data_5YDR
#
_model_server_result.job_id            rfFIu43aqZXh-iOQApyEdA 
_model_server_result.datetime_utc      '2024-10-19 23:59:10' 
_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          5ydr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":601}' 
#
_entry.id    5YDR 
#
_exptl.entry_id    5YDR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              65.409 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'ZINC ION' 
_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         120 
_cell.entry_id            5YDR 
_cell.length_a            131.76 
_cell.length_b            131.76 
_cell.length_c            61.025 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YDR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
_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 
#
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
metalc ? metalc1 B SG CYS 4 B CYS 353 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? 
metalc ? metalc2 B SG CYS 7 B CYS 356 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? 
metalc ? metalc3 B SG CYS 65 B CYS 414 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc4 B ND1 HIS 69 B HIS 418 1_555 E ZN ZN . B ZN 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
#
_chem_comp.formula           'Zn 2' 
_chem_comp.formula_weight    65.409 
_chem_comp.id                ZN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'ZINC ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     5YDR 
_atom_sites.fract_transf_matrix[1][1]    0.00759 
_atom_sites.fract_transf_matrix[1][2]    0.004382 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008764 
_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]    0.016387 
_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 3 PO4 A 1 101 1 PO4 PO4 . 
E 4 ZN B 1 601 1 ZN ZN . 
F 3 PO4 B 1 602 1 PO4 PO4 . 
G 5 HOH A 1 201 253 HOH HOH . 
G 5 HOH A 2 202 215 HOH HOH . 
G 5 HOH A 3 203 94 HOH HOH . 
G 5 HOH A 4 204 243 HOH HOH . 
G 5 HOH A 5 205 139 HOH HOH . 
G 5 HOH A 6 206 22 HOH HOH . 
G 5 HOH A 7 207 267 HOH HOH . 
G 5 HOH A 8 208 125 HOH HOH . 
G 5 HOH A 9 209 138 HOH HOH . 
G 5 HOH A 10 210 213 HOH HOH . 
G 5 HOH A 11 211 23 HOH HOH . 
G 5 HOH A 12 212 185 HOH HOH . 
G 5 HOH A 13 213 178 HOH HOH . 
G 5 HOH A 14 214 207 HOH HOH . 
G 5 HOH A 15 215 134 HOH HOH . 
G 5 HOH A 16 216 68 HOH HOH . 
G 5 HOH A 17 217 195 HOH HOH . 
G 5 HOH A 18 218 254 HOH HOH . 
G 5 HOH A 19 219 117 HOH HOH . 
G 5 HOH A 20 220 162 HOH HOH . 
G 5 HOH A 21 221 240 HOH HOH . 
G 5 HOH A 22 222 18 HOH HOH . 
G 5 HOH A 23 223 148 HOH HOH . 
G 5 HOH A 24 224 266 HOH HOH . 
G 5 HOH A 25 225 263 HOH HOH . 
H 5 HOH B 1 701 272 HOH HOH . 
H 5 HOH B 2 702 275 HOH HOH . 
H 5 HOH B 3 703 191 HOH HOH . 
H 5 HOH B 4 704 46 HOH HOH . 
H 5 HOH B 5 705 218 HOH HOH . 
H 5 HOH B 6 706 149 HOH HOH . 
H 5 HOH B 7 707 116 HOH HOH . 
H 5 HOH B 8 708 204 HOH HOH . 
H 5 HOH B 9 709 16 HOH HOH . 
H 5 HOH B 10 710 54 HOH HOH . 
H 5 HOH B 11 711 61 HOH HOH . 
H 5 HOH B 12 712 85 HOH HOH . 
H 5 HOH B 13 713 174 HOH HOH . 
H 5 HOH B 14 714 230 HOH HOH . 
H 5 HOH B 15 715 171 HOH HOH . 
H 5 HOH B 16 716 183 HOH HOH . 
H 5 HOH B 17 717 159 HOH HOH . 
H 5 HOH B 18 718 84 HOH HOH . 
