data_3B9S
#
_model_server_result.job_id            P0ZJCdaXMoOiY2ySJKYfrw 
_model_server_result.datetime_utc      '2025-06-12 15:05:27' 
_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          3b9s 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":116}' 
#
_entry.id    3B9S 
#
_exptl.entry_id    3B9S 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          2 
_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            3B9S 
_cell.length_a            67.891 
_cell.length_b            67.995 
_cell.length_c            88.296 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3B9S 
_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    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,O,P 
_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
? 2 D N N 
? 2 I N N 
? 2 L 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 N PRO 1 A PRO 1 1_555 E C4 RW1 . A RW1 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale2 B N PRO 1 B PRO 1 1_555 J C4 RW1 . B RW1 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? 
covale ? covale3 C N PRO 1 C PRO 1 1_555 M C4 RW1 . C RW1 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.372 ? 
#
_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                     3B9S 
_atom_sites.fract_transf_matrix[1][1]    0.014729 
_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]    0.014707 
_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]    0.011326 
_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
D 2 GOL A 1 119 2 GOL GOL . 
E 3 RW1 A 1 118 1 RW1 RW . 
F 4 SO4 A 1 115 2 SO4 SO4 . 
G 4 SO4 A 1 116 3 SO4 SO4 . 
H 4 SO4 A 1 117 4 SO4 SO4 . 
I 2 GOL B 1 117 1 GOL GOL . 
J 3 RW1 B 1 116 2 RW1 RW . 
K 4 SO4 B 1 115 1 SO4 SO4 . 
L 2 GOL C 1 116 3 GOL GOL . 
M 3 RW1 C 1 115 3 RW1 RW . 
N 5 HOH A 1 120 1 HOH HOH . 
N 5 HOH A 2 121 2 HOH HOH . 
N 5 HOH A 3 122 3 HOH HOH . 
N 5 HOH A 4 123 4 HOH HOH . 
N 5 HOH A 5 124 8 HOH HOH . 
N 5 HOH A 6 125 10 HOH HOH . 
N 5 HOH A 7 126 14 HOH HOH . 
N 5 HOH A 8 127 21 HOH HOH . 
N 5 HOH A 9 128 27 HOH HOH . 
N 5 HOH A 10 129 30 HOH HOH . 
N 5 HOH A 11 130 31 HOH HOH . 
N 5 HOH A 12 131 36 HOH HOH . 
N 5 HOH A 13 132 40 HOH HOH . 
N 5 HOH A 14 133 42 HOH HOH . 
N 5 HOH A 15 134 44 HOH HOH . 
N 5 HOH A 16 135 45 HOH HOH . 
N 5 HOH A 17 136 46 HOH HOH . 
N 5 HOH A 18 137 47 HOH HOH . 
N 5 HOH A 19 138 53 HOH HOH . 
N 5 HOH A 20 139 57 HOH HOH . 
N 5 HOH A 21 140 59 HOH HOH . 
N 5 HOH A 22 141 60 HOH HOH . 
N 5 HOH A 23 142 61 HOH HOH . 
N 5 HOH A 24 143 63 HOH HOH . 
N 5 HOH A 25 144 64 HOH HOH . 
N 5 HOH A 26 145 68 HOH HOH . 
N 5 HOH A 27 146 71 HOH HOH . 
N 5 HOH A 28 147 73 HOH HOH . 
N 5 HOH A 29 148 75 HOH HOH . 
N 5 HOH A 30 149 79 HOH HOH . 
N 5 HOH A 31 150 80 HOH HOH . 
N 5 HOH A 32 151 81 HOH HOH . 
N 5 HOH A 33 152 83 HOH HOH . 
N 5 HOH A 34 153 84 HOH HOH . 
N 5 HOH A 35 154 85 HOH HOH . 
N 5 HOH A 36 155 87 HOH HOH . 
N 5 HOH A 37 156 91 HOH HOH . 
