data_4D77
#
_model_server_result.job_id            qbIt9Hg2q7BNOke9k7ELSQ 
_model_server_result.datetime_utc      '2025-01-10 16:32:19' 
_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          4d77 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1544}' 
#
_entry.id    4D77 
#
_exptl.entry_id    4D77 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_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            4D77 
_cell.length_a            45.84 
_cell.length_b            62.48 
_cell.length_c            88.29 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4D77 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
#
_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
? 3 C N N 
? 3 D N N 
? 3 E 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
metalc ? metalc1 A OD1 ASN 165 A ASN 423 1_555 B NA NA . A NA 1543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc2 A OD1 ASN 213 A ASN 471 1_555 B NA NA . A NA 1543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc3 A O ALA 214 A ALA 472 1_555 B NA NA . A NA 1543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc4 A O LEU 259 A LEU 517 1_555 B NA NA . A NA 1543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc5 B NA NA . A NA 1543 1_555 F O HOH . A HOH 2063 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.437 ? 
#
_chem_comp.formula           'C6 H14 O2' 
_chem_comp.formula_weight    118.174 
_chem_comp.id                MPD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4S)-2-METHYL-2,4-PENTANEDIOL 
_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
C1 C2 MPD sing 237 n n 
C1 H11 MPD sing 238 n n 
C1 H12 MPD sing 239 n n 
C1 H13 MPD sing 240 n n 
C2 O2 MPD sing 241 n n 
C2 CM MPD sing 242 n n 
C2 C3 MPD sing 243 n n 
O2 HO2 MPD sing 244 n n 
CM HM1 MPD sing 245 n n 
CM HM2 MPD sing 246 n n 
CM HM3 MPD sing 247 n n 
C3 C4 MPD sing 248 n n 
C3 H31 MPD sing 249 n n 
C3 H32 MPD sing 250 n n 
C4 O4 MPD sing 251 n n 
C4 C5 MPD sing 252 n n 
C4 H4 MPD sing 253 n n 
O4 HO4 MPD sing 254 n n 
C5 H51 MPD sing 255 n n 
C5 H52 MPD sing 256 n n 
C5 H53 MPD sing 257 n n 
#
_atom_sites.entry_id                     4D77 
_atom_sites.fract_transf_matrix[1][1]    0.021815 
_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]    0.016005 
_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
B 2 NA A 1 1543 1543 NA NA . 
C 3 MPD A 1 1544 1544 MPD MPD . 
D 3 MPD A 1 1545 1545 MPD MPD . 
E 3 MPD A 1 1546 1546 MPD MPD . 
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 2023 2023 HOH HOH . 
F 4 HOH A 23 2024 2024 HOH HOH . 
F 4 HOH A 24 2025 2025 HOH HOH . 
F 4 HOH A 25 2026 2026 HOH HOH . 
F 4 HOH A 26 2027 2027 HOH HOH . 
F 4 HOH A 27 2028 2028 HOH HOH . 
F 4 HOH A 28 2029 2029 HOH HOH . 
F 4 HOH A 29 2030 2030 HOH HOH . 
F 4 HOH A 30 2031 2031 HOH HOH . 
F 4 HOH A 31 2032 2032 HOH HOH . 
F 4 HOH A 32 2033 2033 HOH HOH . 
F 4 HOH A 33 2034 2034 HOH HOH . 
F 4 HOH A 34 2035 2035 HOH HOH . 
F 4 HOH A 35 2036 2036 HOH HOH . 
F 4 HOH A 36 2037 2037 HOH HOH . 
F 4 HOH A 37 2038 2038 HOH HOH . 
F 4 HOH A 38 2039 2039 HOH HOH . 
F 4 HOH A 39 2040 2040 HOH HOH . 
F 4 HOH A 40 2041 2041 HOH HOH . 
F 4 HOH A 41 2042 2042 HOH HOH . 
F 4 HOH A 42 2043 2043 HOH HOH . 
F 4 HOH A 43 2044 2044 HOH HOH . 
F 4 HOH A 44 2045 2045 HOH HOH . 
F 4 HOH A 45 2046 2046 HOH HOH . 
F 4 HOH A 46 2047 2047 HOH HOH . 