H 5 HOH B 19 719 48 HOH HOH . 
H 5 HOH B 20 720 14 HOH HOH . 
H 5 HOH B 21 721 247 HOH HOH . 
H 5 HOH B 22 722 15 HOH HOH . 
H 5 HOH B 23 723 160 HOH HOH . 
H 5 HOH B 24 724 3 HOH HOH . 
H 5 HOH B 25 725 60 HOH HOH . 
H 5 HOH B 26 726 44 HOH HOH . 
H 5 HOH B 27 727 8 HOH HOH . 
H 5 HOH B 28 728 31 HOH HOH . 
H 5 HOH B 29 729 128 HOH HOH . 
H 5 HOH B 30 730 41 HOH HOH . 
H 5 HOH B 31 731 123 HOH HOH . 
H 5 HOH B 32 732 184 HOH HOH . 
H 5 HOH B 33 733 222 HOH HOH . 
H 5 HOH B 34 734 235 HOH HOH . 
H 5 HOH B 35 735 51 HOH HOH . 
H 5 HOH B 36 736 21 HOH HOH . 
H 5 HOH B 37 737 188 HOH HOH . 
H 5 HOH B 38 738 241 HOH HOH . 
H 5 HOH B 39 739 219 HOH HOH . 
H 5 HOH B 40 740 50 HOH HOH . 
H 5 HOH B 41 741 69 HOH HOH . 
H 5 HOH B 42 742 86 HOH HOH . 
H 5 HOH B 43 743 57 HOH HOH . 
H 5 HOH B 44 744 269 HOH HOH . 
H 5 HOH B 45 745 211 HOH HOH . 
H 5 HOH B 46 746 28 HOH HOH . 
H 5 HOH B 47 747 17 HOH HOH . 
H 5 HOH B 48 748 11 HOH HOH . 
H 5 HOH B 49 749 59 HOH HOH . 
H 5 HOH B 50 750 201 HOH HOH . 
H 5 HOH B 51 751 52 HOH HOH . 
H 5 HOH B 52 752 256 HOH HOH . 
H 5 HOH B 53 753 29 HOH HOH . 
H 5 HOH B 54 754 20 HOH HOH . 
H 5 HOH B 55 755 35 HOH HOH . 
H 5 HOH B 56 756 33 HOH HOH . 
H 5 HOH B 57 757 172 HOH HOH . 
H 5 HOH B 58 758 73 HOH HOH . 
H 5 HOH B 59 759 79 HOH HOH . 
H 5 HOH B 60 760 63 HOH HOH . 
H 5 HOH B 61 761 87 HOH HOH . 
H 5 HOH B 62 762 27 HOH HOH . 
H 5 HOH B 63 763 186 HOH HOH . 
H 5 HOH B 64 764 276 HOH HOH . 
H 5 HOH B 65 765 58 HOH HOH . 
H 5 HOH B 66 766 26 HOH HOH . 
H 5 HOH B 67 767 19 HOH HOH . 
H 5 HOH B 68 768 97 HOH HOH . 
H 5 HOH B 69 769 120 HOH HOH . 
H 5 HOH B 70 770 10 HOH HOH . 
H 5 HOH B 71 771 96 HOH HOH . 
H 5 HOH B 72 772 55 HOH HOH . 
H 5 HOH B 73 773 34 HOH HOH . 
H 5 HOH B 74 774 49 HOH HOH . 
H 5 HOH B 75 775 141 HOH HOH . 
H 5 HOH B 76 776 177 HOH HOH . 
H 5 HOH B 77 777 81 HOH HOH . 
H 5 HOH B 78 778 25 HOH HOH . 
H 5 HOH B 79 779 2 HOH HOH . 
H 5 HOH B 80 780 90 HOH HOH . 
H 5 HOH B 81 781 72 HOH HOH . 
H 5 HOH B 82 782 239 HOH HOH . 
H 5 HOH B 83 783 158 HOH HOH . 
H 5 HOH B 84 784 197 HOH HOH . 