N 5 HOH A 38 157 92 HOH HOH . 
N 5 HOH A 39 158 93 HOH HOH . 
N 5 HOH A 40 159 100 HOH HOH . 
N 5 HOH A 41 160 103 HOH HOH . 
N 5 HOH A 42 161 106 HOH HOH . 
N 5 HOH A 43 162 107 HOH HOH . 
N 5 HOH A 44 163 108 HOH HOH . 
N 5 HOH A 45 164 109 HOH HOH . 
N 5 HOH A 46 165 110 HOH HOH . 
N 5 HOH A 47 166 116 HOH HOH . 
N 5 HOH A 48 167 125 HOH HOH . 
N 5 HOH A 49 168 128 HOH HOH . 
N 5 HOH A 50 169 129 HOH HOH . 
N 5 HOH A 51 170 132 HOH HOH . 
N 5 HOH A 52 171 134 HOH HOH . 
N 5 HOH A 53 172 139 HOH HOH . 
N 5 HOH A 54 173 140 HOH HOH . 
N 5 HOH A 55 174 142 HOH HOH . 
N 5 HOH A 56 175 143 HOH HOH . 
N 5 HOH A 57 176 144 HOH HOH . 
N 5 HOH A 58 177 145 HOH HOH . 
N 5 HOH A 59 178 146 HOH HOH . 
N 5 HOH A 60 179 148 HOH HOH . 
N 5 HOH A 61 180 153 HOH HOH . 
N 5 HOH A 62 181 156 HOH HOH . 
N 5 HOH A 63 182 160 HOH HOH . 
N 5 HOH A 64 183 162 HOH HOH . 
N 5 HOH A 65 184 165 HOH HOH . 
N 5 HOH A 66 185 166 HOH HOH . 
N 5 HOH A 67 186 167 HOH HOH . 
N 5 HOH A 68 187 168 HOH HOH . 
N 5 HOH A 69 188 180 HOH HOH . 
N 5 HOH A 70 189 185 HOH HOH . 
N 5 HOH A 71 190 186 HOH HOH . 
N 5 HOH A 72 191 191 HOH HOH . 
N 5 HOH A 73 192 194 HOH HOH . 
N 5 HOH A 74 193 196 HOH HOH . 
N 5 HOH A 75 194 203 HOH HOH . 
N 5 HOH A 76 195 207 HOH HOH . 
N 5 HOH A 77 196 208 HOH HOH . 
N 5 HOH A 78 197 210 HOH HOH . 
N 5 HOH A 79 198 214 HOH HOH . 
N 5 HOH A 80 199 216 HOH HOH . 
N 5 HOH A 81 200 206 HOH HOH . 
N 5 HOH A 82 201 217 HOH HOH . 
O 5 HOH B 1 118 5 HOH HOH . 
O 5 HOH B 2 119 9 HOH HOH . 
O 5 HOH B 3 120 15 HOH HOH . 
O 5 HOH B 4 121 16 HOH HOH . 
O 5 HOH B 5 122 19 HOH HOH . 
O 5 HOH B 6 123 23 HOH HOH . 
O 5 HOH B 7 124 24 HOH HOH . 
O 5 HOH B 8 125 25 HOH HOH . 
O 5 HOH B 9 126 26 HOH HOH . 
O 5 HOH B 10 127 28 HOH HOH . 
O 5 HOH B 11 128 34 HOH HOH . 
O 5 HOH B 12 129 37 HOH HOH . 
O 5 HOH B 13 130 38 HOH HOH . 
O 5 HOH B 14 131 41 HOH HOH . 
O 5 HOH B 15 132 43 HOH HOH . 
O 5 HOH B 16 133 48 HOH HOH . 
O 5 HOH B 17 134 50 HOH HOH . 
O 5 HOH B 18 135 51 HOH HOH . 
O 5 HOH B 19 136 54 HOH HOH . 
O 5 HOH B 20 137 58 HOH HOH . 