F 4 HOH A 47 2048 2048 HOH HOH . 
F 4 HOH A 48 2049 2049 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 2094 2094 HOH HOH . 
F 4 HOH A 94 2095 2095 HOH HOH . 
F 4 HOH A 95 2096 2096 HOH HOH . 
F 4 HOH A 96 2097 2097 HOH HOH . 
F 4 HOH A 97 2098 2098 HOH HOH . 
F 4 HOH A 98 2099 2099 HOH HOH . 
F 4 HOH A 99 2100 2100 HOH HOH . 
F 4 HOH A 100 2101 2101 HOH HOH . 
F 4 HOH A 101 2102 2102 HOH HOH . 
F 4 HOH A 102 2103 2103 HOH HOH . 
F 4 HOH A 103 2104 2104 HOH HOH . 
F 4 HOH A 104 2105 2105 HOH HOH . 
F 4 HOH A 105 2106 2106 HOH HOH . 
F 4 HOH A 106 2107 2107 HOH HOH . 
F 4 HOH A 107 2108 2108 HOH HOH . 
F 4 HOH A 108 2109 2109 HOH HOH . 
F 4 HOH A 109 2110 2110 HOH HOH . 
F 4 HOH A 110 2111 2111 HOH HOH . 
F 4 HOH A 111 2112 2112 HOH HOH . 
F 4 HOH A 112 2113 2113 HOH HOH . 
F 4 HOH A 113 2114 2114 HOH HOH . 
F 4 HOH A 114 2115 2115 HOH HOH . 
F 4 HOH A 115 2116 2116 HOH HOH . 
F 4 HOH A 116 2117 2117 HOH HOH . 
F 4 HOH A 117 2118 2118 HOH HOH . 
F 4 HOH A 118 2119 2119 HOH HOH . 
F 4 HOH A 119 2120 2120 HOH HOH . 
F 4 HOH A 120 2121 2121 HOH HOH . 
F 4 HOH A 121 2122 2122 HOH HOH . 
F 4 HOH A 122 2123 2123 HOH HOH . 
F 4 HOH A 123 2124 2124 HOH HOH . 
F 4 HOH A 124 2125 2125 HOH HOH . 
F 4 HOH A 125 2126 2126 HOH HOH . 
F 4 HOH A 126 2127 2127 HOH HOH . 
F 4 HOH A 127 2128 2128 HOH HOH . 
F 4 HOH A 128 2129 2129 HOH HOH . 
F 4 HOH A 129 2130 2130 HOH HOH . 
F 4 HOH A 130 2131 2131 HOH HOH . 
F 4 HOH A 131 2132 2132 HOH HOH . 
F 4 HOH A 132 2133 2133 HOH HOH . 
F 4 HOH A 133 2134 2134 HOH HOH . 
F 4 HOH A 134 2135 2135 HOH HOH . 
F 4 HOH A 135 2136 2136 HOH HOH . 
F 4 HOH A 136 2137 2137 HOH HOH . 
F 4 HOH A 137 2138 2138 HOH HOH . 
F 4 HOH A 138 2139 2139 HOH HOH . 
F 4 HOH A 139 2140 2140 HOH HOH . 
F 4 HOH A 140 2141 2141 HOH HOH . 
F 4 HOH A 141 2142 2142 HOH HOH . 
F 4 HOH A 142 2143 2143 HOH HOH . 
F 4 HOH A 143 2144 2144 HOH HOH . 
F 4 HOH A 144 2145 2145 HOH HOH . 
F 4 HOH A 145 2146 2146 HOH HOH . 
F 4 HOH A 146 2147 2147 HOH HOH . 
F 4 HOH A 147 2148 2148 HOH HOH . 
F 4 HOH A 148 2149 2149 HOH HOH . 
F 4 HOH A 149 2150 2150 HOH HOH . 
F 4 HOH A 150 2151 2151 HOH HOH . 
F 4 HOH A 151 2152 2152 HOH HOH . 
F 4 HOH A 152 2153 2153 HOH HOH . 
F 4 HOH A 153 2154 2154 HOH HOH . 
F 4 HOH A 154 2155 2155 HOH HOH . 
F 4 HOH A 155 2156 2156 HOH HOH . 
