data_8RDK
#
_model_server_result.job_id            YfGkFgrBFJVjliMisjzNtQ 
_model_server_result.datetime_utc      '2024-11-28 13:16:52' 
_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          8rdk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":802}' 
#
_entry.id    8RDK 
#
_exptl.entry_id    8RDK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_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         90 
_cell.entry_id            8RDK 
_cell.length_a            69.509 
_cell.length_b            78.199 
_cell.length_c            86.872 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8RDK 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E 
_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                      3 
_struct_asym.id                             C 
_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 A NE2 HIS 36 A HIS 477 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? 
metalc ? metalc2 A NE2 HIS 122 A HIS 563 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
#
_chem_comp.formula           'C6 H14 O2' 
_chem_comp.formula_weight    118.174 
_chem_comp.id                MPD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4S)-2-METHYL-2,4-PENTANEDIOL 
_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
C1 C2 MPD sing 237 n n 
C1 H11 MPD sing 238 n n 
C1 H12 MPD sing 239 n n 
C1 H13 MPD sing 240 n n 
C2 O2 MPD sing 241 n n 
C2 CM MPD sing 242 n n 
C2 C3 MPD sing 243 n n 
O2 HO2 MPD sing 244 n n 
CM HM1 MPD sing 245 n n 
CM HM2 MPD sing 246 n n 
CM HM3 MPD sing 247 n n 
C3 C4 MPD sing 248 n n 
C3 H31 MPD sing 249 n n 
C3 H32 MPD sing 250 n n 
C4 O4 MPD sing 251 n n 
C4 C5 MPD sing 252 n n 
C4 H4 MPD sing 253 n n 
O4 HO4 MPD sing 254 n n 
C5 H51 MPD sing 255 n n 
C5 H52 MPD sing 256 n n 
C5 H53 MPD sing 257 n n 
#
_atom_sites.entry_id                     8RDK 
_atom_sites.fract_transf_matrix[1][1]    0.014387 
_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]    0.012788 
_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]    0.011511 
_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 ZN A 1 801 1 ZN ZN . 
C 3 MPD A 1 802 808 MPD MPD . 
D 4 YQT A 1 803 811 YQT 420 . 
E 5 HOH A 1 901 114 HOH HOH . 
E 5 HOH A 2 902 110 HOH HOH . 
E 5 HOH A 3 903 105 HOH HOH . 
E 5 HOH A 4 904 101 HOH HOH . 
E 5 HOH A 5 905 9 HOH HOH . 
E 5 HOH A 6 906 60 HOH HOH . 
E 5 HOH A 7 907 139 HOH HOH . 
E 5 HOH A 8 908 82 HOH HOH . 
E 5 HOH A 9 909 45 HOH HOH . 
E 5 HOH A 10 910 125 HOH HOH . 
E 5 HOH A 11 911 44 HOH HOH . 
E 5 HOH A 12 912 134 HOH HOH . 
E 5 HOH A 13 913 98 HOH HOH . 
E 5 HOH A 14 914 72 HOH HOH . 
E 5 HOH A 15 915 22 HOH HOH . 
E 5 HOH A 16 916 137 HOH HOH . 
E 5 HOH A 17 917 55 HOH HOH . 
E 5 HOH A 18 918 13 HOH HOH . 
E 5 HOH A 19 919 113 HOH HOH . 
E 5 HOH A 20 920 58 HOH HOH . 
E 5 HOH A 21 921 108 HOH HOH . 
E 5 HOH A 22 922 117 HOH HOH . 
E 5 HOH A 23 923 10 HOH HOH . 
E 5 HOH A 24 924 88 HOH HOH . 
E 5 HOH A 25 925 18 HOH HOH . 
E 5 HOH A 26 926 24 HOH HOH . 
E 5 HOH A 27 927 19 HOH HOH . 
E 5 HOH A 28 928 128 HOH HOH . 
E 5 HOH A 29 929 42 HOH HOH . 
E 5 HOH A 30 930 23 HOH HOH . 
E 5 HOH A 31 931 35 HOH HOH . 
E 5 HOH A 32 932 4 HOH HOH . 
E 5 HOH A 33 933 46 HOH HOH . 
E 5 HOH A 34 934 30 HOH HOH . 
E 5 HOH A 35 935 56 HOH HOH . 
E 5 HOH A 36 936 73 HOH HOH . 
E 5 HOH A 37 937 64 HOH HOH . 
E 5 HOH A 38 938 90 HOH HOH . 
E 5 HOH A 39 939 49 HOH HOH . 
E 5 HOH A 40 940 91 HOH HOH . 
E 5 HOH A 41 941 6 HOH HOH . 
E 5 HOH A 42 942 95 HOH HOH . 
E 5 HOH A 43 943 80 HOH HOH . 
E 5 HOH A 44 944 21 HOH HOH . 
E 5 HOH A 45 945 14 HOH HOH . 
E 5 HOH A 46 946 27 HOH HOH . 
E 5 HOH A 47 947 109 HOH HOH . 
E 5 HOH A 48 948 87 HOH HOH . 
E 5 HOH A 49 949 63 HOH HOH . 
E 5 HOH A 50 950 7 HOH HOH . 
E 5 HOH A 51 951 102 HOH HOH . 
E 5 HOH A 52 952 38 HOH HOH . 
E 5 HOH A 53 953 17 HOH HOH . 
E 5 HOH A 54 954 16 HOH HOH . 
E 5 HOH A 55 955 37 HOH HOH . 
E 5 HOH A 56 956 100 HOH HOH . 
E 5 HOH A 57 957 84 HOH HOH . 
E 5 HOH A 58 958 92 HOH HOH . 
E 5 HOH A 59 959 5 HOH HOH . 
E 5 HOH A 60 960 83 HOH HOH . 
E 5 HOH A 61 961 26 HOH HOH . 
E 5 HOH A 62 962 127 HOH HOH . 
E 5 HOH A 63 963 39 HOH HOH . 
E 5 HOH A 64 964 138 HOH HOH . 
E 5 HOH A 65 965 28 HOH HOH . 
E 5 HOH A 66 966 32 HOH HOH . 
E 5 HOH A 67 967 93 HOH HOH . 
E 5 HOH A 68 968 140 HOH HOH . 
E 5 HOH A 69 969 106 HOH HOH . 
E 5 HOH A 70 970 40 HOH HOH . 
E 5 HOH A 71 971 31 HOH HOH . 
E 5 HOH A 72 972 103 HOH HOH . 
E 5 HOH A 73 973 126 HOH HOH . 
E 5 HOH A 74 974 3 HOH HOH . 
E 5 HOH A 75 975 122 HOH HOH . 
E 5 HOH A 76 976 34 HOH HOH . 
E 5 HOH A 77 977 119 HOH HOH . 
E 5 HOH A 78 978 41 HOH HOH . 
E 5 HOH A 79 979 70 HOH HOH . 
E 5 HOH A 80 980 1 HOH HOH . 
E 5 HOH A 81 981 2 HOH HOH . 
E 5 HOH A 82 982 54 HOH HOH . 
E 5 HOH A 83 983 86 HOH HOH . 
E 5 HOH A 84 984 132 HOH HOH . 
E 5 HOH A 85 985 97 HOH HOH . 
E 5 HOH A 86 986 20 HOH HOH . 
E 5 HOH A 87 987 121 HOH HOH . 
E 5 HOH A 88 988 89 HOH HOH . 
E 5 HOH A 89 989 43 HOH HOH . 
E 5 HOH A 90 990 81 HOH HOH . 
E 5 HOH A 91 991 47 HOH HOH . 
E 5 HOH A 92 992 29 HOH HOH . 
E 5 HOH A 93 993 15 HOH HOH . 
E 5 HOH A 94 994 66 HOH HOH . 
E 5 HOH A 95 995 11 HOH HOH . 
E 5 HOH A 96 996 52 HOH HOH . 
E 5 HOH A 97 997 8 HOH HOH . 
E 5 HOH A 98 998 50 HOH HOH . 
E 5 HOH A 99 999 104 HOH HOH . 
E 5 HOH A 100 1000 51 HOH HOH . 
E 5 HOH A 101 1001 67 HOH HOH . 
E 5 HOH A 102 1002 136 HOH HOH . 
E 5 HOH A 103 1003 129 HOH HOH . 
E 5 HOH A 104 1004 124 HOH HOH . 
E 5 HOH A 105 1005 57 HOH HOH . 
E 5 HOH A 106 1006 69 HOH HOH . 
E 5 HOH A 107 1007 116 HOH HOH . 
E 5 HOH A 108 1008 120 HOH HOH . 
E 5 HOH A 109 1009 85 HOH HOH . 
E 5 HOH A 110 1010 53 HOH HOH . 
E 5 HOH A 111 1011 130 HOH HOH . 
E 5 HOH A 112 1012 94 HOH HOH . 
E 5 HOH A 113 1013 112 HOH HOH . 
E 5 HOH A 114 1014 111 HOH HOH . 
E 5 HOH A 115 1015 68 HOH HOH . 
E 5 HOH A 116 1016 65 HOH HOH . 
E 5 HOH A 117 1017 135 HOH HOH . 
E 5 HOH A 118 1018 123 HOH HOH . 
E 5 HOH A 119 1019 96 HOH HOH . 
E 5 HOH A 120 1020 48 HOH HOH . 
E 5 HOH A 121 1021 118 HOH HOH . 
E 5 HOH A 122 1022 71 HOH HOH . 
E 5 HOH A 123 1023 62 HOH HOH . 
E 5 HOH A 124 1024 131 HOH HOH . 
E 5 HOH A 125 1025 133 HOH HOH . 
E 5 HOH A 126 1026 33 HOH HOH . 
E 5 HOH A 127 1027 99 HOH HOH . 
E 5 HOH A 128 1028 79 HOH HOH . 
E 5 HOH A 129 1029 12 HOH HOH . 
E 5 HOH A 130 1030 78 HOH HOH . 
E 5 HOH A 131 1031 25 HOH HOH . 
E 5 HOH A 132 1032 115 HOH HOH . 
E 5 HOH A 133 1033 75 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 MPD . . . C 3 -30.329 7.911 15.864 1 52.36 ? C1 MPD 802 A 1 
HETATM 2 C C2 MPD . . . C 3 -29.537 7.025 16.821 1 59.41 ? C2 MPD 802 A 1 
HETATM 3 O O2 MPD . . . C 3 -28.204 6.973 16.327 1 55.68 ? O2 MPD 802 A 1 
HETATM 4 C CM MPD . . . C 3 -29.477 7.614 18.221 1 63.33 ? CM MPD 802 A 1 
HETATM 5 C C3 MPD . . . C 3 -29.783 5.508 16.775 1 67.22 ? C3 MPD 802 A 1 
HETATM 6 C C4 MPD . . . C 3 -31.104 4.839 17.033 1 68.98 ? C4 MPD 802 A 1 
HETATM 7 O O4 MPD . . . C 3 -31.392 4.285 15.802 1 64.91 ? O4 MPD 802 A 1 
HETATM 8 C C5 MPD . . . C 3 -31.219 3.703 18.023 1 71.77 ? C5 MPD 802 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           8 
#