H 5 HOH B 85 785 144 HOH HOH . 
H 5 HOH B 86 786 39 HOH HOH . 
H 5 HOH B 87 787 93 HOH HOH . 
H 5 HOH B 88 788 37 HOH HOH . 
H 5 HOH B 89 789 12 HOH HOH . 
H 5 HOH B 90 790 13 HOH HOH . 
H 5 HOH B 91 791 121 HOH HOH . 
H 5 HOH B 92 792 4 HOH HOH . 
H 5 HOH B 93 793 36 HOH HOH . 
H 5 HOH B 94 794 40 HOH HOH . 
H 5 HOH B 95 795 261 HOH HOH . 
H 5 HOH B 96 796 82 HOH HOH . 
H 5 HOH B 97 797 244 HOH HOH . 
H 5 HOH B 98 798 45 HOH HOH . 
H 5 HOH B 99 799 234 HOH HOH . 
H 5 HOH B 100 800 47 HOH HOH . 
H 5 HOH B 101 801 1 HOH HOH . 
H 5 HOH B 102 802 152 HOH HOH . 
H 5 HOH B 103 803 255 HOH HOH . 
H 5 HOH B 104 804 56 HOH HOH . 
H 5 HOH B 105 805 227 HOH HOH . 
H 5 HOH B 106 806 62 HOH HOH . 
H 5 HOH B 107 807 53 HOH HOH . 
H 5 HOH B 108 808 216 HOH HOH . 
H 5 HOH B 109 809 115 HOH HOH . 
H 5 HOH B 110 810 24 HOH HOH . 
H 5 HOH B 111 811 208 HOH HOH . 
H 5 HOH B 112 812 102 HOH HOH . 
H 5 HOH B 113 813 9 HOH HOH . 
H 5 HOH B 114 814 189 HOH HOH . 
H 5 HOH B 115 815 30 HOH HOH . 
H 5 HOH B 116 816 210 HOH HOH . 
H 5 HOH B 117 817 99 HOH HOH . 
H 5 HOH B 118 818 193 HOH HOH . 
H 5 HOH B 119 819 133 HOH HOH . 
H 5 HOH B 120 820 108 HOH HOH . 
H 5 HOH B 121 821 249 HOH HOH . 
H 5 HOH B 122 822 5 HOH HOH . 
H 5 HOH B 123 823 181 HOH HOH . 
H 5 HOH B 124 824 190 HOH HOH . 
H 5 HOH B 125 825 38 HOH HOH . 
H 5 HOH B 126 826 6 HOH HOH . 
H 5 HOH B 127 827 252 HOH HOH . 
H 5 HOH B 128 828 42 HOH HOH . 
H 5 HOH B 129 829 106 HOH HOH . 
H 5 HOH B 130 830 212 HOH HOH . 
H 5 HOH B 131 831 67 HOH HOH . 
H 5 HOH B 132 832 75 HOH HOH . 
H 5 HOH B 133 833 113 HOH HOH . 
H 5 HOH B 134 834 202 HOH HOH . 
H 5 HOH B 135 835 161 HOH HOH . 
H 5 HOH B 136 836 220 HOH HOH . 
H 5 HOH B 137 837 203 HOH HOH . 
H 5 HOH B 138 838 251 HOH HOH . 
H 5 HOH B 139 839 71 HOH HOH . 
H 5 HOH B 140 840 214 HOH HOH . 
H 5 HOH B 141 841 156 HOH HOH . 
H 5 HOH B 142 842 228 HOH HOH . 
H 5 HOH B 143 843 7 HOH HOH . 
H 5 HOH B 144 844 262 HOH HOH . 
H 5 HOH B 145 845 64 HOH HOH . 
H 5 HOH B 146 846 154 HOH HOH . 
H 5 HOH B 147 847 78 HOH HOH . 
H 5 HOH B 148 848 131 HOH HOH . 
H 5 HOH B 149 849 236 HOH HOH . 
H 5 HOH B 150 850 32 HOH HOH . 
H 5 HOH B 151 851 43 HOH HOH . 
