data_8DA9
#
_model_server_result.job_id            VwwLVXzfg_OWivl4tnxwHA 
_model_server_result.datetime_utc      '2024-11-12 20:27:56' 
_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          8da9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":101}' 
#
_entry.id    8DA9 
#
_exptl.entry_id    8DA9 
_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          94.41 
_cell.angle_gamma         90 
_cell.entry_id            8DA9 
_cell.length_a            53.403 
_cell.length_b            54.259 
_cell.length_c            68.601 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8DA9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    'C 2y' 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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,B,E,F,J,K 1 1 
C,D,G,H,I,L,M 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
? 4 E N N 
? 4 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 A C ASN 4 A ASN 3 1_555 A N MLY 5 A MLY 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale2 A C MLY 5 A MLY 4 1_555 A N PHE 6 A PHE 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale3 A C LEU 35 A LEU 34 1_555 A N MLY 36 A MLY 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? 
covale ? covale4 A C MLY 36 A MLY 35 1_555 A N ASP 37 A ASP 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale5 B C ASN 4 B ASN 3 1_555 B N MLY 5 B MLY 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale6 B C MLY 5 B MLY 4 1_555 B N PHE 6 B PHE 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? 
covale ? covale7 B C GLN 27 B GLN 26 1_555 B N MLY 28 B MLY 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale8 B C MLY 28 B MLY 27 1_555 B N LYS 29 B LYS 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale9 C C ASN 4 C ASN 3 1_555 C N MLY 5 C MLY 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale10 C C MLY 5 C MLY 4 1_555 C N PHE 6 C PHE 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale11 C C LEU 35 C LEU 34 1_555 C N MLY 36 C MLY 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale12 C C MLY 36 C MLY 35 1_555 C N ASP 37 C ASP 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale13 D C ASN 4 D ASN 3 1_555 D N MLY 5 D MLY 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? 
covale ? covale14 D C MLY 5 D MLY 4 1_555 D N PHE 6 D PHE 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.317 ? 
covale ? covale15 D C GLN 27 D GLN 26 1_555 D N MLY 28 D MLY 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale16 D C MLY 28 D MLY 27 1_555 D N MLY 29 D MLY 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale17 D C MLY 29 D MLY 28 1_555 D N ALA 30 D ALA 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? 
#
_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 116 n n 
C1 C2 GOL sing 117 n n 
C1 H11 GOL sing 118 n n 
C1 H12 GOL sing 119 n n 
O1 HO1 GOL sing 120 n n 
C2 O2 GOL sing 121 n n 
C2 C3 GOL sing 122 n n 
C2 H2 GOL sing 123 n n 
O2 HO2 GOL sing 124 n n 
C3 O3 GOL sing 125 n n 
C3 H31 GOL sing 126 n n 
C3 H32 GOL sing 127 n n 
O3 HO3 GOL sing 128 n n 
#
_atom_sites.entry_id                     8DA9 
_atom_sites.fract_transf_matrix[1][1]    0.018726 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001444 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01843 
_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]    0.01462 
_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 GOL A 1 101 101 GOL GOL . 
F 5 SO4 A 1 102 1 SO4 SO4 . 
G 4 GOL C 1 101 101 GOL GOL . 
H 5 SO4 C 1 102 2 SO4 SO4 . 
I 5 SO4 D 1 101 3 SO4 SO4 . 
J 6 HOH A 1 201 85 HOH HOH . 
J 6 HOH A 2 202 121 HOH HOH . 
J 6 HOH A 3 203 45 HOH HOH . 
J 6 HOH A 4 204 97 HOH HOH . 
J 6 HOH A 5 205 3 HOH HOH . 
J 6 HOH A 6 206 44 HOH HOH . 
J 6 HOH A 7 207 91 HOH HOH . 
J 6 HOH A 8 208 112 HOH HOH . 
J 6 HOH A 9 209 49 HOH HOH . 
J 6 HOH A 10 210 47 HOH HOH . 
J 6 HOH A 11 211 28 HOH HOH . 
J 6 HOH A 12 212 59 HOH HOH . 
J 6 HOH A 13 213 10 HOH HOH . 
J 6 HOH A 14 214 37 HOH HOH . 
J 6 HOH A 15 215 20 HOH HOH . 
J 6 HOH A 16 216 65 HOH HOH . 
J 6 HOH A 17 217 92 HOH HOH . 
J 6 HOH A 18 218 33 HOH HOH . 
