data_5LA7 # _model_server_result.job_id i2jbvSWQe-zrB-i8hhCg8Q _model_server_result.datetime_utc '2024-11-26 17:02:45' _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 5la7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":601}' # _entry.id 5LA7 # _exptl.entry_id 5LA7 _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 3 _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 5LA7 _cell.length_a 50.41 _cell.length_b 88.02 _cell.length_c 118.2 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LA7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,L,M _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 ? 3 C N N ? 3 D N N ? 3 E N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type 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 ? 2 3 1 FUC NAG C1 O1 . O6 HO6 . 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 B 1 NAG C 4 NAG 2 n B NAG 2 B 2 NAG B 1 NAG 2 n B FUC 3 B 3 FUC C 5 FUC # 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 93 A CYS 127 1_555 A SG CYS 145 A CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf2 A SG CYS 403 A CYS 437 1_555 A SG CYS 508 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? covale ? covale1 A ND2 ASN 128 A ASN 162 1_555 C C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 A ND2 ASN 166 A ASN 200 1_555 D C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 A ND2 ASN 204 A ASN 238 1_555 E C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 A OE2 GLU 309 A GLU 343 1_555 L C1 6S6 . A 6S6 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale5 A ND2 ASN 425 A ASN 459 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale6 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? # _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 322 n n C1 O1 NAG sing 323 n n C1 O5 NAG sing 324 n n C1 H1 NAG sing 325 n n C2 C3 NAG sing 326 n n C2 N2 NAG sing 327 n n C2 H2 NAG sing 328 n n C3 C4 NAG sing 329 n n C3 O3 NAG sing 330 n n C3 H3 NAG sing 331 n n C4 C5 NAG sing 332 n n C4 O4 NAG sing 333 n n C4 H4 NAG sing 334 n n C5 C6 NAG sing 335 n n C5 O5 NAG sing 336 n n C5 H5 NAG sing 337 n n C6 O6 NAG sing 338 n n C6 H61 NAG sing 339 n n C6 H62 NAG sing 340 n n C7 C8 NAG sing 341 n n C7 N2 NAG sing 342 n n C7 O7 NAG doub 343 n n C8 H81 NAG sing 344 n n C8 H82 NAG sing 345 n n C8 H83 NAG sing 346 n n N2 HN2 NAG sing 347 n n O1 HO1 NAG sing 348 n n O3 HO3 NAG sing 349 n n O4 HO4 NAG sing 350 n n O6 HO6 NAG sing 351 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 5LA7 _atom_sites.fract_transf_matrix[1][1] 0.019837 _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] 0.011361 _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] 0.00846 _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 C 3 NAG A 1 601 1 NAG NAG . D 3 NAG A 1 602 2 NAG NAG . E 3 NAG A 1 603 3 NAG NAG . F 4 EDO A 1 607 1 EDO EDO . G 4 EDO A 1 608 2 EDO EDO . H 4 EDO A 1 609 3 EDO EDO . I 4 EDO A 1 610 4 EDO EDO . J 4 EDO A 1 611 5 EDO EDO . K 4 EDO A 1 612 6 EDO EDO . L 5 6S6 A 1 613 1 6S6 355 . M 6 HOH A 1 701 168 HOH HOH . M 6 HOH A 2 702 159 HOH HOH . M 6 HOH A 3 703 113 HOH HOH . M 6 HOH A 4 704 78 HOH HOH . M 6 HOH A 5 705 121 HOH HOH . M 6 HOH A 6 706 13 HOH HOH . M 6 HOH A 7 707 118 HOH HOH . M 6 HOH A 8 708 6 HOH HOH . M 6 HOH A 9 709 14 HOH HOH . M 6 HOH A 10 710 141 HOH HOH . M 6 HOH A 11 711 162 HOH HOH . M 6 HOH A 12 712 169 HOH HOH . M 6 HOH A 13 713 111 HOH HOH . M 6 HOH A 14 714 59 HOH HOH . M 6 HOH A 15 715 94 HOH HOH . M 6 HOH A 16 716 103 HOH HOH . M 6 HOH A 17 717 20 HOH HOH . M 6 HOH A 18 718 47 HOH HOH . M 6 HOH A 19 719 22 HOH HOH . M 6 HOH A 20 720 11 HOH HOH . M 6 HOH A 21 721 23 HOH HOH . M 6 HOH A 22 722 39 HOH HOH . M 6 HOH A 23 723 157 HOH HOH . M 6 HOH A 24 724 175 HOH HOH . M 6 HOH A 25 725 54 HOH HOH . M 6 HOH A 26 726 95 HOH HOH . M 6 HOH A 27 727 79 HOH HOH . M 6 HOH A 28 728 188 HOH HOH . M 6 HOH A 29 729 48 HOH HOH . M 6 HOH A 30 730 46 HOH HOH . M 6 HOH A 31 731 3 HOH HOH . M 6 HOH A 32 732 170 HOH HOH . M 6 HOH A 33 733 36 HOH HOH . M 6 HOH A 34 734 7 HOH HOH . M 6 HOH A 35 735 58 HOH HOH . M 6 HOH A 36 736 31 HOH HOH . M 6 HOH A 37 737 119 HOH HOH . M 6 HOH A 38 738 104 HOH HOH . M 6 HOH A 39 739 123 HOH HOH . M 6 HOH A 40 740 114 HOH HOH . M 6 HOH A 41 741 69 HOH HOH . M 6 HOH A 42 742 52 HOH HOH . M 6 HOH A 43 743 98 HOH HOH . M 6 HOH A 44 744 18 HOH HOH . M 6 HOH A 45 745 53 HOH HOH . M 6 HOH A 46 746 93 HOH HOH . M 6 HOH A 47 747 51 HOH HOH . M 6 HOH A 48 748 107 HOH HOH . M 6 HOH A 49 749 89 HOH HOH . M 6 HOH A 50 750 172 HOH HOH . M 6 HOH A 51 751 173 HOH HOH . M 6 HOH A 52 752 109 HOH HOH . M 6 HOH A 53 753 42 HOH HOH . M 6 HOH A 54 754 5 HOH HOH . M 6 HOH A 55 755 124 HOH HOH . M 6 HOH A 56 756 35 HOH HOH . M 6 HOH A 57 757 50 HOH HOH . M 6 HOH A 58 758 9 HOH HOH . M 6 HOH A 59 759 16 HOH HOH . M 6 HOH A 60 760 152 HOH HOH . M 6 HOH A 61 761 90 HOH HOH . M 6 HOH A 62 762 19 HOH HOH . M 6 HOH A 63 763 182 HOH HOH . M 6 HOH A 64 764 154 HOH HOH . M 6 HOH A 65 765 117 HOH HOH . M 6 HOH A 66 766 43 HOH HOH . M 6 HOH A 67 767 26 HOH HOH . M 6 HOH A 68 768 12 HOH HOH . M 6 HOH A 69 769 145 HOH HOH . M 6 HOH A 70 770 8 HOH HOH . M 6 HOH A 71 771 55 HOH HOH . M 6 HOH A 72 772 75 HOH HOH . M 6 HOH A 73 773 28 HOH HOH . M 6 HOH A 74 774 184 HOH HOH . M 6 HOH A 75 775 68 HOH HOH . M 6 HOH A 76 776 166 HOH HOH . M 6 HOH A 77 777 126 HOH HOH . M 6 HOH A 78 778 110 HOH HOH . M 6 HOH A 79 779 88 HOH HOH . M 6 HOH A 80 780 33 HOH HOH . M 6 HOH A 81 781 57 HOH HOH . M 6 HOH A 82 782 41 HOH HOH . M 6 HOH A 83 783 49 HOH HOH . M 6 HOH A 84 784 142 HOH HOH . M 6 HOH A 85 785 70 HOH HOH . M 6 HOH A 86 786 156 HOH HOH . M 6 HOH A 87 787 34 HOH HOH . M 6 HOH A 88 788 1 HOH HOH . M 6 HOH A 89 789 160 HOH HOH . M 6 HOH A 90 790 146 HOH HOH . M 6 HOH A 91 791 105 HOH HOH . M 6 HOH A 92 792 81 HOH HOH . M 6 HOH A 93 793 99 HOH HOH . M 6 HOH A 94 794 17 HOH HOH . M 6 HOH A 95 795 167 HOH HOH . M 6 HOH A 96 796 40 HOH HOH . M 6 HOH A 97 797 92 HOH HOH . M 6 HOH A 98 798 2 HOH HOH . M 6 HOH A 99 799 102 HOH HOH . M 6 HOH A 100 800 158 HOH HOH . M 6 HOH A 101 801 32 HOH HOH . M 6 HOH A 102 802 15 HOH HOH . M 6 HOH A 103 803 125 HOH HOH . M 6 HOH A 104 804 130 HOH HOH . M 6 HOH A 105 805 38 HOH HOH . M 6 HOH A 106 806 62 HOH HOH . M 6 HOH A 107 807 131 HOH HOH . M 6 HOH A 108 808 181 HOH HOH . M 6 HOH A 109 809 37 HOH HOH . M 6 HOH A 110 810 45 HOH HOH . M 6 HOH A 111 811 147 HOH HOH . M 6 HOH A 112 812 164 HOH HOH . M 6 HOH A 113 813 133 HOH HOH . M 6 HOH A 114 814 127 HOH HOH . M 6 HOH A 115 815 27 HOH HOH . M 6 HOH A 116 816 186 HOH HOH . M 6 HOH A 117 817 185 HOH HOH . M 6 HOH A 118 818 112 HOH HOH . M 6 HOH A 119 819 21 HOH HOH . M 6 HOH A 120 820 64 HOH HOH . M 6 HOH A 121 821 25 HOH HOH . M 6 HOH A 122 822 63 HOH HOH . M 6 HOH A 123 823 179 HOH HOH . M 6 HOH A 124 824 120 HOH HOH . M 6 HOH A 125 825 77 HOH HOH . M 6 HOH A 126 826 72 HOH HOH . M 6 HOH A 127 827 85 HOH HOH . M 6 HOH A 128 828 65 HOH HOH . M 6 HOH A 129 829 161 HOH HOH . M 6 HOH A 130 830 116 HOH HOH . M 6 HOH A 131 831 106 HOH HOH . M 6 HOH A 132 832 108 HOH HOH . M 6 HOH A 133 833 91 HOH HOH . M 6 HOH A 134 834 153 HOH HOH . M 6 HOH A 135 835 10 HOH HOH . M 6 HOH A 136 836 174 HOH HOH . M 6 HOH A 137 837 96 HOH HOH . M 6 HOH A 138 838 128 HOH HOH . M 6 HOH A 139 839 180 HOH HOH . M 6 HOH A 140 840 183 HOH HOH . M 6 HOH A 141 841 140 HOH HOH . M 6 HOH A 142 842 82 HOH HOH . M 6 HOH A 143 843 97 HOH HOH . M 6 HOH A 144 844 178 HOH HOH . M 6 HOH A 145 845 187 HOH HOH . M 6 HOH A 146 846 148 HOH HOH . M 6 HOH A 147 847 84 HOH HOH . M 6 HOH A 148 848 80 HOH HOH . M 6 HOH A 149 849 100 HOH HOH . M 6 HOH A 150 850 176 HOH HOH . M 6 HOH A 151 851 83 HOH HOH . M 6 HOH A 152 852 56 HOH HOH . M 6 HOH A 153 853 177 HOH HOH . M 6 HOH A 154 854 150 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 38.471 -2.655 5.479 1 63.48 ? C1 NAG 601 A 1 HETATM 2 C C2 NAG . . . C 3 39.994 -2.599 5.636 1 64.19 ? C2 NAG 601 A 1 HETATM 3 C C3 NAG . . . C 3 40.494 -1.326 4.942 1 65.45 ? C3 NAG 601 A 1 HETATM 4 C C4 NAG . . . C 3 40.103 -1.354 3.471 1 64.46 ? C4 NAG 601 A 1 HETATM 5 C C5 NAG . . . C 3 38.58 -1.385 3.39 1 64.42 ? C5 NAG 601 A 1 HETATM 6 C C6 NAG . . . C 3 38.057 -1.348 1.951 1 61.41 ? C6 NAG 601 A 1 HETATM 7 C C7 NAG . . . C 3 40.563 -3.775 7.741 1 64.42 ? C7 NAG 601 A 1 HETATM 8 C C8 NAG . . . C 3 41.006 -3.601 9.167 1 63.91 ? C8 NAG 601 A 1 HETATM 9 N N2 NAG . . . C 3 40.411 -2.64 7.035 1 64.04 ? N2 NAG 601 A 1 HETATM 10 O O3 NAG . . . C 3 41.909 -1.172 5.036 1 68.34 ? O3 NAG 601 A 1 HETATM 11 O O4 NAG . . . C 3 40.611 -0.189 2.811 1 64.12 ? O4 NAG 601 A 1 HETATM 12 O O5 NAG . . . C 3 38.103 -2.546 4.076 1 60.04 ? O5 NAG 601 A 1 HETATM 13 O O6 NAG . . . C 3 38.189 -2.654 1.42 1 62.13 ? O6 NAG 601 A 1 HETATM 14 O O7 NAG . . . C 3 40.361 -4.892 7.286 1 63.88 ? O7 NAG 601 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #