data_6PDG
#
_model_server_result.job_id            M8NAhdfI2B4rYLdWMdSzOw 
_model_server_result.datetime_utc      '2024-11-14 21:10:19' 
_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          6pdg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":803}' 
#
_entry.id    6PDG 
#
_exptl.entry_id    6PDG 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            6PDG 
_cell.length_a            45.923 
_cell.length_b            56.284 
_cell.length_c            123.743 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PDG 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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
? 4 D N N 
? 4 E 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
covale ? covale1 A C HIS 97 A HIS 603 1_555 A N ALY 98 A ALY 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A C ALY 98 A ALY 604 1_555 A N THR 99 A THR 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
metalc ? metalc1 A SG CYS 34 A CYS 540 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc2 A SG CYS 37 A CYS 543 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc3 A NE2 HIS 50 A HIS 556 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? 
metalc ? metalc4 A SG CYS 54 A CYS 560 1_555 B ZN ZN . A ZN 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? 
metalc ? metalc5 C NA NA . A NA 802 1_555 H O HOH . A HOH 913 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.028 ? 
metalc ? metalc6 C NA NA . A NA 802 1_555 H O HOH . A HOH 923 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? 
metalc ? metalc7 C NA NA . A NA 802 1_555 H O HOH . A HOH 1039 4_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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 O1 GOL sing 157 n n 
C1 C2 GOL sing 158 n n 
C1 H11 GOL sing 159 n n 
C1 H12 GOL sing 160 n n 
O1 HO1 GOL sing 161 n n 
C2 O2 GOL sing 162 n n 
C2 C3 GOL sing 163 n n 
C2 H2 GOL sing 164 n n 
O2 HO2 GOL sing 165 n n 
C3 O3 GOL sing 166 n n 
C3 H31 GOL sing 167 n n 
C3 H32 GOL sing 168 n n 
O3 HO3 GOL sing 169 n n 
#
_atom_sites.entry_id                     6PDG 
_atom_sites.fract_transf_matrix[1][1]    0.021776 
_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]    0.017767 
_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]    0.008081 
_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 1 801 506 ZN ZN . 
C 3 NA A 1 802 507 NA NA . 
D 4 GOL A 1 803 510 GOL GOL . 
E 4 GOL A 1 804 511 GOL GOL . 
F 5 SO4 A 1 805 512 SO4 SO4 . 
G 6 O9A A 1 806 506 O9A LIG . 
H 7 HOH A 1 901 53 HOH HOH . 
H 7 HOH A 2 902 71 HOH HOH . 
H 7 HOH A 3 903 8 HOH HOH . 
H 7 HOH A 4 904 146 HOH HOH . 
H 7 HOH A 5 905 45 HOH HOH . 
H 7 HOH A 6 906 171 HOH HOH . 
H 7 HOH A 7 907 29 HOH HOH . 
H 7 HOH A 8 908 138 HOH HOH . 
H 7 HOH A 9 909 85 HOH HOH . 
H 7 HOH A 10 910 40 HOH HOH . 
H 7 HOH A 11 911 149 HOH HOH . 
H 7 HOH A 12 912 44 HOH HOH . 
H 7 HOH A 13 913 161 HOH HOH . 
H 7 HOH A 14 914 82 HOH HOH . 
H 7 HOH A 15 915 13 HOH HOH . 
H 7 HOH A 16 916 11 HOH HOH . 
H 7 HOH A 17 917 73 HOH HOH . 
H 7 HOH A 18 918 7 HOH HOH . 
H 7 HOH A 19 919 56 HOH HOH . 
H 7 HOH A 20 920 166 HOH HOH . 
H 7 HOH A 21 921 69 HOH HOH . 
H 7 HOH A 22 922 32 HOH HOH . 
H 7 HOH A 23 923 160 HOH HOH . 
H 7 HOH A 24 924 159 HOH HOH . 
H 7 HOH A 25 925 23 HOH HOH . 
H 7 HOH A 26 926 31 HOH HOH . 
H 7 HOH A 27 927 9 HOH HOH . 
H 7 HOH A 28 928 2 HOH HOH . 
H 7 HOH A 29 929 37 HOH HOH . 
H 7 HOH A 30 930 167 HOH HOH . 
H 7 HOH A 31 931 46 HOH HOH . 
H 7 HOH A 32 932 65 HOH HOH . 
H 7 HOH A 33 933 19 HOH HOH . 
H 7 HOH A 34 934 1 HOH HOH . 
H 7 HOH A 35 935 12 HOH HOH . 
H 7 HOH A 36 936 10 HOH HOH . 
H 7 HOH A 37 937 79 HOH HOH . 
H 7 HOH A 38 938 60 HOH HOH . 
H 7 HOH A 39 939 55 HOH HOH . 
H 7 HOH A 40 940 36 HOH HOH . 
H 7 HOH A 41 941 87 HOH HOH . 
H 7 HOH A 42 942 30 HOH HOH . 
H 7 HOH A 43 943 59 HOH HOH . 
H 7 HOH A 44 944 20 HOH HOH . 
H 7 HOH A 45 945 151 HOH HOH . 
H 7 HOH A 46 946 49 HOH HOH . 
H 7 HOH A 47 947 139 HOH HOH . 
H 7 HOH A 48 948 22 HOH HOH . 
H 7 HOH A 49 949 42 HOH HOH . 
H 7 HOH A 50 950 35 HOH HOH . 
H 7 HOH A 51 951 83 HOH HOH . 
H 7 HOH A 52 952 64 HOH HOH . 
H 7 HOH A 53 953 77 HOH HOH . 
H 7 HOH A 54 954 47 HOH HOH . 
H 7 HOH A 55 955 39 HOH HOH . 
H 7 HOH A 56 956 133 HOH HOH . 
H 7 HOH A 57 957 127 HOH HOH . 
H 7 HOH A 58 958 143 HOH HOH . 
H 7 HOH A 59 959 28 HOH HOH . 
H 7 HOH A 60 960 21 HOH HOH . 
H 7 HOH A 61 961 25 HOH HOH . 
H 7 HOH A 62 962 75 HOH HOH . 
H 7 HOH A 63 963 52 HOH HOH . 
H 7 HOH A 64 964 3 HOH HOH . 
H 7 HOH A 65 965 6 HOH HOH . 
H 7 HOH A 66 966 51 HOH HOH . 
H 7 HOH A 67 967 116 HOH HOH . 
H 7 HOH A 68 968 157 HOH HOH . 
H 7 HOH A 69 969 66 HOH HOH . 
H 7 HOH A 70 970 110 HOH HOH . 
H 7 HOH A 71 971 4 HOH HOH . 
H 7 HOH A 72 972 101 HOH HOH . 
H 7 HOH A 73 973 123 HOH HOH . 
H 7 HOH A 74 974 63 HOH HOH . 
H 7 HOH A 75 975 132 HOH HOH . 
H 7 HOH A 76 976 99 HOH HOH . 
H 7 HOH A 77 977 78 HOH HOH . 
H 7 HOH A 78 978 26 HOH HOH . 
H 7 HOH A 79 979 90 HOH HOH . 
H 7 HOH A 80 980 134 HOH HOH . 
H 7 HOH A 81 981 41 HOH HOH . 
H 7 HOH A 82 982 50 HOH HOH . 
H 7 HOH A 83 983 155 HOH HOH . 
H 7 HOH A 84 984 131 HOH HOH . 
H 7 HOH A 85 985 58 HOH HOH . 
H 7 HOH A 86 986 140 HOH HOH . 
H 7 HOH A 87 987 130 HOH HOH . 
H 7 HOH A 88 988 88 HOH HOH . 
H 7 HOH A 89 989 164 HOH HOH . 
H 7 HOH A 90 990 117 HOH HOH . 
H 7 HOH A 91 991 43 HOH HOH . 
H 7 HOH A 92 992 80 HOH HOH . 
H 7 HOH A 93 993 150 HOH HOH . 
H 7 HOH A 94 994 16 HOH HOH . 
H 7 HOH A 95 995 142 HOH HOH . 
H 7 HOH A 96 996 105 HOH HOH . 
H 7 HOH A 97 997 76 HOH HOH . 
H 7 HOH A 98 998 38 HOH HOH . 
H 7 HOH A 99 999 108 HOH HOH . 
H 7 HOH A 100 1000 68 HOH HOH . 
H 7 HOH A 101 1001 72 HOH HOH . 
H 7 HOH A 102 1002 136 HOH HOH . 
H 7 HOH A 103 1003 48 HOH HOH . 
H 7 HOH A 104 1004 18 HOH HOH . 
H 7 HOH A 105 1005 112 HOH HOH . 
H 7 HOH A 106 1006 98 HOH HOH . 
H 7 HOH A 107 1007 92 HOH HOH . 
H 7 HOH A 108 1008 74 HOH HOH . 
H 7 HOH A 109 1009 137 HOH HOH . 
H 7 HOH A 110 1010 84 HOH HOH . 
H 7 HOH A 111 1011 93 HOH HOH . 
H 7 HOH A 112 1012 70 HOH HOH . 
H 7 HOH A 113 1013 5 HOH HOH . 
H 7 HOH A 114 1014 27 HOH HOH . 
H 7 HOH A 115 1015 120 HOH HOH . 
H 7 HOH A 116 1016 125 HOH HOH . 
H 7 HOH A 117 1017 61 HOH HOH . 
H 7 HOH A 118 1018 168 HOH HOH . 
H 7 HOH A 119 1019 118 HOH HOH . 
H 7 HOH A 120 1020 169 HOH HOH . 
H 7 HOH A 121 1021 106 HOH HOH . 
H 7 HOH A 122 1022 91 HOH HOH . 
H 7 HOH A 123 1023 14 HOH HOH . 
H 7 HOH A 124 1024 54 HOH HOH . 
H 7 HOH A 125 1025 152 HOH HOH . 
H 7 HOH A 126 1026 121 HOH HOH . 
H 7 HOH A 127 1027 126 HOH HOH . 
H 7 HOH A 128 1028 62 HOH HOH . 
H 7 HOH A 129 1029 141 HOH HOH . 
H 7 HOH A 130 1030 129 HOH HOH . 
H 7 HOH A 131 1031 94 HOH HOH . 
H 7 HOH A 132 1032 15 HOH HOH . 
H 7 HOH A 133 1033 153 HOH HOH . 
H 7 HOH A 134 1034 17 HOH HOH . 
H 7 HOH A 135 1035 113 HOH HOH . 
H 7 HOH A 136 1036 109 HOH HOH . 
H 7 HOH A 137 1037 102 HOH HOH . 
H 7 HOH A 138 1038 156 HOH HOH . 
H 7 HOH A 139 1039 33 HOH HOH . 
H 7 HOH A 140 1040 111 HOH HOH . 
H 7 HOH A 141 1041 154 HOH HOH . 
H 7 HOH A 142 1042 34 HOH HOH . 
H 7 HOH A 143 1043 163 HOH HOH . 
H 7 HOH A 144 1044 86 HOH HOH . 
H 7 HOH A 145 1045 24 HOH HOH . 
H 7 HOH A 146 1046 135 HOH HOH . 
H 7 HOH A 147 1047 95 HOH HOH . 
H 7 HOH A 148 1048 147 HOH HOH . 
H 7 HOH A 149 1049 165 HOH HOH . 
H 7 HOH A 150 1050 67 HOH HOH . 
H 7 HOH A 151 1051 107 HOH HOH . 
H 7 HOH A 152 1052 124 HOH HOH . 
H 7 HOH A 153 1053 97 HOH HOH . 
H 7 HOH A 154 1054 57 HOH HOH . 
H 7 HOH A 155 1055 119 HOH HOH . 
H 7 HOH A 156 1056 103 HOH HOH . 
H 7 HOH A 157 1057 158 HOH HOH . 
H 7 HOH A 158 1058 114 HOH HOH . 
H 7 HOH A 159 1059 122 HOH HOH . 
H 7 HOH A 160 1060 170 HOH HOH . 
H 7 HOH A 161 1061 89 HOH HOH . 
H 7 HOH A 162 1062 115 HOH HOH . 
H 7 HOH A 163 1063 104 HOH HOH . 
H 7 HOH A 164 1064 100 HOH HOH . 
H 7 HOH A 165 1065 162 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 GOL . . . D 4 -1.621 -10.683 -21.463 1 39.97 ? C1 GOL 803 A 1 
HETATM 2 O O1 GOL . . . D 4 -2.671 -9.99 -22.1 1 48.12 ? O1 GOL 803 A 1 
HETATM 3 C C2 GOL . . . D 4 -1.109 -9.827 -20.311 1 43.6 ? C2 GOL 803 A 1 
HETATM 4 O O2 GOL . . . D 4 -2.182 -9.493 -19.456 1 45.53 ? O2 GOL 803 A 1 
HETATM 5 C C3 GOL . . . D 4 -0.076 -10.61 -19.517 1 36.98 ? C3 GOL 803 A 1 
HETATM 6 O O3 GOL . . . D 4 0.33 -9.825 -18.418 1 35.47 ? O3 GOL 803 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           469 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           6 
#