data_3ZI8
#
_model_server_result.job_id            MjLmak7KSO4eY4Vqgf7dnw 
_model_server_result.datetime_utc      '2024-11-05 23:06:25' 
_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          3zi8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":102}' 
#
_entry.id    3ZI8 
#
_exptl.entry_id    3ZI8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4R)-2-METHYLPENTANE-2,4-DIOL 
_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         120 
_cell.entry_id            3ZI8 
_cell.length_a            72.399 
_cell.length_b            72.399 
_cell.length_c            35.99 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3ZI8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 3 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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    1,2,3 
#
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' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 36.1995 62.699373 0 
3 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 72.399 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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
metalc ? metalc1 A O ALA 7 A ALA 7 1_555 C MG MG . A MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc2 A O VAL 50 A VAL 50 3_665 C MG MG . A MG 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc3 C MG MG . A MG 101 1_555 E O HOH . A HOH 2018 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.686 ? 
metalc ? metalc4 C MG MG . A MG 101 1_555 E O HOH . A HOH 2019 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? 
metalc ? metalc5 C MG MG . A MG 101 1_555 E O HOH . A HOH 2020 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? 
metalc ? metalc6 C MG MG . A MG 101 1_555 E O HOH . A HOH 2020 3_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
#
_chem_comp.formula           'C6 H14 O2' 
_chem_comp.formula_weight    118.174 
_chem_comp.id                MRD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4R)-2-METHYLPENTANE-2,4-DIOL 
_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 MRD sing 241 n n 
C1 H1C1 MRD sing 242 n n 
C1 H1C2 MRD sing 243 n n 
C1 H1C3 MRD sing 244 n n 
C2 O2 MRD sing 245 n n 
C2 CM MRD sing 246 n n 
C2 C3 MRD sing 247 n n 
O2 H2 MRD sing 248 n n 
CM HMC1 MRD sing 249 n n 
CM HMC2 MRD sing 250 n n 
CM HMC3 MRD sing 251 n n 
C3 C4 MRD sing 252 n n 
C3 H3C1 MRD sing 253 n n 
C3 H3C2 MRD sing 254 n n 
C4 O4 MRD sing 255 n n 
C4 C5 MRD sing 256 n n 
C4 H4 MRD sing 257 n n 
O4 HA MRD sing 258 n n 
C5 H5C1 MRD sing 259 n n 
C5 H5C2 MRD sing 260 n n 
C5 H5C3 MRD sing 261 n n 
#
_atom_sites.entry_id                     3ZI8 
_atom_sites.fract_transf_matrix[1][1]    0.013812 
_atom_sites.fract_transf_matrix[1][2]    0.007975 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015949 
_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]    0.027785 
_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 FUL A 1 100 100 FUL FU4 . 
C 3 MG A 1 101 101 MG MG . 
D 4 MRD A 1 102 102 MRD MRD . 
E 5 HOH A 1 2001 2001 HOH HOH . 
E 5 HOH A 2 2002 2002 HOH HOH . 
E 5 HOH A 3 2003 2003 HOH HOH . 
E 5 HOH A 4 2004 2004 HOH HOH . 
E 5 HOH A 5 2005 2005 HOH HOH . 
E 5 HOH A 6 2006 2006 HOH HOH . 
E 5 HOH A 7 2007 2007 HOH HOH . 
E 5 HOH A 8 2008 2008 HOH HOH . 
E 5 HOH A 9 2009 2009 HOH HOH . 
E 5 HOH A 10 2010 2010 HOH HOH . 
E 5 HOH A 11 2011 2011 HOH HOH . 
E 5 HOH A 12 2012 2012 HOH HOH . 
E 5 HOH A 13 2013 2013 HOH HOH . 
E 5 HOH A 14 2014 2014 HOH HOH . 
E 5 HOH A 15 2015 2015 HOH HOH . 
E 5 HOH A 16 2016 2016 HOH HOH . 
E 5 HOH A 17 2017 2017 HOH HOH . 
E 5 HOH A 18 2018 2018 HOH HOH . 
E 5 HOH A 19 2019 2019 HOH HOH . 
E 5 HOH A 20 2020 2020 HOH HOH . 
E 5 HOH A 21 2021 2021 HOH HOH . 
E 5 HOH A 22 2022 2022 HOH HOH . 
E 5 HOH A 23 2023 2023 HOH HOH . 
E 5 HOH A 24 2024 2024 HOH HOH . 
E 5 HOH A 25 2025 2025 HOH HOH . 
E 5 HOH A 26 2026 2026 HOH HOH . 
E 5 HOH A 27 2027 2027 HOH HOH . 
E 5 HOH A 28 2028 2028 HOH HOH . 
E 5 HOH A 29 2029 2029 HOH HOH . 
E 5 HOH A 30 2030 2030 HOH HOH . 
E 5 HOH A 31 2031 2031 HOH HOH . 
E 5 HOH A 32 2032 2032 HOH HOH . 
E 5 HOH A 33 2033 2033 HOH HOH . 
E 5 HOH A 34 2034 2034 HOH HOH . 
E 5 HOH A 35 2035 2035 HOH HOH . 
E 5 HOH A 36 2036 2036 HOH HOH . 
E 5 HOH A 37 2037 2037 HOH HOH . 
E 5 HOH A 38 2038 2038 HOH HOH . 
E 5 HOH A 39 2039 2039 HOH HOH . 
E 5 HOH A 40 2040 2040 HOH HOH . 
E 5 HOH A 41 2041 2041 HOH HOH . 
E 5 HOH A 42 2042 2042 HOH HOH . 
E 5 HOH A 43 2043 2043 HOH HOH . 
E 5 HOH A 44 2044 2044 HOH HOH . 
E 5 HOH A 45 2045 2045 HOH HOH . 
E 5 HOH A 46 2046 2046 HOH HOH . 
E 5 HOH A 47 2047 2047 HOH HOH . 
E 5 HOH A 48 2048 2048 HOH HOH . 
E 5 HOH A 49 2049 2049 HOH HOH . 
E 5 HOH A 50 2050 2050 HOH HOH . 
E 5 HOH A 51 2051 2051 HOH HOH . 
E 5 HOH A 52 2052 2052 HOH HOH . 
E 5 HOH A 53 2053 2053 HOH HOH . 
E 5 HOH A 54 2054 2054 HOH HOH . 
E 5 HOH A 55 2055 2055 HOH HOH . 
E 5 HOH A 56 2056 2056 HOH HOH . 
E 5 HOH A 57 2057 2057 HOH HOH . 
E 5 HOH A 58 2058 2058 HOH HOH . 
E 5 HOH A 59 2059 2059 HOH HOH . 
E 5 HOH A 60 2060 2060 HOH HOH . 
E 5 HOH A 61 2061 2061 HOH HOH . 
E 5 HOH A 62 2062 2062 HOH HOH . 
E 5 HOH A 63 2063 2063 HOH HOH . 
E 5 HOH A 64 2064 2064 HOH HOH . 
E 5 HOH A 65 2065 2065 HOH HOH . 
E 5 HOH A 66 2066 2066 HOH HOH . 
E 5 HOH A 67 2067 2067 HOH HOH . 
E 5 HOH A 68 2068 2068 HOH HOH . 
E 5 HOH A 69 2069 2069 HOH HOH . 
E 5 HOH A 70 2070 2070 HOH HOH . 
E 5 HOH A 71 2071 2071 HOH HOH . 
E 5 HOH A 72 2072 2072 HOH HOH . 
E 5 HOH A 73 2073 2073 HOH HOH . 
E 5 HOH A 74 2074 2074 HOH HOH . 
E 5 HOH A 75 2075 2075 HOH HOH . 
E 5 HOH A 76 2076 2076 HOH HOH . 
E 5 HOH A 77 2077 2077 HOH HOH . 
E 5 HOH A 78 2078 2078 HOH HOH . 
E 5 HOH A 79 2079 2079 HOH HOH . 
E 5 HOH A 80 2080 2080 HOH HOH . 
E 5 HOH A 81 2081 2081 HOH HOH . 
E 5 HOH A 82 2082 2082 HOH HOH . 
E 5 HOH A 83 2083 2083 HOH HOH . 
E 5 HOH A 84 2084 2084 HOH HOH . 
E 5 HOH A 85 2085 2085 HOH HOH . 
E 5 HOH A 86 2086 2086 HOH HOH . 
E 5 HOH A 87 2087 2087 HOH HOH . 
E 5 HOH A 88 2088 2088 HOH HOH . 
E 5 HOH A 89 2089 2089 HOH HOH . 
E 5 HOH A 90 2090 2090 HOH HOH . 
E 5 HOH A 91 2091 2091 HOH HOH . 
E 5 HOH A 92 2092 2092 HOH HOH . 
E 5 HOH A 93 2093 2093 HOH HOH . 
E 5 HOH A 94 2094 2094 HOH HOH . 
E 5 HOH A 95 2095 2095 HOH HOH . 
E 5 HOH A 96 2096 2096 HOH HOH . 
E 5 HOH A 97 2097 2097 HOH HOH . 
E 5 HOH A 98 2098 2098 HOH HOH . 
E 5 HOH A 99 2099 2099 HOH HOH . 
E 5 HOH A 100 2100 2100 HOH HOH . 
E 5 HOH A 101 2101 2101 HOH HOH . 
E 5 HOH A 102 2102 2102 HOH HOH . 
E 5 HOH A 103 2103 2103 HOH HOH . 
E 5 HOH A 104 2104 2104 HOH HOH . 
E 5 HOH A 105 2105 2105 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 MRD . . . D 4 23.441 28.228 -19.091 1 28.65 ? C1 MRD 102 A 1 
HETATM 2 C C2 MRD . . . D 4 21.982 28.161 -18.623 1 28.41 ? C2 MRD 102 A 1 
HETATM 3 O O2 MRD . . . D 4 21.885 28.947 -17.442 1 29.16 ? O2 MRD 102 A 1 
HETATM 4 C CM MRD . . . D 4 21.636 26.734 -18.209 1 28.93 ? CM MRD 102 A 1 
HETATM 5 C C3 MRD . . . D 4 21.001 28.74 -19.646 1 26.86 ? C3 MRD 102 A 1 
HETATM 6 C C4 MRD . . . D 4 21.323 30.174 -20.093 1 29.47 ? C4 MRD 102 A 1 
HETATM 7 O O4 MRD . . . D 4 21.344 31.108 -18.988 1 30.57 ? O4 MRD 102 A 1 
HETATM 8 C C5 MRD . . . D 4 20.242 30.669 -21.053 1 34.74 ? C5 MRD 102 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           8 
#