O 5 HOH B 21 138 62 HOH HOH . 
O 5 HOH B 22 139 65 HOH HOH . 
O 5 HOH B 23 140 66 HOH HOH . 
O 5 HOH B 24 141 67 HOH HOH . 
O 5 HOH B 25 142 70 HOH HOH . 
O 5 HOH B 26 143 74 HOH HOH . 
O 5 HOH B 27 144 76 HOH HOH . 
O 5 HOH B 28 145 77 HOH HOH . 
O 5 HOH B 29 146 78 HOH HOH . 
O 5 HOH B 30 147 82 HOH HOH . 
O 5 HOH B 31 148 86 HOH HOH . 
O 5 HOH B 32 149 88 HOH HOH . 
O 5 HOH B 33 150 89 HOH HOH . 
O 5 HOH B 34 151 95 HOH HOH . 
O 5 HOH B 35 152 96 HOH HOH . 
O 5 HOH B 36 153 98 HOH HOH . 
O 5 HOH B 37 154 99 HOH HOH . 
O 5 HOH B 38 155 102 HOH HOH . 
O 5 HOH B 39 156 105 HOH HOH . 
O 5 HOH B 40 157 111 HOH HOH . 
O 5 HOH B 41 158 119 HOH HOH . 
O 5 HOH B 42 159 121 HOH HOH . 
O 5 HOH B 43 160 124 HOH HOH . 
O 5 HOH B 44 161 126 HOH HOH . 
O 5 HOH B 45 162 130 HOH HOH . 
O 5 HOH B 46 163 131 HOH HOH . 
O 5 HOH B 47 164 136 HOH HOH . 
O 5 HOH B 48 165 147 HOH HOH . 
O 5 HOH B 49 166 149 HOH HOH . 
O 5 HOH B 50 167 150 HOH HOH . 
O 5 HOH B 51 168 154 HOH HOH . 
O 5 HOH B 52 169 157 HOH HOH . 
O 5 HOH B 53 170 158 HOH HOH . 
O 5 HOH B 54 171 161 HOH HOH . 
O 5 HOH B 55 172 163 HOH HOH . 
O 5 HOH B 56 173 164 HOH HOH . 
O 5 HOH B 57 174 170 HOH HOH . 
O 5 HOH B 58 175 174 HOH HOH . 
O 5 HOH B 59 176 175 HOH HOH . 
O 5 HOH B 60 177 176 HOH HOH . 
O 5 HOH B 61 178 177 HOH HOH . 
O 5 HOH B 62 179 183 HOH HOH . 
O 5 HOH B 63 180 187 HOH HOH . 
O 5 HOH B 64 181 188 HOH HOH . 
O 5 HOH B 65 182 189 HOH HOH . 
O 5 HOH B 66 183 192 HOH HOH . 
O 5 HOH B 67 185 195 HOH HOH . 
O 5 HOH B 68 186 197 HOH HOH . 
O 5 HOH B 69 187 198 HOH HOH . 
O 5 HOH B 70 188 202 HOH HOH . 
O 5 HOH B 71 189 204 HOH HOH . 
O 5 HOH B 72 191 211 HOH HOH . 
O 5 HOH B 73 192 212 HOH HOH . 
O 5 HOH B 74 193 213 HOH HOH . 
O 5 HOH B 75 194 215 HOH HOH . 
O 5 HOH B 76 200 218 HOH HOH . 
P 5 HOH C 1 117 6 HOH HOH . 
P 5 HOH C 2 118 7 HOH HOH . 
P 5 HOH C 3 119 11 HOH HOH . 
P 5 HOH C 4 120 12 HOH HOH . 
P 5 HOH C 5 121 13 HOH HOH . 
P 5 HOH C 6 122 17 HOH HOH . 
P 5 HOH C 7 123 18 HOH HOH . 
P 5 HOH C 8 124 20 HOH HOH . 
P 5 HOH C 9 125 22 HOH HOH . 
P 5 HOH C 10 126 29 HOH HOH . 
P 5 HOH C 11 127 32 HOH HOH . 
P 5 HOH C 12 128 33 HOH HOH . 
P 5 HOH C 13 129 35 HOH HOH . 
P 5 HOH C 14 130 39 HOH HOH . 
P 5 HOH C 15 131 49 HOH HOH . 
P 5 HOH C 16 132 52 HOH HOH . 
P 5 HOH C 17 133 55 HOH HOH . 
P 5 HOH C 18 134 56 HOH HOH . 
P 5 HOH C 19 135 69 HOH HOH . 
P 5 HOH C 20 136 72 HOH HOH . 
P 5 HOH C 21 137 90 HOH HOH . 
P 5 HOH C 22 138 94 HOH HOH . 
P 5 HOH C 23 139 97 HOH HOH . 
P 5 HOH C 24 140 101 HOH HOH . 
P 5 HOH C 25 141 104 HOH HOH . 
P 5 HOH C 26 142 112 HOH HOH . 
P 5 HOH C 27 143 113 HOH HOH . 
P 5 HOH C 28 144 114 HOH HOH . 
P 5 HOH C 29 145 115 HOH HOH . 
P 5 HOH C 30 146 117 HOH HOH . 
P 5 HOH C 31 147 118 HOH HOH . 
P 5 HOH C 32 148 120 HOH HOH . 
P 5 HOH C 33 149 122 HOH HOH . 
P 5 HOH C 34 150 123 HOH HOH . 
P 5 HOH C 35 151 127 HOH HOH . 
P 5 HOH C 36 152 133 HOH HOH . 
P 5 HOH C 37 153 135 HOH HOH . 
P 5 HOH C 38 154 137 HOH HOH . 
P 5 HOH C 39 155 138 HOH HOH . 
P 5 HOH C 40 156 141 HOH HOH . 
P 5 HOH C 41 157 151 HOH HOH . 
P 5 HOH C 42 158 152 HOH HOH . 
P 5 HOH C 43 159 155 HOH HOH . 
P 5 HOH C 44 160 159 HOH HOH . 
P 5 HOH C 45 161 169 HOH HOH . 
P 5 HOH C 46 162 171 HOH HOH . 
P 5 HOH C 47 163 172 HOH HOH . 
P 5 HOH C 48 164 173 HOH HOH . 
P 5 HOH C 49 165 178 HOH HOH . 
P 5 HOH C 50 166 181 HOH HOH . 
P 5 HOH C 51 167 182 HOH HOH . 
P 5 HOH C 52 168 184 HOH HOH . 
P 5 HOH C 53 169 190 HOH HOH . 
P 5 HOH C 54 170 199 HOH HOH . 
P 5 HOH C 55 171 200 HOH HOH . 
P 5 HOH C 56 172 201 HOH HOH . 
P 5 HOH C 57 173 205 HOH HOH . 
P 5 HOH C 58 174 209 HOH HOH . 
P 5 HOH C 59 184 193 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 . . . L 2 -6.083 20.677 -0.478 1 37.9 ? C1 GOL 116 C 1 
HETATM 2 O O1 GOL . . . L 2 -5.672 19.651 -1.338 1 32.01 ? O1 GOL 116 C 1 
HETATM 3 C C2 GOL . . . L 2 -5.281 21.943 -0.773 1 37.14 ? C2 GOL 116 C 1 
HETATM 4 O O2 GOL . . . L 2 -6.161 23.038 -0.656 1 37.47 ? O2 GOL 116 C 1 
HETATM 5 C C3 GOL . . . L 2 -4.564 21.888 -2.125 1 35.79 ? C3 GOL 116 C 1 
HETATM 6 O O3 GOL . . . L 2 -3.477 22.773 -2.218 1 35.65 ? O3 GOL 116 C 1 
#
_model_server_stats.io_time_ms              87 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           339 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           6 
#