data_3BXZ # _model_server_result.job_id GryUrIumkBUJPOZbvoqrfg _model_server_result.datetime_utc '2024-12-27 00:52:12' _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 3bxz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":906}' # _entry.id 3BXZ # _exptl.entry_id 3BXZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 145.246 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMIDINE _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 128.82 _cell.angle_gamma 90 _cell.entry_id 3BXZ _cell.length_a 177.823 _cell.length_b 71.361 _cell.length_c 119.536 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BXZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 D N N ? 3 G 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 metalc ? metalc1 E O1B ADP . A ADP 901 1_555 C MG MG . A MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc2 C MG MG . A MG 903 1_555 I O HOH . A HOH 966 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc3 C MG MG . A MG 903 1_555 I O HOH . A HOH 967 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? # _chem_comp.formula 'C7 H19 N3' _chem_comp.formula_weight 145.246 _chem_comp.id SPD _chem_comp.mon_nstd_flag . _chem_comp.name SPERMIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;PA(34) # 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 N1 C2 SPD sing 334 n n N1 HN11 SPD sing 335 n n N1 HN12 SPD sing 336 n n C2 C3 SPD sing 337 n n C2 H21 SPD sing 338 n n C2 H22 SPD sing 339 n n C3 C4 SPD sing 340 n n C3 H31 SPD sing 341 n n C3 H32 SPD sing 342 n n C4 C5 SPD sing 343 n n C4 H41 SPD sing 344 n n C4 H42 SPD sing 345 n n C5 N6 SPD sing 346 n n C5 H51 SPD sing 347 n n C5 H52 SPD sing 348 n n N6 C7 SPD sing 349 n n N6 HN6 SPD sing 350 n n C7 C8 SPD sing 351 n n C7 H71 SPD sing 352 n n C7 H72 SPD sing 353 n n C8 C9 SPD sing 354 n n C8 H81 SPD sing 355 n n C8 H82 SPD sing 356 n n C9 N10 SPD sing 357 n n C9 H91 SPD sing 358 n n C9 H92 SPD sing 359 n n N10 H101 SPD sing 360 n n N10 H102 SPD sing 361 n n # _atom_sites.entry_id 3BXZ _atom_sites.fract_transf_matrix[1][1] 0.005624 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004525 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014013 _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] 0.010737 _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 2 MG A 1 903 903 MG MG . D 3 SPD A 1 905 905 SPD SPD . E 4 ADP A 1 901 901 ADP ADP . F 2 MG B 1 904 904 MG MG . G 3 SPD B 1 906 906 SPD SPD . H 4 ADP B 1 902 902 ADP ADP . I 5 HOH A 1 906 1 HOH WAT . I 5 HOH A 2 907 3 HOH WAT . I 5 HOH A 3 908 4 HOH WAT . I 5 HOH A 4 909 5 HOH WAT . I 5 HOH A 5 910 8 HOH WAT . I 5 HOH A 6 911 9 HOH WAT . I 5 HOH A 7 912 10 HOH WAT . I 5 HOH A 8 913 11 HOH WAT . I 5 HOH A 9 914 14 HOH WAT . I 5 HOH A 10 915 22 HOH WAT . I 5 HOH A 11 916 23 HOH WAT . I 5 HOH A 12 917 32 HOH WAT . I 5 HOH A 13 