H 5 HOH B 152 852 112 HOH HOH . 
H 5 HOH B 153 853 170 HOH HOH . 
H 5 HOH B 154 854 107 HOH HOH . 
H 5 HOH B 155 855 194 HOH HOH . 
H 5 HOH B 156 856 91 HOH HOH . 
H 5 HOH B 157 857 129 HOH HOH . 
H 5 HOH B 158 858 164 HOH HOH . 
H 5 HOH B 159 859 179 HOH HOH . 
H 5 HOH B 160 860 242 HOH HOH . 
H 5 HOH B 161 861 111 HOH HOH . 
H 5 HOH B 162 862 223 HOH HOH . 
H 5 HOH B 163 863 65 HOH HOH . 
H 5 HOH B 164 864 196 HOH HOH . 
H 5 HOH B 165 865 146 HOH HOH . 
H 5 HOH B 166 866 66 HOH HOH . 
H 5 HOH B 167 867 104 HOH HOH . 
H 5 HOH B 168 868 209 HOH HOH . 
H 5 HOH B 169 869 260 HOH HOH . 
H 5 HOH B 170 870 101 HOH HOH . 
H 5 HOH B 171 871 259 HOH HOH . 
H 5 HOH B 172 872 119 HOH HOH . 
H 5 HOH B 173 873 257 HOH HOH . 
H 5 HOH B 174 874 167 HOH HOH . 
H 5 HOH B 175 875 151 HOH HOH . 
H 5 HOH B 176 876 127 HOH HOH . 
H 5 HOH B 177 877 250 HOH HOH . 
H 5 HOH B 178 878 98 HOH HOH . 
H 5 HOH B 179 879 150 HOH HOH . 
H 5 HOH B 180 880 157 HOH HOH . 
H 5 HOH B 181 881 245 HOH HOH . 
H 5 HOH B 182 882 100 HOH HOH . 
H 5 HOH B 183 883 175 HOH HOH . 
H 5 HOH B 184 884 76 HOH HOH . 
H 5 HOH B 185 885 200 HOH HOH . 
H 5 HOH B 186 886 126 HOH HOH . 
H 5 HOH B 187 887 271 HOH HOH . 
H 5 HOH B 188 888 206 HOH HOH . 
H 5 HOH B 189 889 163 HOH HOH . 
H 5 HOH B 190 890 130 HOH HOH . 
H 5 HOH B 191 891 168 HOH HOH . 
H 5 HOH B 192 892 192 HOH HOH . 
H 5 HOH B 193 893 205 HOH HOH . 
H 5 HOH B 194 894 77 HOH HOH . 
H 5 HOH B 195 895 176 HOH HOH . 
H 5 HOH B 196 896 92 HOH HOH . 
H 5 HOH B 197 897 124 HOH HOH . 
H 5 HOH B 198 898 135 HOH HOH . 
H 5 HOH B 199 899 118 HOH HOH . 
H 5 HOH B 200 900 187 HOH HOH . 
H 5 HOH B 201 901 198 HOH HOH . 
H 5 HOH B 202 902 248 HOH HOH . 
H 5 HOH B 203 903 80 HOH HOH . 
I 5 HOH D 1 101 246 HOH HOH . 
I 5 HOH D 2 102 231 HOH HOH . 
I 5 HOH D 3 103 83 HOH HOH . 
I 5 HOH D 4 104 270 HOH HOH . 
I 5 HOH D 5 105 145 HOH HOH . 
I 5 HOH D 6 106 147 HOH HOH . 
I 5 HOH D 7 107 265 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           ZN 
_atom_site.label_atom_id         ZN 
_atom_site.label_comp_id         ZN 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         E 
_atom_site.label_entity_id       4 
_atom_site.Cartn_x               46.09 
_atom_site.Cartn_y               -30.057 
_atom_site.Cartn_z               -6.621 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        31.68 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          ZN 
_atom_site.auth_comp_id          ZN 
_atom_site.auth_seq_id           601 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           275 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#