J 6 HOH A 19 219 19 HOH HOH . 
J 6 HOH A 20 220 36 HOH HOH . 
J 6 HOH A 21 221 60 HOH HOH . 
J 6 HOH A 22 222 119 HOH HOH . 
J 6 HOH A 23 223 86 HOH HOH . 
J 6 HOH A 24 224 82 HOH HOH . 
J 6 HOH A 25 225 134 HOH HOH . 
J 6 HOH A 26 226 99 HOH HOH . 
J 6 HOH A 27 227 128 HOH HOH . 
J 6 HOH A 28 228 71 HOH HOH . 
K 6 HOH B 1 101 56 HOH HOH . 
K 6 HOH B 2 102 124 HOH HOH . 
K 6 HOH B 3 103 57 HOH HOH . 
K 6 HOH B 4 104 89 HOH HOH . 
K 6 HOH B 5 105 12 HOH HOH . 
K 6 HOH B 6 106 104 HOH HOH . 
K 6 HOH B 7 107 61 HOH HOH . 
K 6 HOH B 8 108 67 HOH HOH . 
K 6 HOH B 9 109 109 HOH HOH . 
K 6 HOH B 10 110 48 HOH HOH . 
K 6 HOH B 11 111 62 HOH HOH . 
K 6 HOH B 12 112 2 HOH HOH . 
K 6 HOH B 13 113 51 HOH HOH . 
K 6 HOH B 14 114 108 HOH HOH . 
K 6 HOH B 15 115 50 HOH HOH . 
K 6 HOH B 16 116 78 HOH HOH . 
K 6 HOH B 17 117 80 HOH HOH . 
K 6 HOH B 18 118 4 HOH HOH . 
K 6 HOH B 19 119 15 HOH HOH . 
K 6 HOH B 20 120 13 HOH HOH . 
K 6 HOH B 21 121 42 HOH HOH . 
K 6 HOH B 22 122 106 HOH HOH . 
K 6 HOH B 23 123 110 HOH HOH . 
K 6 HOH B 24 124 118 HOH HOH . 
K 6 HOH B 25 125 39 HOH HOH . 
K 6 HOH B 26 126 103 HOH HOH . 
K 6 HOH B 27 127 94 HOH HOH . 
K 6 HOH B 28 128 83 HOH HOH . 
K 6 HOH B 29 129 107 HOH HOH . 
K 6 HOH B 30 130 81 HOH HOH . 
K 6 HOH B 31 131 130 HOH HOH . 
K 6 HOH B 32 132 74 HOH HOH . 
K 6 HOH B 33 133 137 HOH HOH . 
K 6 HOH B 34 134 131 HOH HOH . 
K 6 HOH B 35 135 31 HOH HOH . 
K 6 HOH B 36 136 113 HOH HOH . 
L 6 HOH C 1 201 55 HOH HOH . 
L 6 HOH C 2 202 54 HOH HOH . 
L 6 HOH C 3 203 26 HOH HOH . 
L 6 HOH C 4 204 114 HOH HOH . 
L 6 HOH C 5 205 111 HOH HOH . 
L 6 HOH C 6 206 102 HOH HOH . 
L 6 HOH C 7 207 1 HOH HOH . 
L 6 HOH C 8 208 138 HOH HOH . 
L 6 HOH C 9 209 14 HOH HOH . 
L 6 HOH C 10 210 79 HOH HOH . 
L 6 HOH C 11 211 6 HOH HOH . 
L 6 HOH C 12 212 136 HOH HOH . 
L 6 HOH C 13 213 96 HOH HOH . 
L 6 HOH C 14 214 8 HOH HOH . 
L 6 HOH C 15 215 17 HOH HOH . 
L 6 HOH C 16 216 46 HOH HOH . 
L 6 HOH C 17 217 41 HOH HOH . 
L 6 HOH C 18 218 66 HOH HOH . 
L 6 HOH C 19 219 23 HOH HOH . 
L 6 HOH C 20 220 122 HOH HOH . 
L 6 HOH C 21 221 7 HOH HOH . 
L 6 HOH C 22 222 139 HOH HOH . 
L 6 HOH C 23 223 32 HOH HOH . 
L 6 HOH C 24 224 35 HOH HOH . 
L 6 HOH C 25 225 43 HOH HOH . 
L 6 HOH C 26 226 22 HOH HOH . 
L 6 HOH C 27 227 88 HOH HOH . 
L 6 HOH C 28 228 125 HOH HOH . 
L 6 HOH C 29 229 76 HOH HOH . 
L 6 HOH C 30 230 120 HOH HOH . 
M 6 HOH D 1 201 69 HOH HOH . 
M 6 HOH D 2 202 123 HOH HOH . 
M 6 HOH D 3 203 133 HOH HOH . 
M 6 HOH D 4 204 68 HOH HOH . 
M 6 HOH D 5 205 90 HOH HOH . 
M 6 HOH D 6 206 101 HOH HOH . 
M 6 HOH D 7 207 34 HOH HOH . 
M 6 HOH D 8 208 58 HOH HOH . 
M 6 HOH D 9 209 52 HOH HOH . 
M 6 HOH D 10 210 18 HOH HOH . 
M 6 HOH D 11 211 84 HOH HOH . 
M 6 HOH D 12 212 95 HOH HOH . 
M 6 HOH D 13 213 30 HOH HOH . 
M 6 HOH D 14 214 77 HOH HOH . 
M 6 HOH D 15 215 132 HOH HOH . 
M 6 HOH D 16 216 135 HOH HOH . 
M 6 HOH D 17 217 40 HOH HOH . 
M 6 HOH D 18 218 27 HOH HOH . 
M 6 HOH D 19 219 75 HOH HOH . 
M 6 HOH D 20 220 9 HOH HOH . 
M 6 HOH D 21 221 5 HOH HOH . 
M 6 HOH D 22 222 72 HOH HOH . 
M 6 HOH D 23 223 87 HOH HOH . 
M 6 HOH D 24 224 126 HOH HOH . 
M 6 HOH D 25 225 115 HOH HOH . 
M 6 HOH D 26 226 11 HOH HOH . 
M 6 HOH D 27 227 129 HOH HOH . 
M 6 HOH D 28 228 21 HOH HOH . 
M 6 HOH D 29 229 93 HOH HOH . 
M 6 HOH D 30 230 16 HOH HOH . 
M 6 HOH D 31 231 25 HOH HOH . 
M 6 HOH D 32 232 73 HOH HOH . 
M 6 HOH D 33 233 38 HOH HOH . 
M 6 HOH D 34 234 29 HOH HOH . 
M 6 HOH D 35 235 105 HOH HOH . 
M 6 HOH D 36 236 117 HOH HOH . 
M 6 HOH D 37 237 70 HOH HOH . 
M 6 HOH D 38 238 116 HOH HOH . 
M 6 HOH D 39 239 127 HOH HOH . 
M 6 HOH D 40 240 53 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 . . . E 4 33.063 44.273 -3.369 1 27.3 ? C1 GOL 101 A 1 
HETATM 2 O O1 GOL . . . E 4 31.982 45.222 -3.277 1 28.64 ? O1 GOL 101 A 1 
HETATM 3 C C2 GOL . . . E 4 32.466 42.831 -3.575 1 35.62 ? C2 GOL 101 A 1 
HETATM 4 O O2 GOL . . . E 4 31.466 42.538 -2.671 1 48.7 ? O2 GOL 101 A 1 
HETATM 5 C C3 GOL . . . E 4 33.633 41.869 -3.408 1 41.92 ? C3 GOL 101 A 1 
HETATM 6 O O3 GOL . . . E 4 34.134 42.103 -2.111 1 46.67 ? O3 GOL 101 A 1 
HETATM 7 H H11 GOL . . . E 4 33.616 44.269 -2.572 1 32.81 ? H11 GOL 101 A 1 
HETATM 8 H H12 GOL . . . E 4 33.662 44.47 -4.106 1 32.81 ? H12 GOL 101 A 1 
HETATM 9 H HO1 GOL . . . E 4 32.246 45.952 -3.646 1 34.42 ? HO1 GOL 101 A 1 
HETATM 10 H H2 GOL . . . E 4 32.077 42.775 -4.462 1 42.8 ? H2 GOL 101 A 1 
HETATM 11 H H31 GOL . . . E 4 34.282 42.028 -4.111 1 50.36 ? H31 GOL 101 A 1 
HETATM 12 H H32 GOL . . . E 4 33.321 40.961 -3.548 1 50.36 ? H32 GOL 101 A 1 
HETATM 13 H HO3 GOL . . . E 4 34.807 41.591 -2.007 1 56.05 ? HO3 GOL 101 A 1 
#
_model_server_stats.io_time_ms              71 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    31 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           13 
#