data_1YRK
#
_model_server_result.job_id            YpFMrRSnXj_sXODRO1Ym3w 
_model_server_result.datetime_utc      '2025-01-07 17:46:42' 
_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          1yrk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":2001}' 
#
_entry.id    1YRK 
#
_exptl.entry_id    1YRK 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              60.052 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'ACETIC ACID' 
_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            1YRK 
_cell.length_a            37.272 
_cell.length_b            41.856 
_cell.length_c            88.463 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1YRK 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 B C ILE 6 B ILE 6 1_555 B N PTR 7 B PTR 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale2 B C PTR 7 B PTR 7 1_555 B N GLN 8 B GLN 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? 
#
_chem_comp.formula           'C2 H4 O2' 
_chem_comp.formula_weight    60.052 
_chem_comp.id                ACY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'ACETIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
C O ACY doub 1 n n 
C OXT ACY sing 2 n n 
C CH3 ACY sing 3 n n 
OXT HXT ACY sing 4 n n 
CH3 H1 ACY sing 5 n n 
CH3 H2 ACY sing 6 n n 
CH3 H3 ACY sing 7 n n 
#
_atom_sites.entry_id                     1YRK 
_atom_sites.fract_transf_matrix[1][1]    0.02683 
_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]    0.023891 
_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]    0.011304 
_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 3 ACY A 1 2001 2001 ACY ACY . 
D 4 HOH A 1 2002 2 HOH TIP . 
D 4 HOH A 2 2003 5 HOH TIP . 
D 4 HOH A 3 2004 6 HOH TIP . 
D 4 HOH A 4 2005 8 HOH TIP . 
D 4 HOH A 5 2006 9 HOH TIP . 
D 4 HOH A 6 2007 10 HOH TIP . 
D 4 HOH A 7 2008 11 HOH TIP . 
D 4 HOH A 8 2009 12 HOH TIP . 
D 4 HOH A 9 2010 13 HOH TIP . 
D 4 HOH A 10 2011 14 HOH TIP . 
D 4 HOH A 11 2012 15 HOH TIP . 
D 4 HOH A 12 2013 16 HOH TIP . 
D 4 HOH A 13 2014 17 HOH TIP . 
D 4 HOH A 14 2015 18 HOH TIP . 
D 4 HOH A 15 2016 19 HOH TIP . 
D 4 HOH A 16 2017 21 HOH TIP . 
D 4 HOH A 17 2018 22 HOH TIP . 
D 4 HOH A 18 2019 23 HOH TIP . 
D 4 HOH A 19 2020 24 HOH TIP . 
D 4 HOH A 20 2021 25 HOH TIP . 
D 4 HOH A 21 2022 26 HOH TIP . 
D 4 HOH A 22 2023 27 HOH TIP . 
D 4 HOH A 23 2024 28 HOH TIP . 
D 4 HOH A 24 2025 30 HOH TIP . 
D 4 HOH A 25 2026 31 HOH TIP . 
D 4 HOH A 26 2027 32 HOH TIP . 
D 4 HOH A 27 2028 33 HOH TIP . 
D 4 HOH A 28 2029 34 HOH TIP . 
D 4 HOH A 29 2030 35 HOH TIP . 
D 4 HOH A 30 2031 36 HOH TIP . 
D 4 HOH A 31 2032 37 HOH TIP . 
D 4 HOH A 32 2033 39 HOH TIP . 
D 4 HOH A 33 2034 41 HOH TIP . 
D 4 HOH A 34 2035 42 HOH TIP . 
D 4 HOH A 35 2036 44 HOH TIP . 
D 4 HOH A 36 2037 45 HOH TIP . 
D 4 HOH A 37 2038 47 HOH TIP . 
D 4 HOH A 38 2039 48 HOH TIP . 
D 4 HOH A 39 2040 49 HOH TIP . 
D 4 HOH A 40 2041 50 HOH TIP . 
D 4 HOH A 41 2042 51 HOH TIP . 