918 33 HOH WAT . I 5 HOH A 14 919 34 HOH WAT . I 5 HOH A 15 920 35 HOH WAT . I 5 HOH A 16 921 36 HOH WAT . I 5 HOH A 17 922 37 HOH WAT . I 5 HOH A 18 923 39 HOH WAT . I 5 HOH A 19 924 41 HOH WAT . I 5 HOH A 20 925 42 HOH WAT . I 5 HOH A 21 926 43 HOH WAT . I 5 HOH A 22 927 44 HOH WAT . I 5 HOH A 23 928 45 HOH WAT . I 5 HOH A 24 929 48 HOH WAT . I 5 HOH A 25 930 52 HOH WAT . I 5 HOH A 26 931 53 HOH WAT . I 5 HOH A 27 932 56 HOH WAT . I 5 HOH A 28 933 57 HOH WAT . I 5 HOH A 29 934 58 HOH WAT . I 5 HOH A 30 935 60 HOH WAT . I 5 HOH A 31 936 62 HOH WAT . I 5 HOH A 32 937 64 HOH WAT . I 5 HOH A 33 938 67 HOH WAT . I 5 HOH A 34 939 70 HOH WAT . I 5 HOH A 35 940 72 HOH WAT . I 5 HOH A 36 941 73 HOH WAT . I 5 HOH A 37 942 76 HOH WAT . I 5 HOH A 38 943 77 HOH WAT . I 5 HOH A 39 944 80 HOH WAT . I 5 HOH A 40 945 82 HOH WAT . I 5 HOH A 41 946 84 HOH WAT . I 5 HOH A 42 947 85 HOH WAT . I 5 HOH A 43 948 88 HOH WAT . I 5 HOH A 44 949 89 HOH WAT . I 5 HOH A 45 950 91 HOH WAT . I 5 HOH A 46 951 93 HOH WAT . I 5 HOH A 47 952 94 HOH WAT . I 5 HOH A 48 953 95 HOH WAT . I 5 HOH A 49 954 98 HOH WAT . I 5 HOH A 50 955 99 HOH WAT . I 5 HOH A 51 956 102 HOH WAT . I 5 HOH A 52 957 104 HOH WAT . I 5 HOH A 53 958 105 HOH WAT . I 5 HOH A 54 959 107 HOH WAT . I 5 HOH A 55 960 108 HOH WAT . I 5 HOH A 56 961 109 HOH WAT . I 5 HOH A 57 962 110 HOH WAT . I 5 HOH A 58 963 111 HOH WAT . I 5 HOH A 59 964 114 HOH WAT . I 5 HOH A 60 965 116 HOH WAT . I 5 HOH A 61 966 117 HOH WAT . I 5 HOH A 62 967 118 HOH WAT . I 5 HOH A 63 968 123 HOH WAT . I 5 HOH A 64 969 125 HOH WAT . I 5 HOH A 65 970 129 HOH WAT . I 5 HOH A 66 971 130 HOH WAT . I 5 HOH A 67 972 132 HOH WAT . I 5 HOH A 68 973 134 HOH WAT . I 5 HOH A 69 974 138 HOH WAT . I 5 HOH A 70 975 140 HOH WAT . I 5 HOH A 71 976 143 HOH WAT . I 5 HOH A 72 977 144 HOH WAT . I 5 HOH A 73 978 145 HOH WAT . I 5 HOH A 74 979 146 HOH WAT . I 5 HOH A 75 980 147 HOH WAT . I 5 HOH A 76 981 148 HOH WAT . I 5 HOH A 77 982 152 HOH WAT . I 5 HOH A 78 983 153 HOH WAT . I 5 HOH A 79 984 154 HOH WAT . I 5 HOH A 80 985 155 HOH WAT . I 5 HOH A 81 986 156 HOH WAT . I 5 HOH A 82 987 157 HOH WAT . I 5 HOH A 83 988 158 HOH WAT . I 5 HOH A 84 989 161 HOH WAT . I 5 HOH A 85 990 162 HOH WAT . I 5 HOH A 86 991 164 HOH WAT . I 5 HOH A 87 992 166 HOH WAT . I 5 HOH A 88 993 169 HOH WAT . I 5 HOH A 89 994 170 HOH WAT . J 5 HOH B 1 907 2 HOH WAT . J 5 HOH B 2 908 6 HOH WAT . J 5 HOH B 3 909 7 HOH WAT . J 5 HOH B 4 910 12 HOH WAT . J 5 HOH B 5 911 13 HOH WAT . J 5 HOH B 6 912 15 HOH WAT . J 5 HOH B 7 913 16 HOH WAT . J 5 HOH B 8 914 17 HOH WAT . J 5 HOH B 9 915 18 HOH WAT . J 5 HOH B 10 916 19 HOH WAT . J 5 HOH B 11 917 20 HOH WAT . J 5 HOH B 12 918 21 HOH WAT . J 5 HOH B 13 919 24 HOH WAT . J 5 HOH B 14 920 25 HOH WAT . J 5 HOH B 15 921 26 HOH WAT . J 5 HOH B 16 922 27 HOH WAT . J 5 HOH B 17 923 28 HOH WAT . J 5 HOH B 18 924 29 HOH WAT . J 5 HOH B 19 925 30 HOH WAT . J 5 HOH B 20 926 31 HOH WAT . J 5 HOH B 21 927 38 HOH WAT . J 5 HOH B 22 928 40 HOH WAT . J 5 HOH B 23 929 46 HOH WAT . J 5 HOH B 24 930 47 HOH WAT . J 5 HOH B 25 931 49 HOH WAT . J 5 HOH B 26 932 50 HOH WAT . J 5 HOH B 27 933 51 HOH WAT . J 5 HOH B 28 934 54 HOH WAT . J 5 HOH B 29 935 55 HOH WAT . J 5 HOH B 30 936 59 HOH WAT . J 5 HOH B 31 937 61 HOH WAT . J 5 HOH B 32 938 63 HOH WAT . J 5 HOH B 33 939 65 HOH WAT . J 5 HOH B 34 940 66 HOH WAT . J 5 HOH B 35 941 68 HOH WAT . J 5 HOH B 36 942 69 HOH WAT . J 5 HOH B 37 943 71 HOH WAT . J 5 HOH B 38 944 74 HOH WAT . J 5 HOH B 39 945 75 HOH WAT . J 5 HOH B 40 946 78 HOH WAT . J 5 HOH B 41 947 79 HOH WAT . J 5 HOH B 42 948 81 HOH WAT . J 5 HOH B 43 949 83 HOH WAT . J 5 HOH B 44 950 86 HOH WAT . J 5 HOH B 45 951 87 HOH WAT . J 5 HOH B 46 952 90 HOH WAT . J 5 HOH B 47 953 92 HOH WAT . J 5 HOH B 48 954 96 HOH WAT . J 5 HOH B 49 955 97 HOH WAT . J 5 HOH B 50 956 100 HOH WAT . J 5 HOH B 51 957 101 HOH WAT . J 5 HOH B 52 958 103 HOH WAT . J 5 HOH B 53 959 106 HOH WAT . J 5 HOH B 54 960 112 HOH WAT . J 5 HOH B 55 961 113 HOH WAT . J 5 HOH B 56 962 115 HOH WAT . J 5 HOH B 57 963 119 HOH WAT . J 5 HOH B 58 964 120 HOH WAT . J 5 HOH B 59 965 121 HOH WAT . J 5 HOH B 60 966 122 HOH WAT . J 5 HOH B 61 967 124 HOH WAT . J 5 HOH B 62 968 126 HOH WAT . J 5 HOH B 63 969 127 HOH WAT . J 5 HOH B 64 970 128 HOH WAT . J 5 HOH B 65 971 131 HOH WAT . J 5 HOH B 66 972 133 HOH WAT . J 5 HOH B 67 973 135 HOH WAT . J 5 HOH B 68 974 136 HOH WAT . J 5 HOH B 69 975 137 HOH WAT . J 5 HOH B 70 976 139 HOH WAT . J 5 HOH B 71 977 141 HOH WAT . J 5 HOH B 72 978 142 HOH WAT . J 5 HOH B 73 979 149 HOH WAT . J 5 HOH B 74 980 150 HOH WAT . J 5 HOH B 75 981 151 HOH WAT . J 5 HOH B 76 982 159 HOH WAT . J 5 HOH B 77 983 160 HOH WAT . J 5 HOH B 78 984 163 HOH WAT . J 5 HOH B 79 985 165 HOH WAT . J 5 HOH B 80 986 167 HOH WAT . J 5 HOH B 81 987 168 HOH WAT . J 5 HOH B 82 988 171 HOH WAT . # 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 N N1 SPD . . . G 3 46.945 18.783 55.253 1 74.23 ? N1 SPD 906 B 1 HETATM 2 C C2 SPD . . . G 3 46.386 18.285 56.53 1 77.07 ? C2 SPD 906 B 1 HETATM 3 C C3 SPD . . . G 3 46.05 19.466 57.471 1 79.84 ? C3 SPD 906 B 1 HETATM 4 C C4 SPD . . . G 3 45.455 19.004 58.818 1 81.38 ? C4 SPD 906 B 1 HETATM 5 C C5 SPD . . . G 3 44.568 20.12 59.438 1 82.35 ? C5 SPD 906 B 1 HETATM 6 N N6 SPD . . . G 3 43.978 19.701 60.737 1 82.29 ? N6 SPD 906 B 1 HETATM 7 C C7 SPD . . . G 3 43.137 20.802 61.265 1 81.63 ? C7 SPD 906 B 1 HETATM 8 C C8 SPD . . . G 3 42.48 20.418 62.616 1 81.78 ? C8 SPD 906 B 1 HETATM 9 C C9 SPD . . . G 3 41.596 21.567 63.161 1 80 ? C9 SPD 906 B 1 HETATM 10 N N10 SPD . . . G 3 40.186 21.48 62.707 1 76.95 ? N10 SPD 906 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 10 #