data_2YXJ
#
_model_server_result.job_id            v1mHQC0IfM5FO3gYgwPF1g 
_model_server_result.datetime_utc      '2025-07-16 13:46:38' 
_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          2yxj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":247}' 
#
_entry.id    2YXJ 
#
_exptl.entry_id    2YXJ 
_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    1 
_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            2YXJ 
_cell.length_a            66.321 
_cell.length_b            75.37 
_cell.length_c            87.778 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YXJ 
_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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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,D,E,G 1 1 
B,F,H 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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                     2YXJ 
_atom_sites.fract_transf_matrix[1][1]    0.015078 
_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]    0.013268 
_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]    0.011392 
_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
C 2 CL A 1 3001 1 CL CL . 
D 3 N3C A 1 1001 1 N3C N3C . 
E 4 GOL A 1 247 247 GOL GOL . 
F 3 N3C B 1 2001 1 N3C N3C . 
G 5 HOH A 1 3002 1 HOH HOH . 
G 5 HOH A 2 3003 5 HOH HOH . 
G 5 HOH A 3 3004 6 HOH HOH . 
G 5 HOH A 4 3005 8 HOH HOH . 
G 5 HOH A 5 3006 9 HOH HOH . 
G 5 HOH A 6 3007 11 HOH HOH . 
G 5 HOH A 7 3008 12 HOH HOH . 
G 5 HOH A 8 3009 14 HOH HOH . 
G 5 HOH A 9 3010 15 HOH HOH . 
G 5 HOH A 10 3011 17 HOH HOH . 
G 5 HOH A 11 3012 19 HOH HOH . 
G 5 HOH A 12 3013 20 HOH HOH . 
G 5 HOH A 13 3014 21 HOH HOH . 
G 5 HOH A 14 3015 22 HOH HOH . 
G 5 HOH A 15 3016 23 HOH HOH . 
G 5 HOH A 16 3017 25 HOH HOH . 
G 5 HOH A 17 3018 26 HOH HOH . 
G 5 HOH A 18 3019 27 HOH HOH . 
G 5 HOH A 19 3020 29 HOH HOH . 
G 5 HOH A 20 3021 30 HOH HOH . 
G 5 HOH A 21 3022 34 HOH HOH . 
G 5 HOH A 22 3023 35 HOH HOH . 
G 5 HOH A 23 3024 36 HOH HOH . 
G 5 HOH A 24 3025 37 HOH HOH . 
G 5 HOH A 25 3026 40 HOH HOH . 
G 5 HOH A 26 3027 41 HOH HOH . 
G 5 HOH A 27 3028 42 HOH HOH . 
G 5 HOH A 28 3029 44 HOH HOH . 
G 5 HOH A 29 3030 47 HOH HOH . 
G 5 HOH A 30 3031 48 HOH HOH . 
G 5 HOH A 31 3032 52 HOH HOH . 
G 5 HOH A 32 3033 54 HOH HOH . 
G 5 HOH A 33 3034 56 HOH HOH . 
G 5 HOH A 34 3035 58 HOH HOH . 
G 5 HOH A 35 3036 59 HOH HOH . 
G 5 HOH A 36 3037 61 HOH HOH . 
G 5 HOH A 37 3038 62 HOH HOH . 
G 5 HOH A 38 3039 63 HOH HOH . 
G 5 HOH A 39 3040 65 HOH HOH . 
G 5 HOH A 40 3041 68 HOH HOH . 
G 5 HOH A 41 3042 70 HOH HOH . 
G 5 HOH A 42 3043 71 HOH HOH . 
G 5 HOH A 43 3044 72 HOH HOH . 
G 5 HOH A 44 3045 78 HOH HOH . 
G 5 HOH A 45 3046 80 HOH HOH . 
G 5 HOH A 46 3047 83 HOH HOH . 
G 5 HOH A 47 3048 86 HOH HOH . 
G 5 HOH A 48 3049 87 HOH HOH . 
G 5 HOH A 49 3050 88 HOH HOH . 
G 5 HOH A 50 3051 93 HOH HOH . 
G 5 HOH A 51 3052 100 HOH HOH . 
G 5 HOH A 52 3053 108 HOH HOH . 
G 5 HOH A 53 3054 111 HOH HOH . 
G 5 HOH A 54 3055 112 HOH HOH . 
G 5 HOH A 55 3056 114 HOH HOH . 
G 5 HOH A 56 3057 115 HOH HOH . 
G 5 HOH A 57 3058 116 HOH HOH . 
G 5 HOH A 58 3059 117 HOH HOH . 
G 5 HOH A 59 3060 128 HOH HOH . 
G 5 HOH A 60 3061 130 HOH HOH . 
G 5 HOH A 61 3062 131 HOH HOH . 
G 5 HOH A 62 3063 132 HOH HOH . 