F 4 HOH A 156 2157 2157 HOH HOH . 
F 4 HOH A 157 2158 2158 HOH HOH . 
F 4 HOH A 158 2159 2159 HOH HOH . 
F 4 HOH A 159 2160 2160 HOH HOH . 
F 4 HOH A 160 2161 2161 HOH HOH . 
F 4 HOH A 161 2162 2162 HOH HOH . 
F 4 HOH A 162 2163 2163 HOH HOH . 
F 4 HOH A 163 2164 2164 HOH HOH . 
F 4 HOH A 164 2165 2165 HOH HOH . 
F 4 HOH A 165 2166 2166 HOH HOH . 
F 4 HOH A 166 2167 2167 HOH HOH . 
F 4 HOH A 167 2168 2168 HOH HOH . 
F 4 HOH A 168 2169 2169 HOH HOH . 
F 4 HOH A 169 2170 2170 HOH HOH . 
F 4 HOH A 170 2171 2171 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 MPD . . . C 3 -10.722 -11.019 -25.057 1 44.98 ? C1 MPD 1544 A 1 
HETATM 2 C C2 MPD . . . C 3 -9.8 -10.161 -25.931 1 43.22 ? C2 MPD 1544 A 1 
HETATM 3 O O2 MPD . . . C 3 -8.564 -9.984 -25.205 1 40.73 ? O2 MPD 1544 A 1 
HETATM 4 C CM MPD . . . C 3 -10.388 -8.776 -26.193 1 43.36 ? CM MPD 1544 A 1 
HETATM 5 C C3 MPD . . . C 3 -9.527 -10.9 -27.24 1 44.16 ? C3 MPD 1544 A 1 
HETATM 6 C C4 MPD . . . C 3 -8.425 -10.273 -28.089 1 42.56 ? C4 MPD 1544 A 1 
HETATM 7 O O4 MPD . . . C 3 -7.229 -10.178 -27.34 1 39.57 ? O4 MPD 1544 A 1 
HETATM 8 C C5 MPD . . . C 3 -8.178 -11.107 -29.345 1 42.69 ? C5 MPD 1544 A 1 
HETATM 9 H H11 MPD . . . C 3 -10.22 -11.25 -24.117 1 53.97 ? H11 MPD 1544 A 1 
HETATM 10 H H12 MPD . . . C 3 -11.642 -10.472 -24.852 1 53.97 ? H12 MPD 1544 A 1 
HETATM 11 H H13 MPD . . . C 3 -10.958 -11.946 -25.579 1 53.97 ? H13 MPD 1544 A 1 
HETATM 12 H HO2 MPD . . . C 3 -7.826 -10.378 -25.715 1 48.87 ? HO2 MPD 1544 A 1 
HETATM 13 H HM1 MPD . . . C 3 -11.37 -8.704 -25.726 1 52.03 ? HM1 MPD 1544 A 1 
HETATM 14 H HM2 MPD . . . C 3 -9.729 -8.017 -25.773 1 52.03 ? HM2 MPD 1544 A 1 
HETATM 15 H HM3 MPD . . . C 3 -10.483 -8.62 -27.267 1 52.03 ? HM3 MPD 1544 A 1 
HETATM 16 H H31 MPD . . . C 3 -9.253 -11.93 -27.013 1 53 ? H31 MPD 1544 A 1 
HETATM 17 H H32 MPD . . . C 3 -10.447 -10.931 -27.825 1 53 ? H32 MPD 1544 A 1 
HETATM 18 H H4 MPD . . . C 3 -8.746 -9.276 -28.393 1 51.07 ? H4 MPD 1544 A 1 
HETATM 19 H HO4 MPD . . . C 3 -6.791 -11.054 -27.314 1 47.48 ? HO4 MPD 1544 A 1 
HETATM 20 H H51 MPD . . . C 3 -8.832 -11.979 -29.336 1 51.22 ? H51 MPD 1544 A 1 
HETATM 21 H H52 MPD . . . C 3 -8.389 -10.504 -30.229 1 51.22 ? H52 MPD 1544 A 1 
HETATM 22 H H53 MPD . . . C 3 -7.138 -11.432 -29.367 1 51.22 ? H53 MPD 1544 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           22 
#