data_2Y3F
#
_model_server_result.job_id            u9ERhK5u45yNvMJb9gLi0g 
_model_server_result.datetime_utc      '2024-12-23 07:46:18' 
_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          2y3f 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1138}' 
#
_entry.id    2Y3F 
#
_exptl.entry_id    2Y3F 
_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            2Y3F 
_cell.length_a            57.34 
_cell.length_b            57.34 
_cell.length_c            77.55 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Y3F 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        94 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 42 21 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_645 -x+1,-y-1,z -1 0 0 0 -1 0 0 0 1 57.34 -57.34 0 
3 'crystal symmetry operation' 7_645 y+1,x-1,-z 0 1 0 1 0 0 0 0 -1 57.34 -57.34 0 
4 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 D N N 
? 3 E 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 149 n n 
C1 C2 GOL sing 150 n n 
C1 H11 GOL sing 151 n n 
C1 H12 GOL sing 152 n n 
O1 HO1 GOL sing 153 n n 
C2 O2 GOL sing 154 n n 
C2 C3 GOL sing 155 n n 
C2 H2 GOL sing 156 n n 
O2 HO2 GOL sing 157 n n 
C3 O3 GOL sing 158 n n 
C3 H31 GOL sing 159 n n 
C3 H32 GOL sing 160 n n 
O3 HO3 GOL sing 161 n n 
#
_atom_sites.entry_id                     2Y3F 
_atom_sites.fract_transf_matrix[1][1]    0.01744 
_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]    0.01744 
_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]    0.012895 
_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 BTN A 1 1136 1136 BTN BTN . 
C 3 GOL A 1 1137 1137 GOL GOL . 
D 3 GOL A 1 1138 1138 GOL GOL . 
E 3 GOL A 1 1139 1139 GOL GOL . 
F 4 HOH A 1 2001 2001 HOH HOH . 
F 4 HOH A 2 2002 2002 HOH HOH . 
F 4 HOH A 3 2003 2003 HOH HOH . 
F 4 HOH A 4 2004 2004 HOH HOH . 
F 4 HOH A 5 2005 2005 HOH HOH . 
F 4 HOH A 6 2006 2006 HOH HOH . 
F 4 HOH A 7 2007 2007 HOH HOH . 
F 4 HOH A 8 2008 2008 HOH HOH . 
F 4 HOH A 9 2009 2009 HOH HOH . 
F 4 HOH A 10 2010 2010 HOH HOH . 
F 4 HOH A 11 2011 2011 HOH HOH . 
F 4 HOH A 12 2012 2012 HOH HOH . 
F 4 HOH A 13 2013 2013 HOH HOH . 
F 4 HOH A 14 2014 2014 HOH HOH . 
F 4 HOH A 15 2015 2015 HOH HOH . 
F 4 HOH A 16 2016 2016 HOH HOH . 
F 4 HOH A 17 2017 2017 HOH HOH . 
F 4 HOH A 18 2018 2018 HOH HOH . 
F 4 HOH A 19 2019 2019 HOH HOH . 
F 4 HOH A 20 2020 2020 HOH HOH . 
F 4 HOH A 21 2021 2021 HOH HOH . 
F 4 HOH A 22 2022 2022 HOH HOH . 
F 4 HOH A 23 2023 2023 HOH HOH . 
F 4 HOH A 24 2024 2024 HOH HOH . 
F 4 HOH A 25 2025 2025 HOH HOH . 
F 4 HOH A 26 2026 2026 HOH HOH . 
F 4 HOH A 27 2027 2027 HOH HOH . 
F 4 HOH A 28 2028 2028 HOH HOH . 
F 4 HOH A 29 2029 2029 HOH HOH . 
F 4 HOH A 30 2030 2030 HOH HOH . 
F 4 HOH A 31 2031 2031 HOH HOH . 
F 4 HOH A 32 2032 2032 HOH HOH . 
F 4 HOH A 33 2033 2033 HOH HOH . 
F 4 HOH A 34 2034 2034 HOH HOH . 
F 4 HOH A 35 2035 2035 HOH HOH . 
F 4 HOH A 36 2036 2036 HOH HOH . 
F 4 HOH A 37 2037 2037 HOH HOH . 
F 4 HOH A 38 2038 2038 HOH HOH . 
F 4 HOH A 39 2039 2039 HOH HOH . 
F 4 HOH A 40 2040 2040 HOH HOH . 
F 4 HOH A 41 2041 2041 HOH HOH . 
F 4 HOH A 42 2042 2042 HOH HOH . 
F 4 HOH A 43 2043 2043 HOH HOH . 
F 4 HOH A 44 2044 2044 HOH HOH . 
F 4 HOH A 45 2045 2045 HOH HOH . 
F 4 HOH A 46 2046 2046 HOH HOH . 
F 4 HOH A 47 2047 2047 HOH HOH . 
F 4 HOH A 48 2048 2048 HOH HOH . 
F 4 HOH A 49 2050 2050 HOH HOH . 
F 4 HOH A 50 2051 2051 HOH HOH . 
F 4 HOH A 51 2052 2052 HOH HOH . 
F 4 HOH A 52 2053 2053 HOH HOH . 
F 4 HOH A 53 2054 2054 HOH HOH . 
F 4 HOH A 54 2055 2055 HOH HOH . 
F 4 HOH A 55 2056 2056 HOH HOH . 
F 4 HOH A 56 2057 2057 HOH HOH . 
F 4 HOH A 57 2058 2058 HOH HOH . 
F 4 HOH A 58 2059 2059 HOH HOH . 
F 4 HOH A 59 2060 2060 HOH HOH . 
F 4 HOH A 60 2061 2061 HOH HOH . 
F 4 HOH A 61 2062 2062 HOH HOH . 
F 4 HOH A 62 2063 2063 HOH HOH . 
F 4 HOH A 63 2064 2064 HOH HOH . 
F 4 HOH A 64 2065 2065 HOH HOH . 
F 4 HOH A 65 2066 2066 HOH HOH . 
F 4 HOH A 66 2067 2067 HOH HOH . 
F 4 HOH A 67 2068 2068 HOH HOH . 
F 4 HOH A 68 2069 2069 HOH HOH . 
F 4 HOH A 69 2070 2070 HOH HOH . 
F 4 HOH A 70 2071 2071 HOH HOH . 
F 4 HOH A 71 2072 2072 HOH HOH . 
F 4 HOH A 72 2073 2073 HOH HOH . 
F 4 HOH A 73 2074 2074 HOH HOH . 
F 4 HOH A 74 2075 2075 HOH HOH . 
F 4 HOH A 75 2076 2076 HOH HOH . 
F 4 HOH A 76 2077 2077 HOH HOH . 
F 4 HOH A 77 2078 2078 HOH HOH . 
F 4 HOH A 78 2079 2079 HOH HOH . 
F 4 HOH A 79 2080 2080 HOH HOH . 
F 4 HOH A 80 2081 2081 HOH HOH . 
F 4 HOH A 81 2082 2082 HOH HOH . 
F 4 HOH A 82 2083 2083 HOH HOH . 
F 4 HOH A 83 2084 2084 HOH HOH . 
F 4 HOH A 84 2085 2085 HOH HOH . 
F 4 HOH A 85 2086 2086 HOH HOH . 
F 4 HOH A 86 2087 2087 HOH HOH . 
F 4 HOH A 87 2088 2088 HOH HOH . 
F 4 HOH A 88 2089 2089 HOH HOH . 
F 4 HOH A 89 2090 2090 HOH HOH . 
F 4 HOH A 90 2091 2091 HOH HOH . 
F 4 HOH A 91 2092 2092 HOH HOH . 
F 4 HOH A 92 2093 2093 HOH HOH . 
F 4 HOH A 93 2095 2095 HOH HOH . 
F 4 HOH A 94 2096 2096 HOH HOH . 
F 4 HOH A 95 2097 2097 HOH HOH . 
F 4 HOH A 96 2098 2098 HOH HOH . 
F 4 HOH A 97 2099 2099 HOH HOH . 
F 4 HOH A 98 2101 2101 HOH HOH . 
F 4 HOH A 99 2102 2102 HOH HOH . 
F 4 HOH A 100 2103 2103 HOH HOH . 
F 4 HOH A 101 2104 2104 HOH HOH . 
F 4 HOH A 102 2105 2105 HOH HOH . 
F 4 HOH A 103 2106 2106 HOH HOH . 
F 4 HOH A 104 2107 2107 HOH HOH . 
F 4 HOH A 105 2108 2108 HOH HOH . 
F 4 HOH A 106 2109 2109 HOH HOH . 
F 4 HOH A 107 2110 2110 HOH HOH . 
F 4 HOH A 108 2111 2111 HOH HOH . 
F 4 HOH A 109 2112 2112 HOH HOH . 
F 4 HOH A 110 2113 2113 HOH HOH . 
F 4 HOH A 111 2115 2115 HOH HOH . 
F 4 HOH A 112 2116 2116 HOH HOH . 
F 4 HOH A 113 2117 2117 HOH HOH . 
F 4 HOH A 114 2118 2118 HOH HOH . 
F 4 HOH A 115 2119 2119 HOH HOH . 
F 4 HOH A 116 2120 2120 HOH HOH . 
F 4 HOH A 117 2121 2121 HOH HOH . 
F 4 HOH A 118 2122 2122 HOH HOH . 
F 4 HOH A 119 2123 2123 HOH HOH . 
F 4 HOH A 120 2124 2124 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 3 31.038 -18.322 7.071 1 25.73 ? C1 GOL 1138 A 1 
HETATM 2 O O1 GOL . . . D 3 32.08 -18.586 7.997 1 23.9 ? O1 GOL 1138 A 1 
HETATM 3 C C2 GOL . . . D 3 31.052 -19.383 5.972 1 26.09 ? C2 GOL 1138 A 1 
HETATM 4 O O2 GOL . . . D 3 32.191 -19.337 5.145 1 29.45 ? O2 GOL 1138 A 1 
HETATM 5 C C3 GOL . . . D 3 29.816 -19.286 5.099 1 21.87 ? C3 GOL 1138 A 1 
HETATM 6 O O3 GOL . . . D 3 29.269 -20.568 4.908 1 14.95 ? O3 GOL 1138 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           316 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           6 
#