D 4 HOH A 42 2043 52 HOH TIP . 
D 4 HOH A 43 2044 53 HOH TIP . 
D 4 HOH A 44 2045 54 HOH TIP . 
D 4 HOH A 45 2046 55 HOH TIP . 
D 4 HOH A 46 2047 56 HOH TIP . 
D 4 HOH A 47 2048 57 HOH TIP . 
D 4 HOH A 48 2049 58 HOH TIP . 
D 4 HOH A 49 2050 59 HOH TIP . 
D 4 HOH A 50 2051 60 HOH TIP . 
D 4 HOH A 51 2052 61 HOH TIP . 
D 4 HOH A 52 2053 62 HOH TIP . 
D 4 HOH A 53 2054 64 HOH TIP . 
D 4 HOH A 54 2055 65 HOH TIP . 
D 4 HOH A 55 2056 66 HOH TIP . 
D 4 HOH A 56 2057 67 HOH TIP . 
D 4 HOH A 57 2058 68 HOH TIP . 
D 4 HOH A 58 2059 70 HOH TIP . 
D 4 HOH A 59 2060 71 HOH TIP . 
D 4 HOH A 60 2061 72 HOH TIP . 
D 4 HOH A 61 2062 73 HOH TIP . 
D 4 HOH A 62 2063 74 HOH TIP . 
D 4 HOH A 63 2064 76 HOH TIP . 
D 4 HOH A 64 2065 77 HOH TIP . 
D 4 HOH A 65 2066 78 HOH TIP . 
D 4 HOH A 66 2067 79 HOH TIP . 
D 4 HOH A 67 2068 80 HOH TIP . 
D 4 HOH A 68 2069 81 HOH TIP . 
D 4 HOH A 69 2070 82 HOH TIP . 
D 4 HOH A 70 2071 83 HOH TIP . 
D 4 HOH A 71 2072 84 HOH TIP . 
D 4 HOH A 72 2073 85 HOH TIP . 
D 4 HOH A 73 2074 87 HOH TIP . 
D 4 HOH A 74 2075 88 HOH TIP . 
D 4 HOH A 75 2076 89 HOH TIP . 
D 4 HOH A 76 2077 90 HOH TIP . 
D 4 HOH A 77 2078 91 HOH TIP . 
D 4 HOH A 78 2079 92 HOH TIP . 
D 4 HOH A 79 2080 93 HOH TIP . 
D 4 HOH A 80 2081 94 HOH TIP . 
D 4 HOH A 81 2082 95 HOH TIP . 
D 4 HOH A 82 2083 96 HOH TIP . 
D 4 HOH A 83 2084 98 HOH TIP . 
D 4 HOH A 84 2085 100 HOH TIP . 
D 4 HOH A 85 2086 101 HOH TIP . 
D 4 HOH A 86 2087 102 HOH TIP . 
D 4 HOH A 87 2088 103 HOH TIP . 
D 4 HOH A 88 2089 104 HOH TIP . 
D 4 HOH A 89 2090 105 HOH TIP . 
D 4 HOH A 90 2091 107 HOH TIP . 
D 4 HOH A 91 2092 108 HOH TIP . 
D 4 HOH A 92 2093 109 HOH TIP . 
D 4 HOH A 93 2094 110 HOH TIP . 
D 4 HOH A 94 2095 111 HOH TIP . 
D 4 HOH A 95 2096 112 HOH TIP . 
D 4 HOH A 96 2097 113 HOH TIP . 
D 4 HOH A 97 2098 114 HOH TIP . 
D 4 HOH A 98 2099 115 HOH TIP . 
D 4 HOH A 99 2100 116 HOH TIP . 
D 4 HOH A 100 2101 117 HOH TIP . 
D 4 HOH A 101 2102 118 HOH TIP . 
D 4 HOH A 102 2103 119 HOH TIP . 
D 4 HOH A 103 2104 120 HOH TIP . 
D 4 HOH A 104 2105 121 HOH TIP . 
D 4 HOH A 105 2106 122 HOH TIP . 
D 4 HOH A 106 2107 123 HOH TIP . 
D 4 HOH A 107 2108 124 HOH TIP . 
D 4 HOH A 108 2109 125 HOH TIP . 
D 4 HOH A 109 2110 126 HOH TIP . 
D 4 HOH A 110 2111 127 HOH TIP . 
D 4 HOH A 111 2112 128 HOH TIP . 
D 4 HOH A 112 2113 129 HOH TIP . 
D 4 HOH A 113 2114 130 HOH TIP . 
D 4 HOH A 114 2115 132 HOH TIP . 
D 4 HOH A 115 2116 133 HOH TIP . 
D 4 HOH A 116 2117 134 HOH TIP . 
D 4 HOH A 117 2118 135 HOH TIP . 
D 4 HOH A 118 2119 136 HOH TIP . 
D 4 HOH A 119 2120 137 HOH TIP . 
D 4 HOH A 120 2121 138 HOH TIP . 
D 4 HOH A 121 2122 139 HOH TIP . 
D 4 HOH A 122 2123 140 HOH TIP . 
D 4 HOH A 123 2124 141 HOH TIP . 
D 4 HOH A 124 2125 142 HOH TIP . 
D 4 HOH A 125 2126 143 HOH TIP . 
D 4 HOH A 126 2127 144 HOH TIP . 
D 4 HOH A 127 2128 145 HOH TIP . 
D 4 HOH A 128 2129 146 HOH TIP . 
D 4 HOH A 129 2130 147 HOH TIP . 
D 4 HOH A 130 2131 148 HOH TIP . 
D 4 HOH A 131 2132 149 HOH TIP . 
D 4 HOH A 132 2133 150 HOH TIP . 
D 4 HOH A 133 2134 151 HOH TIP . 
D 4 HOH A 134 2135 152 HOH TIP . 
D 4 HOH A 135 2136 153 HOH TIP . 
D 4 HOH A 136 2137 154 HOH TIP . 
D 4 HOH A 137 2138 155 HOH TIP . 
D 4 HOH A 138 2139 156 HOH TIP . 
D 4 HOH A 139 2140 157 HOH TIP . 
D 4 HOH A 140 2141 158 HOH TIP . 
D 4 HOH A 141 2142 159 HOH TIP . 
D 4 HOH A 142 2143 160 HOH TIP . 
D 4 HOH A 143 2144 161 HOH TIP . 
D 4 HOH A 144 2145 162 HOH TIP . 
D 4 HOH A 145 2146 163 HOH TIP . 
D 4 HOH A 146 2147 164 HOH TIP . 
D 4 HOH A 147 2148 165 HOH TIP . 
D 4 HOH A 148 2149 166 HOH TIP . 
D 4 HOH A 149 2150 167 HOH TIP . 
D 4 HOH A 150 2151 168 HOH TIP . 
D 4 HOH A 151 2152 169 HOH TIP . 
D 4 HOH A 152 2153 170 HOH TIP . 
D 4 HOH A 153 2154 171 HOH TIP . 
D 4 HOH A 154 2155 173 HOH TIP . 
D 4 HOH A 155 2156 174 HOH TIP . 
D 4 HOH A 156 2157 175 HOH TIP . 
D 4 HOH A 157 2158 176 HOH TIP . 
D 4 HOH A 158 2159 177 HOH TIP . 
D 4 HOH A 159 2160 178 HOH TIP . 
D 4 HOH A 160 2161 179 HOH TIP . 
D 4 HOH A 161 2162 180 HOH TIP . 
D 4 HOH A 162 2163 181 HOH TIP . 
D 4 HOH A 163 2164 182 HOH TIP . 
D 4 HOH A 164 2165 183 HOH TIP . 
D 4 HOH A 165 2166 186 HOH TIP . 
D 4 HOH A 166 2167 187 HOH TIP . 
D 4 HOH A 167 2168 188 HOH TIP . 
D 4 HOH A 168 2169 189 HOH TIP . 
D 4 HOH A 169 2170 190 HOH TIP . 
D 4 HOH A 170 2171 191 HOH TIP . 
D 4 HOH A 171 2172 192 HOH TIP . 
D 4 HOH A 172 2173 193 HOH TIP . 
D 4 HOH A 173 2174 194 HOH TIP . 
D 4 HOH A 174 2175 196 HOH TIP . 
D 4 HOH A 175 2176 198 HOH TIP . 
D 4 HOH A 176 2177 200 HOH TIP . 
D 4 HOH A 177 2178 201 HOH TIP . 
D 4 HOH A 178 2179 202 HOH TIP . 
D 4 HOH A 179 2180 203 HOH TIP . 
D 4 HOH A 180 2181 204 HOH TIP . 
D 4 HOH A 181 2182 205 HOH TIP . 
D 4 HOH A 182 2183 206 HOH TIP . 
D 4 HOH A 183 2184 209 HOH TIP . 
D 4 HOH A 184 2185 210 HOH TIP . 
D 4 HOH A 185 2186 211 HOH TIP . 
D 4 HOH A 186 2187 212 HOH TIP . 
D 4 HOH A 187 2188 214 HOH TIP . 
D 4 HOH A 188 2189 215 HOH TIP . 
D 4 HOH A 189 2190 217 HOH TIP . 
D 4 HOH A 190 2191 218 HOH TIP . 
D 4 HOH A 191 2192 219 HOH TIP . 
E 4 HOH B 1 14 1 HOH TIP . 
E 4 HOH B 2 15 3 HOH TIP . 
E 4 HOH B 3 16 4 HOH TIP . 
E 4 HOH B 4 17 7 HOH TIP . 
E 4 HOH B 5 18 20 HOH TIP . 
E 4 HOH B 6 19 29 HOH TIP . 
E 4 HOH B 7 20 38 HOH TIP . 
E 4 HOH B 8 21 40 HOH TIP . 
E 4 HOH B 9 22 43 HOH TIP . 
E 4 HOH B 10 23 46 HOH TIP . 
E 4 HOH B 11 24 63 HOH TIP . 
E 4 HOH B 12 25 69 HOH TIP . 
E 4 HOH B 13 26 75 HOH TIP . 
E 4 HOH B 14 27 86 HOH TIP . 
E 4 HOH B 15 28 97 HOH TIP . 
E 4 HOH B 16 29 99 HOH TIP . 
E 4 HOH B 17 30 106 HOH TIP . 
E 4 HOH B 18 31 131 HOH TIP . 
E 4 HOH B 19 32 172 HOH TIP . 
E 4 HOH B 20 33 184 HOH TIP . 
E 4 HOH B 21 34 185 HOH TIP . 
E 4 HOH B 22 35 195 HOH TIP . 
E 4 HOH B 23 36 197 HOH TIP . 
E 4 HOH B 24 37 199 HOH TIP . 
E 4 HOH B 25 38 207 HOH TIP . 
E 4 HOH B 26 39 208 HOH TIP . 
E 4 HOH B 27 40 213 HOH TIP . 
E 4 HOH B 28 41 216 HOH TIP . 
E 4 HOH B 29 42 220 HOH TIP . 
#
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 C ACY . . . C 3 26.104 22.547 16.786 1 20.13 ? C ACY 2001 A 1 
HETATM 2 O O ACY . . . C 3 24.992 23.022 16.558 1 22.02 ? O ACY 2001 A 1 
HETATM 3 O OXT ACY . . . C 3 26.212 21.604 17.568 1 23.25 ? OXT ACY 2001 A 1 
HETATM 4 C CH3 ACY . . . C 3 27.339 23.122 16.092 1 22.13 ? CH3 ACY 2001 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           292 
_model_server_stats.encode_time_ms          13 
_model_server_stats.element_count           4 
#