data_5YH1 # _model_server_result.job_id TZVhFT158SOiu4djBG1nVg _model_server_result.datetime_utc '2024-11-26 03:12:08' _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 5yh1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":805}' # _entry.id 5YH1 # _exptl.entry_id 5YH1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) 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 5YH1 _cell.length_a 132.5 _cell.length_b 132.5 _cell.length_c 212.245 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YH1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63 2 2' # _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 _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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 132.5 0 0 3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 66.25 114.748366 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id F _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 covale ? covale1 A C HIS 4 A HIS 303 1_555 A N MSE 5 A MSE 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 A C MSE 5 A MSE 304 1_555 A N ALA 6 A ALA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 A C ILE 41 A ILE 340 1_555 A N MSE 42 A MSE 341 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 A C MSE 42 A MSE 341 1_555 A N LYS 43 A LYS 342 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale5 A C PHE 46 A PHE 345 1_555 A N MSE 47 A MSE 346 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 A C MSE 47 A MSE 346 1_555 A N ILE 48 A ILE 347 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale7 A C PHE 118 A PHE 417 1_555 A N MSE 119 A MSE 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale8 A C MSE 119 A MSE 418 1_555 A N MSE 120 A MSE 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale9 A C MSE 120 A MSE 419 1_555 A N GLU 121 A GLU 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale10 A C HIS 123 A HIS 422 1_555 A N MSE 124 A MSE 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale11 A C MSE 124 A MSE 423 1_555 A N ARG 125 A ARG 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale12 A C GLY 200 A GLY 499 1_555 A N MSE 201 A MSE 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale13 A C MSE 201 A MSE 500 1_555 A N LEU 202 A LEU 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale14 A C PHE 269 A PHE 568 1_555 A N MSE 270 A MSE 569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale15 A C MSE 270 A MSE 569 1_555 A N ASP 271 A ASP 570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale16 A C ARG 290 A ARG 589 1_555 A N MSE 291 A MSE 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale17 A C MSE 291 A MSE 590 1_555 A N LEU 292 A LEU 591 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale18 A C GLY 381 A GLY 680 1_555 A N MSE 382 A MSE 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale19 A C MSE 382 A MSE 681 1_555 A N ALA 383 A ALA 682 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OD2 ASP 67 A ASP 366 1_555 F MN MN . A MN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc2 A OD1 ASP 137 A ASP 436 1_555 F MN MN . A MN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc3 A NE2 HIS 163 A HIS 462 1_555 F MN MN . A MN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc4 