data_6NKM # _model_server_result.job_id MsCDM1bMks3mcNuu9pPXIg _model_server_result.datetime_utc '2025-07-15 16:37:48' _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 6nkm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":802}' # _entry.id 6NKM # _exptl.entry_id 6NKM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-{[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-8H-pyrrolo[1,2-a]pyrazin-5-ium-1-olate _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 107.44 _cell.angle_gamma 90 _cell.entry_id 6NKM _cell.length_a 209.484 _cell.length_b 117.194 _cell.length_c 63.731 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 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 PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_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,G,H,I,J,K,N,O,P,Q 1 1 E,L,R 2 1,3 F,M,S 2 2,4 # 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' 1_545 x,y-1,z 1 0 0 0 1 0 0 0 1 0 -117.194 0 3 'crystal symmetry operation' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -19.100621 0 60.80137 4 'crystal symmetry operation' 2_546 -x,y-1,-z+1 -1 0 0 0 1 0 0 0 -1 -19.100621 -117.194 60.80137 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C21 H21 N3 O' _chem_comp.formula_weight 331.411 _chem_comp.id ZWP _chem_comp.mon_nstd_flag . _chem_comp.name 3-{[2-(2-methylbut-3-en-2-yl)-1H-indol-3-yl]methyl}-8H-pyrrolo[1,2-a]pyrazin-5-ium-1-olate _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 O25 C18 ZWP sing 456 n n N17 C18 ZWP sing 457 n y N17 C16 ZWP doub 458 n y C18 C19 ZWP doub 459 n y C15 C16 ZWP sing 460 n n C15 C7 ZWP sing 461 n n C16 C21 ZWP sing 462 n y C19 C22 ZWP sing 463 n n C19 N20 ZWP sing 464 n y C22 C23 ZWP sing 465 n n C1 C6 ZWP doub 466 n y C1 C2 ZWP sing 467 n y C21 N20 ZWP doub 468 n y N20 C24 ZWP sing 469 n n C6 C5 ZWP sing 470 n y C23 C24 ZWP doub 471 n n C7 C2 ZWP sing 472 n y C7 C8 ZWP doub 473 n y C2 C3 ZWP doub 474 n y C13 C14 ZWP doub 475 n n C13 C10 ZWP sing 476 n n C5 C4 ZWP doub 477 n y C8 C10 ZWP sing 478 n n C8 N9 ZWP sing 479 n y C3 C4 ZWP sing 480 n y C3 N9 ZWP sing 481 n y C12 C10 ZWP sing 482 n n C10 C11 ZWP sing 483 n n C1 H1 ZWP sing 484 n n C11 H2 ZWP sing 485 n n C11 H3 ZWP sing 486 n n C11 H4 ZWP sing 487 n n C12 H5 ZWP sing 488 n n C12 H6 ZWP sing 489 n n C12 H7 ZWP sing 490 n n C13 H8 ZWP sing 491 n n C14 H9 ZWP sing 492 n n C14 H10 ZWP sing 493 n n C15 H11 ZWP sing 494 n n C15 H12 ZWP sing 495 n n C21 H13 ZWP sing 496 n n C22 H14 ZWP sing 497 n n C23 H15 ZWP sing 498 n n C24 H16 ZWP sing 499 n n C4 H17 ZWP sing 500 n n C5 H18 ZWP sing 501 n n C6 H19 ZWP sing 502 n n N9 H21 ZWP sing 503 n n C22 H22 ZWP sing 504 n n # _atom_sites.entry_id 6NKM _atom_sites.fract_transf_matrix[1][1] 0.004774 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0015 