOH . H 6 HOH A 77 777 65 HOH HOH . H 6 HOH A 78 778 81 HOH HOH . H 6 HOH A 79 779 4 HOH HOH . H 6 HOH A 80 780 107 HOH HOH . H 6 HOH A 81 781 14 HOH HOH . H 6 HOH A 82 782 42 HOH HOH . H 6 HOH A 83 783 52 HOH HOH . H 6 HOH A 84 784 30 HOH HOH . H 6 HOH A 85 785 95 HOH HOH . H 6 HOH A 86 786 28 HOH HOH . H 6 HOH A 87 787 46 HOH HOH . H 6 HOH A 88 788 104 HOH HOH . H 6 HOH A 89 789 32 HOH HOH . H 6 HOH A 90 790 140 HOH HOH . H 6 HOH A 91 791 13 HOH HOH . H 6 HOH A 92 792 161 HOH HOH . H 6 HOH A 93 793 50 HOH HOH . H 6 HOH A 94 794 149 HOH HOH . H 6 HOH A 95 795 92 HOH HOH . H 6 HOH A 96 796 96 HOH HOH . H 6 HOH A 97 797 144 HOH HOH . H 6 HOH A 98 798 69 HOH HOH . H 6 HOH A 99 799 45 HOH HOH . H 6 HOH A 100 800 93 HOH HOH . H 6 HOH A 101 801 94 HOH HOH . H 6 HOH A 102 802 75 HOH HOH . H 6 HOH A 103 803 119 HOH HOH . H 6 HOH A 104 804 40 HOH HOH . H 6 HOH A 105 805 27 HOH HOH . H 6 HOH A 106 806 86 HOH HOH . H 6 HOH A 107 807 117 HOH HOH . H 6 HOH A 108 808 87 HOH HOH . H 6 HOH A 109 809 123 HOH HOH . H 6 HOH A 110 810 33 HOH HOH . H 6 HOH A 111 811 48 HOH HOH . H 6 HOH A 112 812 138 HOH HOH . H 6 HOH A 113 813 82 HOH HOH . H 6 HOH A 114 814 91 HOH HOH . H 6 HOH A 115 815 76 HOH HOH . H 6 HOH A 116 816 55 HOH HOH . H 6 HOH A 117 817 88 HOH HOH . H 6 HOH A 118 818 154 HOH HOH . H 6 HOH A 119 819 68 HOH HOH . H 6 HOH A 120 820 105 HOH HOH . H 6 HOH A 121 821 148 HOH HOH . H 6 HOH A 122 822 113 HOH HOH . H 6 HOH A 123 823 151 HOH HOH . H 6 HOH A 124 824 26 HOH HOH . H 6 HOH A 125 825 141 HOH HOH . H 6 HOH A 126 826 67 HOH HOH . H 6 HOH A 127 827 31 HOH HOH . H 6 HOH A 128 828 146 HOH HOH . H 6 HOH A 129 829 102 HOH HOH . H 6 HOH A 130 830 156 HOH HOH . H 6 HOH A 131 831 157 HOH HOH . H 6 HOH A 132 832 111 HOH HOH . H 6 HOH A 133 833 136 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 . . . C 3 79.623 -6.632 8.531 0.5 92.98 ? C1 NAG 601 A 1 HETATM 2 C C2 NAG . . . C 3 81.009 -6.997 9.06 0.5 88.5 ? C2 NAG 601 A 1 HETATM 3 C C3 NAG . . . C 3 81.138 -8.51 9.181 0.5 89.66 ? C3 NAG 601 A 1 HETATM 4 C C4 NAG . . . C 3 80.009 -9.069 10.035 0.5 95.28 ? C4 NAG 601 A 1 HETATM 5 C C5 NAG . . . C 3 78.65 -8.602 9.516 0.5 98.85 ? C5 NAG 601 A 1 HETATM 6 C C6 NAG . . . C 3 77.516 -9.001 10.433 0.5 100.37 ? C6 NAG 601 A 1 HETATM 7 C C7 NAG . . . C 3 83.329 -6.317 8.61 0.5 85.35 ? C7 NAG 601 A 1 HETATM 8 C C8 NAG . . . C 3 84.275 -5.74 7.602 0.5 81.9 ? C8 NAG 601 A 1 HETATM 9 N N2 NAG . . . C 3 82.059 -6.455 8.211 0.5 86.6 ? N2 NAG 601 A 1 HETATM 10 O O3 NAG . . . C 3 82.388 -8.834 9.777 0.5 86.28 ? O3 NAG 601 A 1 HETATM 11 O O4 NAG . . . C 3 80.051 -10.491 10.027 0.5 99.29 ? O4 NAG 601 A 1 HETATM 12 O O5 NAG . . . C 3 78.617 -7.169 9.405 0.5 94.34 ? O5 NAG 601 A 1 HETATM 13 O O6 NAG . . . C 3 76.658 -7.909 10.731 0.5 95.41 ? O6 NAG 601 A 1 HETATM 14 O O7 NAG . . . C 3 83.698 -6.651 9.732 0.5 85.98 ? O7 NAG 601 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 38 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #