data_5YPO
#
_model_server_result.job_id            jutIXkOPhY_2hv3Z5nGqdA 
_model_server_result.datetime_utc      '2024-11-13 06:17:30' 
_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          5ypo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":801}' 
#
_entry.id    5YPO 
#
_exptl.entry_id    5YPO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    3 
_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            5YPO 
_cell.length_a            33.776 
_cell.length_b            84.063 
_cell.length_c            165.123 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YPO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,C,E,G,H,J 1 1 
B,D,F,I,K 2 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 E N N 
? 3 F 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
covale ? covale1 C C GLU 5 C GLU 0 1_555 C N SEP 6 C SEP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale2 C C SEP 6 C SEP 1 1_555 C N TYR 7 C TYR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale3 D C GLU 5 D GLU 0 1_555 D N SEP 6 D SEP 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale4 D C SEP 6 D SEP 1 1_555 D N TYR 7 D TYR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
#
_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 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     5YPO 
_atom_sites.fract_transf_matrix[1][1]    0.029607 
_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]    0.011896 
_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]    0.006056 
_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
E 3 GOL B 1 801 1 GOL GOL . 
F 3 GOL A 1 801 1 GOL GOL . 
G 3 GOL C 1 101 1 GOL GOL . 
H 4 HOH B 1 901 223 HOH HOH . 
H 4 HOH B 2 902 201 HOH HOH . 
H 4 HOH B 3 903 20 HOH HOH . 
H 4 HOH B 4 904 168 HOH HOH . 
H 4 HOH B 5 905 127 HOH HOH . 
H 4 HOH B 6 906 114 HOH HOH . 
H 4 HOH B 7 907 212 HOH HOH . 
H 4 HOH B 8 908 6 HOH HOH . 
H 4 HOH B 9 909 171 HOH HOH . 
H 4 HOH B 10 910 40 HOH HOH . 
H 4 HOH B 11 911 103 HOH HOH . 
H 4 HOH B 12 912 10 HOH HOH . 
H 4 HOH B 13 913 83 HOH HOH . 
H 4 HOH B 14 914 174 HOH HOH . 
H 4 HOH B 15 915 111 HOH HOH . 
H 4 HOH B 16 916 80 HOH HOH . 
H 4 HOH B 17 917 87 HOH HOH . 
H 4 HOH B 18 918 90 HOH HOH . 
H 4 HOH B 19 919 119 HOH HOH . 
H 4 HOH B 20 920 78 HOH HOH . 
H 4 HOH B 21 921 123 HOH HOH . 
H 4 HOH B 22 922 132 HOH HOH . 
H 4 HOH B 23 923 32 HOH HOH . 
H 4 HOH B 24 924 3 HOH HOH . 
H 4 HOH B 25 925 57 HOH HOH . 
H 4 HOH B 26 926 26 HOH HOH . 
H 4 HOH B 27 927 13 HOH HOH . 
H 4 HOH B 28 928 142 HOH HOH . 
H 4 HOH B 29 929 27 HOH HOH . 
H 4 HOH B 30 930 150 HOH HOH . 
H 4 HOH B 31 931 202 HOH HOH . 
H 4 HOH B 32 932 129 HOH HOH . 
H 4 HOH B 33 933 4 HOH HOH . 
H 4 HOH B 34 934 125 HOH HOH . 
H 4 HOH B 35 935 84 HOH HOH . 
H 4 HOH B 36 936 39 HOH HOH . 
H 4 HOH B 37 937 196 HOH HOH . 
H 4 HOH B 38 938 108 HOH HOH . 
H 4 HOH B 39 939 143 HOH HOH . 
H 4 HOH B 40 940 79 HOH HOH . 
H 4 HOH B 41 941 66 HOH HOH . 
H 4 HOH B 42 942 175 HOH HOH . 
H 4 HOH B 43 943 1 HOH HOH . 
H 4 HOH B 44 944 68 HOH HOH . 
H 4 HOH B 45 945 128 HOH HOH . 
H 4 HOH B 46 946 189 HOH HOH . 
H 4 HOH B 47 947 52 HOH HOH . 
H 4 HOH B 48 948 55 HOH HOH . 
H 4 HOH B 49 949 37 HOH HOH . 
H 4 HOH B 50 950 211 HOH HOH . 
H 4 HOH B 51 951 61 HOH HOH . 
H 4 HOH B 52 952 81 HOH HOH . 
H 4 HOH B 53 953 28 HOH HOH . 
H 4 HOH B 54 954 109 HOH HOH . 
H 4 HOH B 55 955 58 HOH HOH . 
H 4 HOH B 56 956 164 HOH HOH . 
H 4 HOH B 57 957 188 HOH HOH . 
H 4 HOH B 58 958 7 HOH HOH . 
H 4 HOH B 59 959 165 HOH HOH . 
H 4 HOH B 60 960 12 HOH HOH . 
H 4 HOH B 61 961 115 HOH HOH . 
H 4 HOH B 62 962 195 HOH HOH . 
H 4 HOH B 63 963 46 HOH HOH . 
H 4 HOH B 64 964 148 HOH HOH . 
H 4 HOH B 65 965 8 HOH HOH . 
H 4 HOH B 66 966 131 HOH HOH . 
H 4 HOH B 67 967 31 HOH HOH . 
H 4 HOH B 68 968 34 HOH HOH . 
H 4 HOH B 69 969 60 HOH HOH . 
H 4 HOH B 70 970 138 HOH HOH . 
H 4 HOH B 71 971 102 HOH HOH . 
H 4 HOH B 72 972 70 HOH HOH . 
H 4 HOH B 73 973 173 HOH HOH . 
H 4 HOH B 74 974 64 HOH HOH . 
H 4 HOH B 75 975 93 HOH HOH . 
H 4 HOH B 76 976 98 HOH HOH . 
H 4 HOH B 77 977 95 HOH HOH . 
H 4 HOH B 78 978 162 HOH HOH . 
H 4 HOH B 79 979 89 HOH HOH . 
H 4 HOH B 80 980 19 HOH HOH . 
H 4 HOH B 81 981 107 HOH HOH . 
H 4 HOH B 82 982 2 HOH HOH . 
H 4 HOH B 83 983 96 HOH HOH . 
H 4 HOH B 84 984 18 HOH HOH . 
H 4 HOH B 85 985 133 HOH HOH . 
H 4 HOH B 86 986 94 HOH HOH . 
H 4 HOH B 87 987 86 HOH HOH . 
H 4 HOH B 88 988 25 HOH HOH . 
H 4 HOH B 89 989 136 HOH HOH . 
H 4 HOH B 90 990 100 HOH HOH . 
H 4 HOH B 91 991 122 HOH HOH . 
H 4 HOH B 92 992 30 HOH HOH . 
H 4 HOH B 93 993 49 HOH HOH . 
H 4 HOH B 94 994 56 HOH HOH . 
H 4 HOH B 95 995 82 HOH HOH . 
H 4 HOH B 96 996 170 HOH HOH . 
H 4 HOH B 97 997 121 HOH HOH . 
H 4 HOH B 98 998 190 HOH HOH . 
H 4 HOH B 99 999 154 HOH HOH . 
H 4 HOH B 100 1000 43 HOH HOH . 
H 4 HOH B 101 1001 169 HOH HOH . 
H 4 HOH B 102 1002 156 HOH HOH . 
H 4 HOH B 103 1003 140 HOH HOH . 
H 4 HOH B 104 1004 224 HOH HOH . 
H 4 HOH B 105 1005 139 HOH HOH . 
H 4 HOH B 106 1006 205 HOH HOH . 
H 4 HOH B 107 1007 116 HOH HOH . 
H 4 HOH B 108 1008 222 HOH HOH . 
H 4 HOH B 109 1009 92 HOH HOH . 
H 4 HOH B 110 1010 206 HOH HOH . 
H 4 HOH B 111 1011 161 HOH HOH . 
H 4 HOH B 112 1012 153 HOH HOH . 
H 4 HOH B 113 1013 210 HOH HOH . 
I 4 HOH A 1 901 183 HOH HOH . 
I 4 HOH A 2 902 216 HOH HOH . 
I 4 HOH A 3 903 198 HOH HOH . 
I 4 HOH A 4 904 182 HOH HOH . 
I 4 HOH A 5 905 88 HOH HOH . 
I 4 HOH A 6 906 50 HOH HOH . 
I 4 HOH A 7 907 101 HOH HOH . 
I 4 HOH A 8 908 106 HOH HOH . 
I 4 HOH A 9 909 76 HOH HOH . 
I 4 HOH A 10 910 179 HOH HOH . 
I 4 HOH A 11 911 11 HOH HOH . 
I 4 HOH A 12 912 186 HOH HOH . 
I 4 HOH A 13 913 47 HOH HOH . 
I 4 HOH A 14 914 17 HOH HOH . 
I 4 HOH A 15 915 21 HOH HOH . 
I 4 HOH A 16 916 24 HOH HOH . 
I 4 HOH A 17 917 41 HOH HOH . 
I 4 HOH A 18 918 53 HOH HOH . 
I 4 HOH A 19 919 75 HOH HOH . 
I 4 HOH A 20 920 62 HOH HOH . 
I 4 HOH A 21 921 124 HOH HOH . 
I 4 HOH A 22 922 42 HOH HOH . 
I 4 HOH A 23 923 16 HOH HOH . 
I 4 HOH A 24 924 172 HOH HOH . 
I 4 HOH A 25 925 44 HOH HOH . 
I 4 HOH A 26 926 15 HOH HOH . 
I 4 HOH A 27 927 151 HOH HOH . 
I 4 HOH A 28 928 117 HOH HOH . 
I 4 HOH A 29 929 72 HOH HOH . 
I 4 HOH A 30 930 67 HOH HOH . 
I 4 HOH A 31 931 134 HOH HOH . 
I 4 HOH A 32 932 203 HOH HOH . 
I 4 HOH A 33 933 59 HOH HOH . 
I 4 HOH A 34 934 45 HOH HOH . 
I 4 HOH A 35 935 204 HOH HOH . 
I 4 HOH A 36 936 181 HOH HOH . 
I 4 HOH A 37 937 38 HOH HOH . 
I 4 HOH A 38 938 48 HOH HOH . 
I 4 HOH A 39 939 225 HOH HOH . 
I 4 HOH A 40 940 51 HOH HOH . 
I 4 HOH A 41 941 33 HOH HOH . 
I 4 HOH A 42 942 9 HOH HOH . 
I 4 HOH A 43 943 35 HOH HOH . 
I 4 HOH A 44 944 218 HOH HOH . 
I 4 HOH A 45 945 163 HOH HOH . 
I 4 HOH A 46 946 149 HOH HOH . 
I 4 HOH A 47 947 73 HOH HOH . 
I 4 HOH A 48 948 104 HOH HOH . 
I 4 HOH A 49 949 105 HOH HOH . 
I 4 HOH A 50 950 217 HOH HOH . 
I 4 HOH A 51 951 147 HOH HOH . 
I 4 HOH A 52 952 97 HOH HOH . 
I 4 HOH A 53 953 199 HOH HOH . 
I 4 HOH A 54 954 178 HOH HOH . 
I 4 HOH A 55 955 177 HOH HOH . 
I 4 HOH A 56 956 23 HOH HOH . 
I 4 HOH A 57 957 192 HOH HOH . 
I 4 HOH A 58 958 191 HOH HOH . 
I 4 HOH A 59 959 193 HOH HOH . 
I 4 HOH A 60 960 113 HOH HOH . 
I 4 HOH A 61 961 144 HOH HOH . 
I 4 HOH A 62 962 157 HOH HOH . 
I 4 HOH A 63 963 176 HOH HOH . 
I 4 HOH A 64 964 209 HOH HOH . 
I 4 HOH A 65 965 120 HOH HOH . 
I 4 HOH A 66 966 110 HOH HOH . 
I 4 HOH A 67 967 220 HOH HOH . 
I 4 HOH A 68 968 187 HOH HOH . 
I 4 HOH A 69 969 118 HOH HOH . 
I 4 HOH A 70 970 160 HOH HOH . 
I 4 HOH A 71 971 77 HOH HOH . 
I 4 HOH A 72 972 180 HOH HOH . 
I 4 HOH A 73 973 184 HOH HOH . 
I 4 HOH A 74 974 167 HOH HOH . 
I 4 HOH A 75 975 194 HOH HOH . 
I 4 HOH A 76 976 219 HOH HOH . 
J 4 HOH C 1 201 214 HOH HOH . 
J 4 HOH C 2 202 215 HOH HOH . 
J 4 HOH C 3 203 36 HOH HOH . 
J 4 HOH C 4 204 63 HOH HOH . 
J 4 HOH C 5 205 146 HOH HOH . 
J 4 HOH C 6 206 85 HOH HOH . 
J 4 HOH C 7 207 159 HOH HOH . 
J 4 HOH C 8 208 213 HOH HOH . 
J 4 HOH C 9 209 200 HOH HOH . 
K 4 HOH D 1 101 54 HOH HOH . 
K 4 HOH D 2 102 22 HOH HOH . 
K 4 HOH D 3 103 152 HOH HOH . 
K 4 HOH D 4 104 158 HOH HOH . 
K 4 HOH D 5 105 99 HOH HOH . 
K 4 HOH D 6 106 207 HOH HOH . 
K 4 HOH D 7 107 166 HOH HOH . 
K 4 HOH D 8 108 197 HOH HOH . 
K 4 HOH D 9 109 221 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 . . . F 3 6.557 11.975 24.507 1 29.51 ? C1 GOL 801 A 1 
HETATM 2 O O1 GOL . . . F 3 5.331 12.098 23.788 1 21.25 ? O1 GOL 801 A 1 
HETATM 3 C C2 GOL . . . F 3 6.757 13.221 25.432 1 26.27 ? C2 GOL 801 A 1 
HETATM 4 O O2 GOL . . . F 3 6.902 14.376 24.69 1 29.67 ? O2 GOL 801 A 1 
HETATM 5 C C3 GOL . . . F 3 8.049 12.887 26.228 1 28.23 ? C3 GOL 801 A 1 
HETATM 6 O O3 GOL . . . F 3 8.137 13.799 27.287 1 30.91 ? O3 GOL 801 A 1 
#
_model_server_stats.io_time_ms              50 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           258 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           6 
#