data_5YBV
#
_model_server_result.job_id            X3Y88Veg5dg17kVooDxn4g 
_model_server_result.datetime_utc      '2024-11-04 20:35:18' 
_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          5ybv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":903}' 
#
_entry.id    5YBV 
#
_exptl.entry_id    5YBV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         73.02 
_cell.angle_beta          89.67 
_cell.angle_gamma         84.91 
_cell.entry_id            5YBV 
_cell.length_a            45.956 
_cell.length_b            52.834 
_cell.length_c            53.478 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YBV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,K,L,M,N 
_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
? 5 F N N 
? 5 G N N 
? 5 H N N 
? 5 J N N 
#
_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                     5YBV 
_atom_sites.fract_transf_matrix[1][1]    0.02176 
_atom_sites.fract_transf_matrix[1][2]    -0.001939 
_atom_sites.fract_transf_matrix[1][3]    0.000464 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019002 
_atom_sites.fract_transf_matrix[2][3]    -0.005818 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.019557 
_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 4 SO4 A 1 901 1 SO4 SO4 . 
F 5 GOL A 1 902 4 GOL GOL . 
G 5 GOL A 1 903 7 GOL GOL . 
H 5 GOL B 1 901 2 GOL GOL . 
I 4 SO4 B 1 902 5 SO4 SO4 . 
J 5 GOL B 1 903 6 GOL GOL . 
K 6 HOH A 1 1001 1 HOH HOH . 
K 6 HOH A 2 1002 228 HOH HOH . 
K 6 HOH A 3 1003 56 HOH HOH . 
K 6 HOH A 4 1004 40 HOH HOH . 
K 6 HOH A 5 1005 5 HOH HOH . 
K 6 HOH A 6 1006 15 HOH HOH . 
K 6 HOH A 7 1007 24 HOH HOH . 
K 6 HOH A 8 1008 36 HOH HOH . 
K 6 HOH A 9 1009 81 HOH HOH . 
K 6 HOH A 10 1010 2 HOH HOH . 
K 6 HOH A 11 1011 121 HOH HOH . 
K 6 HOH A 12 1012 59 HOH HOH . 
K 6 HOH A 13 1013 32 HOH HOH . 
K 6 HOH A 14 1014 9 HOH HOH . 
K 6 HOH A 15 1015 55 HOH HOH . 
K 6 HOH A 16 1016 107 HOH HOH . 
K 6 HOH A 17 1017 229 HOH HOH . 
K 6 HOH A 18 1018 27 HOH HOH . 
K 6 HOH A 19 1019 112 HOH HOH . 
K 6 HOH A 20 1020 44 HOH HOH . 
K 6 HOH A 21 1021 145 HOH HOH . 
K 6 HOH A 22 1022 35 HOH HOH . 
K 6 HOH A 23 1023 76 HOH HOH . 
K 6 HOH A 24 1024 51 HOH HOH . 
K 6 HOH A 25 1025 21 HOH HOH . 
K 6 HOH A 26 1026 138 HOH HOH . 
K 6 HOH A 27 1027 31 HOH HOH . 
K 6 HOH A 28 1028 144 HOH HOH . 
K 6 HOH A 29 1029 82 HOH HOH . 
K 6 HOH A 30 1030 71 HOH HOH . 
K 6 HOH A 31 1031 84 HOH HOH . 
K 6 HOH A 32 1032 77 HOH HOH . 
K 6 HOH A 33 1033 149 HOH HOH . 
K 6 HOH A 34 1034 186 HOH HOH . 
K 6 HOH A 35 1035 46 HOH HOH . 
K 6 HOH A 36 1036 189 HOH HOH . 
K 6 HOH A 37 1037 97 HOH HOH . 
K 6 HOH A 38 1038 179 HOH HOH . 
K 6 HOH A 39 1039 159 HOH HOH . 
K 6 HOH A 40 1040 83 HOH HOH . 
K 6 HOH A 41 1041 70 HOH HOH . 
K 6 HOH A 42 1042 69 HOH HOH . 
K 6 HOH A 43 1043 7 HOH HOH . 
K 6 HOH A 44 1044 131 HOH HOH . 
K 6 HOH A 45 1045 17 HOH HOH . 
K 6 HOH A 46 1046 37 HOH HOH . 
K 6 HOH A 47 1047 14 HOH HOH . 
K 6 HOH A 48 1048 239 HOH HOH . 
K 6 HOH A 49 1049 4 HOH HOH . 
K 6 HOH A 50 1050 8 HOH HOH . 
K 6 HOH A 51 1051 6 HOH HOH . 
K 6 HOH A 52 1052 19 HOH HOH . 
K 6 HOH A 53 1053 11 HOH HOH . 
K 6 HOH A 54 1054 58 HOH HOH . 
K 6 HOH A 55 1055 152 HOH HOH . 
K 6 HOH A 56 1056 39 HOH HOH . 
K 6 HOH A 57 1057 75 HOH HOH . 
K 6 HOH A 58 1058 168 HOH HOH . 
K 6 HOH A 59 1059 103 HOH HOH . 
K 6 HOH A 60 1060 42 HOH HOH . 
K 6 HOH A 61 1061 66 HOH HOH . 
K 6 HOH A 62 1062 49 HOH HOH . 
K 6 HOH A 63 1063 169 HOH HOH . 
K 6 HOH A 64 1064 217 HOH HOH . 
K 6 HOH A 65 1065 222 HOH HOH . 
K 6 HOH A 66 1066 86 HOH HOH . 
K 6 HOH A 67 1067 67 HOH HOH . 
K 6 HOH A 68 1068 47 HOH HOH . 
K 6 HOH A 69 1069 43 HOH HOH . 
K 6 HOH A 70 1070 94 HOH HOH . 
K 6 HOH A 71 1071 238 HOH HOH . 
K 6 HOH A 72 1072 63 HOH HOH . 
K 6 HOH A 73 1073 104 HOH HOH . 
K 6 HOH A 74 1074 164 HOH HOH . 
K 6 HOH A 75 1075 198 HOH HOH . 
K 6 HOH A 76 1076 225 HOH HOH . 
K 6 HOH A 77 1077 41 HOH HOH . 
K 6 HOH A 78 1078 33 HOH HOH . 
K 6 HOH A 79 1079 106 HOH HOH . 
K 6 HOH A 80 1080 87 HOH HOH . 
K 6 HOH A 81 1081 195 HOH HOH . 
K 6 HOH A 82 1082 215 HOH HOH . 
K 6 HOH A 83 1083 25 HOH HOH . 
K 6 HOH A 84 1084 48 HOH HOH . 
K 6 HOH A 85 1085 119 HOH HOH . 
K 6 HOH A 86 1086 62 HOH HOH . 
K 6 HOH A 87 1087 230 HOH HOH . 
K 6 HOH A 88 1088 53 HOH HOH . 
K 6 HOH A 89 1089 88 HOH HOH . 
K 6 HOH A 90 1090 139 HOH HOH . 
K 6 HOH A 91 1091 141 HOH HOH . 
K 6 HOH A 92 1092 133 HOH HOH . 
K 6 HOH A 93 1093 91 HOH HOH . 
K 6 HOH A 94 1094 102 HOH HOH . 
K 6 HOH A 95 1095 110 HOH HOH . 
K 6 HOH A 96 1096 118 HOH HOH . 
K 6 HOH A 97 1097 184 HOH HOH . 
K 6 HOH A 98 1098 160 HOH HOH . 
K 6 HOH A 99 1099 177 HOH HOH . 
K 6 HOH A 100 1100 173 HOH HOH . 
K 6 HOH A 101 1101 192 HOH HOH . 
K 6 HOH A 102 1102 202 HOH HOH . 
K 6 HOH A 103 1103 98 HOH HOH . 
K 6 HOH A 104 1104 185 HOH HOH . 
K 6 HOH A 105 1105 151 HOH HOH . 
K 6 HOH A 106 1106 135 HOH HOH . 
K 6 HOH A 107 1107 176 HOH HOH . 
K 6 HOH A 108 1108 72 HOH HOH . 
K 6 HOH A 109 1109 90 HOH HOH . 
K 6 HOH A 110 1110 157 HOH HOH . 
K 6 HOH A 111 1111 156 HOH HOH . 
K 6 HOH A 112 1112 146 HOH HOH . 
L 6 HOH B 1 1001 29 HOH HOH . 
L 6 HOH B 2 1002 74 HOH HOH . 
L 6 HOH B 3 1003 3 HOH HOH . 
L 6 HOH B 4 1004 167 HOH HOH . 
L 6 HOH B 5 1005 150 HOH HOH . 
L 6 HOH B 6 1006 235 HOH HOH . 
L 6 HOH B 7 1007 12 HOH HOH . 
L 6 HOH B 8 1008 175 HOH HOH . 
L 6 HOH B 9 1009 153 HOH HOH . 
L 6 HOH B 10 1010 20 HOH HOH . 
L 6 HOH B 11 1011 163 HOH HOH . 
L 6 HOH B 12 1012 100 HOH HOH . 
L 6 HOH B 13 1013 73 HOH HOH . 
L 6 HOH B 14 1014 105 HOH HOH . 
L 6 HOH B 15 1015 120 HOH HOH . 
L 6 HOH B 16 1016 65 HOH HOH . 
L 6 HOH B 17 1017 117 HOH HOH . 
L 6 HOH B 18 1018 95 HOH HOH . 
L 6 HOH B 19 1019 18 HOH HOH . 
L 6 HOH B 20 1020 34 HOH HOH . 
L 6 HOH B 21 1021 60 HOH HOH . 
L 6 HOH B 22 1022 30 HOH HOH . 
L 6 HOH B 23 1023 28 HOH HOH . 
L 6 HOH B 24 1024 174 HOH HOH . 
L 6 HOH B 25 1025 45 HOH HOH . 
L 6 HOH B 26 1026 155 HOH HOH . 
L 6 HOH B 27 1027 132 HOH HOH . 
L 6 HOH B 28 1028 115 HOH HOH . 
L 6 HOH B 29 1029 16 HOH HOH . 
L 6 HOH B 30 1030 57 HOH HOH . 
L 6 HOH B 31 1031 10 HOH HOH . 
L 6 HOH B 32 1032 78 HOH HOH . 
L 6 HOH B 33 1033 190 HOH HOH . 
L 6 HOH B 34 1034 64 HOH HOH . 
L 6 HOH B 35 1035 26 HOH HOH . 
L 6 HOH B 36 1036 80 HOH HOH . 
L 6 HOH B 37 1037 182 HOH HOH . 
L 6 HOH B 38 1038 23 HOH HOH . 
L 6 HOH B 39 1039 13 HOH HOH . 
L 6 HOH B 40 1040 99 HOH HOH . 
L 6 HOH B 41 1041 101 HOH HOH . 
L 6 HOH B 42 1042 96 HOH HOH . 
L 6 HOH B 43 1043 54 HOH HOH . 
L 6 HOH B 44 1044 68 HOH HOH . 
L 6 HOH B 45 1045 79 HOH HOH . 
L 6 HOH B 46 1046 50 HOH HOH . 
L 6 HOH B 47 1047 85 HOH HOH . 
L 6 HOH B 48 1048 93 HOH HOH . 
L 6 HOH B 49 1049 61 HOH HOH . 
L 6 HOH B 50 1050 38 HOH HOH . 
L 6 HOH B 51 1051 224 HOH HOH . 
L 6 HOH B 52 1052 126 HOH HOH . 
L 6 HOH B 53 1053 236 HOH HOH . 
L 6 HOH B 54 1054 203 HOH HOH . 
L 6 HOH B 55 1055 196 HOH HOH . 
L 6 HOH B 56 1056 233 HOH HOH . 
L 6 HOH B 57 1057 109 HOH HOH . 
L 6 HOH B 58 1058 142 HOH HOH . 
L 6 HOH B 59 1059 114 HOH HOH . 
L 6 HOH B 60 1060 244 HOH HOH . 
L 6 HOH B 61 1061 193 HOH HOH . 
L 6 HOH B 62 1062 243 HOH HOH . 
L 6 HOH B 63 1063 52 HOH HOH . 
L 6 HOH B 64 1064 108 HOH HOH . 
L 6 HOH B 65 1065 124 HOH HOH . 
M 6 HOH C 1 1201 22 HOH HOH . 
N 6 HOH D 1 1201 140 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 . . . G 5 -20.364 5.424 -5.537 1 63.71 ? C1 GOL 903 A 1 
HETATM 2 O O1 GOL . . . G 5 -21.566 5.987 -4.999 1 66.41 ? O1 GOL 903 A 1 
HETATM 3 C C2 GOL . . . G 5 -20.208 5.728 -7.023 1 64.19 ? C2 GOL 903 A 1 
HETATM 4 O O2 GOL . . . G 5 -20.331 4.509 -7.76 1 76.78 ? O2 GOL 903 A 1 
HETATM 5 C C3 GOL . . . G 5 -18.842 6.328 -7.348 1 53.68 ? C3 GOL 903 A 1 
HETATM 6 O O3 GOL . . . G 5 -17.798 5.386 -7.072 1 47.02 ? O3 GOL 903 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           296 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           6 
#