G 5 HOH A 63 3064 133 HOH HOH . 
G 5 HOH A 64 3065 135 HOH HOH . 
G 5 HOH A 65 3066 137 HOH HOH . 
G 5 HOH A 66 3067 139 HOH HOH . 
G 5 HOH A 67 3068 140 HOH HOH . 
G 5 HOH A 68 3069 144 HOH HOH . 
G 5 HOH A 69 3070 145 HOH HOH . 
G 5 HOH A 70 3071 146 HOH HOH . 
G 5 HOH A 71 3072 148 HOH HOH . 
G 5 HOH A 72 3073 149 HOH HOH . 
G 5 HOH A 73 3074 150 HOH HOH . 
G 5 HOH A 74 3075 152 HOH HOH . 
G 5 HOH A 75 3076 153 HOH HOH . 
G 5 HOH A 76 3077 161 HOH HOH . 
G 5 HOH A 77 3078 170 HOH HOH . 
G 5 HOH A 78 3079 171 HOH HOH . 
G 5 HOH A 79 3080 172 HOH HOH . 
G 5 HOH A 80 3081 173 HOH HOH . 
G 5 HOH A 81 3082 174 HOH HOH . 
G 5 HOH A 82 3083 175 HOH HOH . 
G 5 HOH A 83 3084 177 HOH HOH . 
G 5 HOH A 84 3085 178 HOH HOH . 
G 5 HOH A 85 3086 179 HOH HOH . 
G 5 HOH A 86 3087 182 HOH HOH . 
G 5 HOH A 87 3088 183 HOH HOH . 
G 5 HOH A 88 3089 184 HOH HOH . 
G 5 HOH A 89 3090 185 HOH HOH . 
G 5 HOH A 90 3091 187 HOH HOH . 
G 5 HOH A 91 3092 188 HOH HOH . 
G 5 HOH A 92 3093 192 HOH HOH . 
G 5 HOH A 93 3094 194 HOH HOH . 
G 5 HOH A 94 3095 195 HOH HOH . 
G 5 HOH A 95 3096 197 HOH HOH . 
G 5 HOH A 96 3097 204 HOH HOH . 
G 5 HOH A 97 3098 209 HOH HOH . 
G 5 HOH A 98 3099 210 HOH HOH . 
G 5 HOH A 99 3100 211 HOH HOH . 
G 5 HOH A 100 3101 212 HOH HOH . 
G 5 HOH A 101 3102 215 HOH HOH . 
G 5 HOH A 102 3103 216 HOH HOH . 
G 5 HOH A 103 3104 222 HOH HOH . 
G 5 HOH A 104 3105 223 HOH HOH . 
H 5 HOH B 1 2002 2 HOH HOH . 
H 5 HOH B 2 2003 7 HOH HOH . 
H 5 HOH B 3 2004 10 HOH HOH . 
H 5 HOH B 4 2005 13 HOH HOH . 
H 5 HOH B 5 2006 16 HOH HOH . 
H 5 HOH B 6 2007 24 HOH HOH . 
H 5 HOH B 7 2008 28 HOH HOH . 
H 5 HOH B 8 2009 31 HOH HOH . 
H 5 HOH B 9 2010 33 HOH HOH . 
H 5 HOH B 10 2011 38 HOH HOH . 
H 5 HOH B 11 2012 39 HOH HOH . 
H 5 HOH B 12 2013 43 HOH HOH . 
H 5 HOH B 13 2014 45 HOH HOH . 
H 5 HOH B 14 2015 46 HOH HOH . 
H 5 HOH B 15 2016 49 HOH HOH . 
H 5 HOH B 16 2017 50 HOH HOH . 
H 5 HOH B 17 2018 51 HOH HOH . 
H 5 HOH B 18 2019 53 HOH HOH . 
H 5 HOH B 19 2020 55 HOH HOH . 
H 5 HOH B 20 2021 57 HOH HOH . 
H 5 HOH B 21 2022 60 HOH HOH . 
H 5 HOH B 22 2023 64 HOH HOH . 
H 5 HOH B 23 2024 67 HOH HOH . 
H 5 HOH B 24 2025 69 HOH HOH . 
H 5 HOH B 25 2026 73 HOH HOH . 
H 5 HOH B 26 2027 74 HOH HOH . 
H 5 HOH B 27 2028 77 HOH HOH . 
H 5 HOH B 28 2029 79 HOH HOH . 
H 5 HOH B 29 2030 81 HOH HOH . 
H 5 HOH B 30 2031 82 HOH HOH . 
H 5 HOH B 31 2032 84 HOH HOH . 
H 5 HOH B 32 2033 85 HOH HOH . 
H 5 HOH B 33 2034 89 HOH HOH . 
H 5 HOH B 34 2035 90 HOH HOH . 
H 5 HOH B 35 2036 91 HOH HOH . 
H 5 HOH B 36 2037 92 HOH HOH . 
H 5 HOH B 37 2038 94 HOH HOH . 
H 5 HOH B 38 2039 95 HOH HOH . 
H 5 HOH B 39 2040 97 HOH HOH . 
H 5 HOH B 40 2041 98 HOH HOH . 
H 5 HOH B 41 2042 99 HOH HOH . 
H 5 HOH B 42 2043 101 HOH HOH . 
H 5 HOH B 43 2044 102 HOH HOH . 
H 5 HOH B 44 2045 104 HOH HOH . 
H 5 HOH B 45 2046 105 HOH HOH . 
H 5 HOH B 46 2047 106 HOH HOH . 
H 5 HOH B 47 2048 107 HOH HOH . 
H 5 HOH B 48 2049 109 HOH HOH . 
H 5 HOH B 49 2050 110 HOH HOH . 
H 5 HOH B 50 2051 113 HOH HOH . 
H 5 HOH B 51 2052 118 HOH HOH . 
H 5 HOH B 52 2053 119 HOH HOH . 
H 5 HOH B 53 2054 121 HOH HOH . 
H 5 HOH B 54 2055 122 HOH HOH . 
H 5 HOH B 55 2056 123 HOH HOH . 
H 5 HOH B 56 2057 124 HOH HOH . 
H 5 HOH B 57 2058 125 HOH HOH . 
H 5 HOH B 58 2059 126 HOH HOH . 
H 5 HOH B 59 2060 127 HOH HOH . 
H 5 HOH B 60 2061 129 HOH HOH . 
H 5 HOH B 61 2062 134 HOH HOH . 
H 5 HOH B 62 2063 141 HOH HOH . 
H 5 HOH B 63 2064 143 HOH HOH . 
H 5 HOH B 64 2065 147 HOH HOH . 
H 5 HOH B 65 2066 151 HOH HOH . 
H 5 HOH B 66 2067 154 HOH HOH . 
H 5 HOH B 67 2068 156 HOH HOH . 
H 5 HOH B 68 2069 157 HOH HOH . 
H 5 HOH B 69 2070 158 HOH HOH . 
H 5 HOH B 70 2071 159 HOH HOH . 
H 5 HOH B 71 2072 160 HOH HOH . 
H 5 HOH B 72 2073 163 HOH HOH . 
H 5 HOH B 73 2074 164 HOH HOH . 
H 5 HOH B 74 2075 165 HOH HOH . 
H 5 HOH B 75 2076 166 HOH HOH . 
H 5 HOH B 76 2077 167 HOH HOH . 
H 5 HOH B 77 2078 168 HOH HOH . 
H 5 HOH B 78 2079 169 HOH HOH . 
H 5 HOH B 79 2080 181 HOH HOH . 
H 5 HOH B 80 2081 189 HOH HOH . 
H 5 HOH B 81 2082 190 HOH HOH . 
H 5 HOH B 82 2083 191 HOH HOH . 
H 5 HOH B 83 2084 193 HOH HOH . 
H 5 HOH B 84 2085 198 HOH HOH . 
H 5 HOH B 85 2086 199 HOH HOH . 
H 5 HOH B 86 2087 200 HOH HOH . 
H 5 HOH B 87 2088 201 HOH HOH . 
H 5 HOH B 88 2089 202 HOH HOH . 
H 5 HOH B 89 2090 203 HOH HOH . 
H 5 HOH B 90 2091 205 HOH HOH . 
H 5 HOH B 91 2092 206 HOH HOH . 
H 5 HOH B 92 2093 208 HOH HOH . 
H 5 HOH B 93 2094 213 HOH HOH . 
H 5 HOH B 94 2095 218 HOH HOH . 
H 5 HOH B 95 2096 219 HOH HOH . 
H 5 HOH B 96 2097 220 HOH HOH . 
H 5 HOH B 97 2098 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 . . . E 4 -9.712 -38.772 11.057 1 53.94 ? C1 GOL 247 A 1 
HETATM 2 O O1 GOL . . . E 4 -10.71 -38.594 12.059 1 52.62 ? O1 GOL 247 A 1 
HETATM 3 C C2 GOL . . . E 4 -8.315 -38.368 11.548 1 54.16 ? C2 GOL 247 A 1 
HETATM 4 O O2 GOL . . . E 4 -8.054 -38.841 12.858 1 54.61 ? O2 GOL 247 A 1 
HETATM 5 C C3 GOL . . . E 4 -7.209 -38.851 10.61 1 54.71 ? C3 GOL 247 A 1 
HETATM 6 O O3 GOL . . . E 4 -5.948 -38.803 11.254 1 55.24 ? O3 GOL 247 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           6 
#