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008533 _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] 0.016447 _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 G 2 NAP A 1 801 801 NAP NAP . H 3 ZWP A 1 802 901 ZWP ZWP . I 2 NAP B 1 801 801 NAP NAP . J 2 NAP C 1 801 801 NAP NAP . K 2 NAP D 1 801 801 NAP NAP . L 2 NAP E 1 801 801 NAP NAP . M 2 NAP F 1 801 801 NAP NAP . N 4 HOH A 1 901 89 HOH HOH . N 4 HOH A 2 902 104 HOH HOH . N 4 HOH A 3 903 173 HOH HOH . N 4 HOH A 4 904 101 HOH HOH . N 4 HOH A 5 905 52 HOH HOH . N 4 HOH A 6 906 57 HOH HOH . N 4 HOH A 7 907 9 HOH HOH . N 4 HOH A 8 908 130 HOH HOH . N 4 HOH A 9 909 78 HOH HOH . N 4 HOH A 10 910 105 HOH HOH . N 4 HOH A 11 911 55 HOH HOH . N 4 HOH A 12 912 164 HOH HOH . N 4 HOH A 13 913 56 HOH HOH . N 4 HOH A 14 914 5 HOH HOH . N 4 HOH A 15 915 21 HOH HOH . N 4 HOH A 16 916 144 HOH HOH . N 4 HOH A 17 917 165 HOH HOH . N 4 HOH A 18 918 193 HOH HOH . N 4 HOH A 19 919 171 HOH HOH . N 4 HOH A 20 920 22 HOH HOH . N 4 HOH A 21 921 179 HOH HOH . N 4 HOH A 22 922 17 HOH HOH . N 4 HOH A 23 923 23 HOH HOH . N 4 HOH A 24 924 102 HOH HOH . N 4 HOH A 25 925 90 HOH HOH . N 4 HOH A 26 926 14 HOH HOH . N 4 HOH A 27 927 82 HOH HOH . N 4 HOH A 28 928 103 HOH HOH . N 4 HOH A 29 929 18 HOH HOH . N 4 HOH A 30 930 65 HOH HOH . N 4 HOH A 31 931 192 HOH HOH . N 4 HOH A 32 932 190 HOH HOH . N 4 HOH A 33 933 188 HOH HOH . N 4 HOH A 34 934 86 HOH HOH . N 4 HOH A 35 935 58 HOH HOH . N 4 HOH A 36 936 189 HOH HOH . N 4 HOH A 37 937 6 HOH HOH . N 4 HOH A 38 938 49 HOH HOH . N 4 HOH A 39 939 80 HOH HOH . N 4 HOH A 40 940 3 HOH HOH . N 4 HOH A 41 941 163 HOH HOH . N 4 HOH A 42 942 98 HOH HOH . N 4 HOH A 43 943 51 HOH HOH . N 4 HOH A 44 944 88 HOH HOH . N 4 HOH A 45 945 170 HOH HOH . N 4 HOH A 46 946 81 HOH HOH . N 4 HOH A 47 947 53 HOH HOH . N 4 HOH A 48 948 16 HOH HOH . N 4 HOH A 49 949 100 HOH HOH . N 4 HOH A 50 950 145 HOH HOH . N 4 HOH A 51 951 106 HOH HOH . N 4 HOH A 52 952 151 HOH HOH . N 4 HOH A 53 953 169 HOH HOH . N 4 HOH A 54 954 152 HOH HOH . N 4 HOH A 55 955 113 HOH HOH . N 4 HOH A 56 956 50 HOH HOH . N 4 HOH A 57 957 168 HOH HOH . N 4 HOH A 58 958 167 HOH HOH . N 4 HOH A 59 959 172 HOH HOH . N 4 HOH A 60 960 159 HOH HOH . O 4 HOH B 1 901 123 HOH HOH . O 4 HOH B 2 902 32 HOH HOH . O 4 HOH B 3 903 109 HOH HOH . O 4 HOH B 4 904 77 HOH HOH . O 4 HOH B 5 905 44 HOH HOH . O 4 HOH B 6 906 177 HOH HOH . O 4 HOH B 7 907 11 HOH HOH . O 4 HOH B 8 908 12 HOH HOH . O 4 HOH B 9 909 111 HOH HOH . O 4 HOH B 10 910 122 HOH HOH . O 4 HOH B 11 911 26 HOH HOH . O 4 HOH B 12 912 128 HOH HOH . O 4 HOH B 13 913 108 HOH HOH . O 4 HOH B 14 914 74 HOH HOH . O 4 HOH B 15 915 42 HOH HOH . O 4 HOH B 16 916 119 HOH HOH . O 4 HOH B 17 917 120 HOH HOH . O 4 HOH B 18 918 2 HOH HOH . O 4 HOH B 19 919 70 HOH HOH . O 4 HOH B 20 920 196 HOH HOH . O 4 HOH B 21 921 43 HOH HOH . O 4 HOH B 22 922 124 HOH HOH . O 4 HOH B 23 923 121 HOH HOH . O 4 HOH B 24 924 34 HOH HOH . O 4 HOH B 25 925 93 HOH HOH . O 4 HOH B 26 926 60 HOH HOH . O 4 HOH B 27 927 33 HOH HOH . O 4 HOH B 28 928 13 HOH HOH . O 4 HOH B 29 929 191 HOH HOH . O 4 HOH B 30 930 36 HOH HOH . O 4 HOH B 31 931 37 HOH HOH . O 4 HOH B 32 932 107 HOH HOH . O 4 HOH B 33 933 154 HOH HOH . O 4 HOH B 34 934 20 HOH HOH . O 4 HOH B 35 935 76 HOH HOH . O 4 HOH B 36 936 112 HOH HOH . O 4 HOH B 37 937 79 HOH HOH . O 4 HOH B 38 938 155 HOH HOH . O 4 HOH B 39 939 29 HOH HOH . O 4 HOH B 40 940 35 HOH HOH . O 4 HOH B 41 941 174 HOH HOH . O 4 HOH B 42 942 140 HOH HOH . O 4 HOH B 43 943 143 HOH HOH . O 4 HOH B 44 944 185 HOH HOH . O 4 HOH B 45 945 141 HOH HOH . O 4 HOH B 46 946 175 HOH HOH . O 4 HOH B 47 947 131 HOH HOH . O 4 HOH B 48 948 176 HOH HOH . O 4 HOH B 49 949 99 HOH HOH . P 4 HOH C 1 901 146 HOH HOH . P 4 HOH C 2 902 161 HOH HOH . P 4 HOH C 3 903 69 HOH HOH . P 4 HOH C 4 904 84 HOH HOH . P 4 HOH C 5 905 48 HOH HOH . P 4 HOH C 6 906 8 HOH HOH . P 4 HOH C 7 907 87 HOH HOH . P 4 HOH C 8 908 118 HOH HOH . P 4 HOH C 9 909 129 HOH HOH . P 4 HOH C 10 910 91 HOH HOH . P 4 HOH C 11 911 195 HOH HOH . P 4 HOH C 12 912 85 HOH HOH . P 4 HOH C 13 913 54 HOH HOH . P 4 HOH C 14 914 25 HOH HOH . P 4 HOH C 15 915 116 HOH HOH . P 4 HOH C 16 916 96 HOH HOH . P 4 HOH C 17 917 115 HOH HOH . P 4 HOH C 18 918 153 HOH HOH . P 4 HOH C 19 919 187 HOH HOH . P 4 HOH C 20 920 194 HOH HOH . P 4 HOH C 21 921 24 HOH HOH . P 4 HOH C 22 922 67 HOH HOH . P 4 HOH C 23 923 83 HOH HOH . P 4 HOH C 24 924 66 HOH HOH . P 4 HOH C 25 925 95 HOH HOH . P 4 HOH C 26 926 1 HOH HOH . P 4 HOH C 27 927 114 HOH HOH . P 4 HOH C 28 928 156 HOH HOH . P 4 HOH C 29 929 47 HOH HOH . P 4 HOH C 30 930 160 HOH HOH . P 4 HOH C 31 931 97 HOH HOH . P 4 HOH C 32 932 137 HOH HOH . P 4 HOH C 33 933 178 HOH HOH . P 4 HOH C 34 934 136 HOH HOH . P 4 HOH C 35 935 180 HOH HOH . P 4 HOH C 36 936 117 HOH HOH . P 4 HOH C 37 937 68 HOH HOH . P 4 HOH C 38 938 157 HOH HOH . P 4 HOH C 39 939 147 HOH HOH . P 4 HOH C 40 940 158 HOH HOH . Q 4 HOH D 1 901 46 HOH HOH . Q 4 HOH D 2 902 94 HOH HOH . Q 4 HOH D 3 903 62 HOH HOH . Q 4 HOH D 4 904 162 HOH HOH . Q 4 HOH D 5 905 71 HOH HOH . Q 4 HOH D 6 906 64 HOH HOH . Q 4 HOH D 7 907 40 HOH HOH . Q 4 HOH D 8 908 110 HOH HOH . Q 4 HOH D 9 909 181 HOH HOH . Q 4 HOH D 10 910 150 HOH HOH . Q 4 HOH D 11 911 38 HOH HOH . Q 4 HOH D 12 912 182 HOH HOH . Q 4 HOH D 13 913 59 HOH HOH . Q 4 HOH D 14 914 28 HOH HOH . Q 4 HOH D 15 915 73 HOH HOH . Q 4 HOH D 16 916 166 HOH HOH . Q 4 HOH D 17 917 7 HOH HOH . Q 4 HOH D 18 918 149 HOH HOH . Q 4 HOH D 19 919 125 HOH HOH . Q 4 HOH D 20 920 142 HOH HOH . Q 4 HOH D 21 921 45 HOH HOH . Q 4 HOH D 22 922 126 HOH HOH . Q 4 HOH D 23 923 63 HOH HOH . Q 4 HOH D 24 924 10 HOH HOH . Q 4 HOH D 25 925 31 HOH HOH . Q 4 HOH D 26 926 4 HOH HOH . Q 4 HOH D 27 927 39 HOH HOH . Q 4 HOH D 28 928 61 HOH HOH . Q 4 HOH D 29 929 15 HOH HOH . Q 4 HOH D 30 930 19 HOH HOH . Q 4 HOH D 31 931 134 HOH HOH . Q 4 HOH D 32 932 148 HOH HOH . Q 4 HOH D 33 933 72 HOH HOH . Q 4 HOH D 34 934 30 HOH HOH . Q 4 HOH D 35 935 139 HOH HOH . Q 4 HOH D 36 936 41 HOH HOH . Q 4 HOH D 37 937 92 HOH HOH . Q 4 HOH D 38 938 27 HOH HOH . Q 4 HOH D 39 939 135 HOH HOH . Q 4 HOH D 40 940 184 HOH HOH . Q 4 HOH D 41 941 183 HOH HOH . R 4 HOH E 1 901 127 HOH HOH . R 4 HOH E 2 902 132 HOH HOH . R 4 HOH E 3 903 186 HOH HOH . R 4 HOH E 4 904 133 HOH HOH . R 4 HOH E 5 905 75 HOH HOH . S 4 HOH F 1 901 138 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 ZWP . . . H 3 3.449 52.246 38.075 1 68.2 ? C1 ZWP 802 A 1 HETATM 2 C C10 ZWP . . . H 3 1.564 48.291 40.596 1 78.06 ? C10 ZWP 802 A 1 HETATM 3 C C11 ZWP . . . H 3 2.033 48.158 42.042 1 79.45 ? C11 ZWP 802 A 1 HETATM 4 C C12 ZWP . . . H 3 0.041 48.34 40.527 1 80.42 ? C12 ZWP 802 A 1 HETATM 5 C C13 ZWP . . . H 3 2.039 47.058 39.859 1 79.76 ? C13 ZWP 802 A 1 HETATM 6 C C14 ZWP . . . H 3 3.229 46.539 40.098 1 81.89 ? C14 ZWP 802 A 1 HETATM 7 C C15 ZWP . . . H 3 2.563 49.253 37.468 1 75.61 ? C15 ZWP 802 A 1 HETATM 8 C C16 ZWP . . . H 3 3.818 48.427 37.498 1 78.02 ? C16 ZWP 802 A 1 HETATM 9 C C18 ZWP . . . H 3 5.037 46.531 36.904 1 80.69 ? C18 ZWP 802 A 1 HETATM 10 C C19 ZWP . . . H 3 6.098 47.037 37.646 1 78.66 ? C19 ZWP 802 A 1 HETATM 11 C C2 ZWP . . . H 3 2.933 51.326 38.974 1 71.29 ? C2 ZWP 802 A 1 HETATM 12 C C21 ZWP . . . H 3 4.892 48.902 38.241 1 78.44 ? C21 ZWP 802 A 1 HETATM 13 C C22 ZWP . . . H 3 7.451 46.407 37.841 1 76.91 ? C22 ZWP 802 A 1 HETATM 14 C C23 ZWP . . . H 3 8.174 47.408 38.749 1 75.48 ? C23 ZWP 802 A 1 HETATM 15 C C24 ZWP . . . H 3 7.216 48.57 39.02 1 76.83 ? C24 ZWP 802 A 1 HETATM 16 C C3 ZWP . . . H 3 2.749 51.645 40.312 1 70.83 ? C3 ZWP 802 A 1 HETATM 17 C C4 ZWP . . . H 3 3.08 52.919 40.76 1 68.38 ? C4 ZWP 802 A 1 HETATM 18 C C5 ZWP . . . H 3 3.588 53.855 39.867 1 66.16 ? C5 ZWP 802 A 1 HETATM 19 C C6 ZWP . . . H 3 3.766 53.52 38.529 1 65.75 ? C6 ZWP 802 A 1 HETATM 20 C C7 ZWP . . . H 3 2.53 50.016 38.77 1 72.92 ? C7 ZWP 802 A 1 HETATM 21 C C8 ZWP . . . H 3 2.126 49.571 40.026 1 72.88 ? C8 ZWP 802 A 1 HETATM 22 N N17 ZWP . . . H 3 3.893 47.249 36.842 1 79.91 ? N17 ZWP 802 A 1 HETATM 23 N N20 ZWP . . . H 3 6.009 48.188 38.286 1 78.04 ? N20 ZWP 802 A 1 HETATM 24 N N9 ZWP . . . H 3 2.245 50.556 40.941 1 71.06 ? N9 ZWP 802 A 1 HETATM 25 O O25 ZWP . . . H 3 5.126 45.371 36.256 1 82.67 ? O25 ZWP 802 A 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 439 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 25 #