A OD2 ASP 229 A ASP 528 1_555 F MN MN . A MN 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc5 F MN MN . A MN 805 1_555 G O HOH . A HOH 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc6 F MN MN . A MN 805 1_555 G O HOH . A HOH 929 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? # _chem_comp.formula 'Mn 2' _chem_comp.formula_weight 54.938 _chem_comp.id MN _chem_comp.mon_nstd_flag . _chem_comp.name 'MANGANESE (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5YH1 _atom_sites.fract_transf_matrix[1][1] 0.007547 _atom_sites.fract_transf_matrix[1][2] 0.004357 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008715 _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] 0.004712 _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 GOL A 1 801 801 GOL GOL . C 2 GOL A 1 802 802 GOL GOL . D 2 GOL A 1 803 803 GOL GOL . E 2 GOL A 1 804 804 GOL GOL . F 3 MN A 1 805 805 MN MN . G 4 HOH A 1 901 901 HOH HOH . G 4 HOH A 2 902 902 HOH HOH . G 4 HOH A 3 903 903 HOH HOH . G 4 HOH A 4 904 904 HOH HOH . G 4 HOH A 5 905 905 HOH HOH . G 4 HOH A 6 906 906 HOH HOH . G 4 HOH A 7 907 907 HOH HOH . G 4 HOH A 8 908 908 HOH HOH . G 4 HOH A 9 909 909 HOH HOH . G 4 HOH A 10 910 910 HOH HOH . G 4 HOH A 11 911 911 HOH HOH . G 4 HOH A 12 912 912 HOH HOH . G 4 HOH A 13 913 913 HOH HOH . G 4 HOH A 14 914 914 HOH HOH . G 4 HOH A 15 915 915 HOH HOH . G 4 HOH A 16 916 916 HOH HOH . G 4 HOH A 17 917 917 HOH HOH . G 4 HOH A 18 918 918 HOH HOH . G 4 HOH A 19 919 919 HOH HOH . G 4 HOH A 20 920 920 HOH HOH . G 4 HOH A 21 921 921 HOH HOH . G 4 HOH A 22 922 922 HOH HOH . G 4 HOH A 23 923 923 HOH HOH . G 4 HOH A 24 924 924 HOH HOH . G 4 HOH A 25 925 925 HOH HOH . G 4 HOH A 26 926 926 HOH HOH . G 4 HOH A 27 927 927 HOH HOH . G 4 HOH A 28 928 928 HOH HOH . G 4 HOH A 29 929 929 HOH HOH . G 4 HOH A 30 930 930 HOH HOH . G 4 HOH A 31 931 931 HOH HOH . G 4 HOH A 32 932 932 HOH HOH . G 4 HOH A 33 933 933 HOH HOH . G 4 HOH A 34 934 934 HOH HOH . G 4 HOH A 35 935 935 HOH HOH . G 4 HOH A 36 936 936 HOH HOH . G 4 HOH A 37 937 937 HOH HOH . G 4 HOH A 38 938 938 HOH HOH . G 4 HOH A 39 939 939 HOH HOH . G 4 HOH A 40 940 940 HOH HOH . G 4 HOH A 41 941 941 HOH HOH . G 4 HOH A 42 942 942 HOH HOH . G 4 HOH A 43 943 943 HOH HOH . G 4 HOH A 44 944 944 HOH HOH . G 4 HOH A 45 945 945 HOH HOH . G 4 HOH A 46 946 946 HOH HOH . G 4 HOH A 47 947 947 HOH HOH . G 4 HOH A 48 948 948 HOH HOH . G 4 HOH A 49 949 949 HOH HOH . G 4 HOH A 50 950 950 HOH HOH . G 4 HOH A 51 951 951 HOH HOH . G 4 HOH A 52 952 952 HOH HOH . G 4 HOH A 53 953 953 HOH HOH . G 4 HOH A 54 954 954 HOH HOH . G 4 HOH A 55 955 955 HOH HOH . G 4 HOH A 56 956 956 HOH HOH . G 4 HOH A 57 957 957 HOH HOH . G 4 HOH A 58 958 958 HOH HOH . G 4 HOH A 59 959 959 HOH HOH . G 4 HOH A 60 960 960 HOH HOH . G 4 HOH A 61 961 961 HOH HOH . G 4 HOH A 62 962 962 HOH HOH . G 4 HOH A 63 963 963 HOH HOH . G 4 HOH A 64 964 964 HOH HOH . G 4 HOH A 65 965 965 HOH HOH . G 4 HOH A 66 966 966 HOH HOH . G 4 HOH A 67 967 967 HOH HOH . G 4 HOH A 68 968 968 HOH HOH . G 4 HOH A 69 969 969 HOH HOH . G 4 HOH A 70 970 970 HOH HOH . G 4 HOH A 71 971 971 HOH HOH . G 4 HOH A 72 972 972 HOH HOH . G 4 HOH A 73 973 973 HOH HOH . G 4 HOH A 74 974 974 HOH HOH . G 4 HOH A 75 975 975 HOH HOH . G 4 HOH A 76 976 976 HOH HOH . G 4 HOH A 77 977 977 HOH HOH . G 4 HOH A 78 978 978 HOH HOH . G 4 HOH A 79 979 979 HOH HOH . G 4 HOH A 80 980 980 HOH HOH . G 4 HOH A 81 981 981 HOH HOH . G 4 HOH A 82 982 982 HOH HOH . G 4 HOH A 83 983 983 HOH HOH . G 4 HOH A 84 984 984 HOH HOH . G 4 HOH A 85 985 985 HOH HOH . G 4 HOH A 86 986 986 HOH HOH . G 4 HOH A 87 987 987 HOH HOH . G 4 HOH A 88 988 988 HOH HOH . G 4 HOH A 89 989 989 HOH HOH . G 4 HOH A 90 990 990 HOH HOH . G 4 HOH A 91 991 991 HOH HOH . G 4 HOH A 92 992 992 HOH HOH . G 4 HOH A 93 993 993 HOH HOH . G 4 HOH A 94 994 994 HOH HOH . G 4 HOH A 95 995 995 HOH HOH . G 4 HOH A 96 996 996 HOH HOH . G 4 HOH A 97 997 997 HOH HOH . G 4 HOH A 98 998 998 HOH HOH . G 4 HOH A 99 999 999 HOH HOH . G 4 HOH A 100 1000 1000 HOH HOH . G 4 HOH A 101 1001 1001 HOH HOH . G 4 HOH A 102 1002 1002 HOH HOH . G 4 HOH A 103 1003 1003 HOH HOH . G 4 HOH A 104 1004 1004 HOH HOH . G 4 HOH A 105 1005 1005 HOH HOH . G 4 HOH A 106 1006 1006 HOH HOH . G 4 HOH A 107 1007 1007 HOH HOH . G 4 HOH A 108 1008 1008 HOH HOH . G 4 HOH A 109 1009 1009 HOH HOH . G 4 HOH A 110 1010 1010 HOH HOH . G 4 HOH A 111 1011 1011 HOH HOH . G 4 HOH A 112 1012 1012 HOH HOH . G 4 HOH A 113 1013 1013 HOH HOH . G 4 HOH A 114 1014 1014 HOH HOH . G 4 HOH A 115 1015 1015 HOH HOH . G 4 HOH A 116 1016 1016 HOH HOH . G 4 HOH A 117 1017 1017 HOH HOH . G 4 HOH A 118 1018 1018 HOH HOH . G 4 HOH A 119 1019 1019 HOH HOH . G 4 HOH A 120 1020 1020 HOH HOH . G 4 HOH A 121 1021 1021 HOH HOH . G 4 HOH A 122 1022 1022 HOH HOH . G 4 HOH A 123 1023 1023 HOH HOH . G 4 HOH A 124 1024 1024 HOH HOH . G 4 HOH A 125 1025 1025 HOH HOH . G 4 HOH A 126 1026 1026 HOH HOH . G 4 HOH A 127 1027 1027 HOH HOH . G 4 HOH A 128 1028 1028 HOH HOH . G 4 HOH A 129 1029 1029 HOH HOH . G 4 HOH A 130 1030 1030 HOH HOH . G 4 HOH A 131 1031 1031 HOH HOH . G 4 HOH A 132 1032 1032 HOH HOH . G 4 HOH A 133 1033 1033 HOH HOH . G 4 HOH A 134 1034 1034 HOH HOH . G 4 HOH A 135 1035 1035 HOH HOH . G 4 HOH A 136 1036 1036 HOH HOH . G 4 HOH A 137 1037 1037 HOH HOH . G 4 HOH A 138 1038 1038 HOH HOH . G 4 HOH A 139 1039 1039 HOH HOH . G 4 HOH A 140 1040 1040 HOH HOH . G 4 HOH A 141 1041 1041 HOH HOH . G 4 HOH A 142 1042 1042 HOH HOH . G 4 HOH A 143 1043 1043 HOH HOH . G 4 HOH A 144 1044 1044 HOH HOH . G 4 HOH A 145 1045 1045 HOH HOH . G 4 HOH A 146 1046 1046 HOH HOH . G 4 HOH A 147 1047 1047 HOH HOH . G 4 HOH A 148 1048 1048 HOH HOH . G 4 HOH A 149 1049 1049 HOH HOH . G 4 HOH A 150 1050 1050 HOH HOH . G 4 HOH A 151 1051 1051 HOH HOH . G 4 HOH A 152 1052 1052 HOH HOH . G 4 HOH A 153 1053 1053 HOH HOH . G 4 HOH A 154 1054 1054 HOH HOH . G 4 HOH A 155 1055 1055 HOH HOH . G 4 HOH A 156 1056 1056 HOH HOH . G 4 HOH A 157 1057 1057 HOH HOH . G 4 HOH A 158 1058 1058 HOH HOH . G 4 HOH A 159 1059 1059 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MN _atom_site.label_atom_id MN _atom_site.label_comp_id MN _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id F _atom_site.label_entity_id 3 _atom_site.Cartn_x 51.513 _atom_site.Cartn_y 59.666 _atom_site.Cartn_z 92.369 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 42.69 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 805 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #