data_3K08
#
_model_server_result.job_id            xF8svLtDbPYRAxzSAM4fDw 
_model_server_result.datetime_utc      '2025-07-13 15:03:03' 
_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          3k08 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":501}' 
#
_entry.id    3K08 
#
_exptl.entry_id    3K08 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_entity.pdbx_number_of_molecules    6 
_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            3K08 
_cell.length_a            67.78 
_cell.length_b            67.78 
_cell.length_c            89.511 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3K08 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 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,F,G,H,I,J,K,L,S 1 1,2,3,4 
B,M,N,O,P,Q,R,T 2 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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_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
? 2 C N N 
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 M N N 
? 2 N 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 S O HOH . A HOH 1 1_555 H NA NA . A NA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? 
metalc ? metalc2 G NA NA . A NA 2 1_555 A O THR 46 A THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc3 H NA NA . A NA 4 1_555 A OG1 THR 46 A THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc4 I NA NA . A NA 5 1_555 A O VAL 47 A VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? 
metalc ? metalc5 J NA NA . A NA 6 1_555 S O HOH . A HOH 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc6 K NA NA . A NA 7 1_555 A O GLY 48 A GLY 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.948 ? 
metalc ? metalc7 L NA NA . A NA 8 1_555 A O GLY 48 A GLY 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.171 ? 
metalc ? metalc8 O NA NA . B NA 1 1_555 B O THR 46 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
metalc ? metalc9 P NA NA . B NA 3 1_555 B OG1 THR 46 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc10 P NA NA . B NA 3 1_555 T O HOH . B HOH 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? 
metalc ? metalc11 Q NA NA . B NA 9 1_555 B O GLY 48 B GLY 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.951 ? 
metalc ? metalc12 R NA NA . B NA 10 1_555 B O VAL 47 B VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? 
#
_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 224 n n 
C1 H11 MPD sing 225 n n 
C1 H12 MPD sing 226 n n 
C1 H13 MPD sing 227 n n 
C2 O2 MPD sing 228 n n 
C2 CM MPD sing 229 n n 
C2 C3 MPD sing 230 n n 
O2 HO2 MPD sing 231 n n 
CM HM1 MPD sing 232 n n 
CM HM2 MPD sing 233 n n 
CM HM3 MPD sing 234 n n 
C3 C4 MPD sing 235 n n 
C3 H31 MPD sing 236 n n 
C3 H32 MPD sing 237 n n 
C4 O4 MPD sing 238 n n 
C4 C5 MPD sing 239 n n 
C4 H4 MPD sing 240 n n 
O4 HO4 MPD sing 241 n n 
C5 H51 MPD sing 242 n n 
C5 H52 MPD sing 243 n n 
C5 H53 MPD sing 244 n n 
#
_atom_sites.entry_id                     3K08 
_atom_sites.fract_transf_matrix[1][1]    0.014754 
_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]    0.014754 
_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]    0.011172 
_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 MPD A 1 502 502 MPD MPD . 
D 2 MPD A 1 504 504 MPD MPD . 
E 2 MPD A 1 505 505 MPD MPD . 
F 2 MPD A 1 506 506 MPD MPD . 
G 3 NA A 1 2 2 NA NA . 
H 3 NA A 1 4 4 NA NA . 
I 3 NA A 1 5 5 NA NA . 
J 3 NA A 1 6 6 NA NA . 
K 3 NA A 1 7 7 NA NA . 
L 3 NA A 1 8 8 NA NA . 
M 2 MPD B 1 501 501 MPD MPD . 
N 2 MPD B 1 503 503 MPD MPD . 
O 3 NA B 1 1 1 NA NA . 
P 3 NA B 1 3 3 NA NA . 
Q 3 NA B 1 9 9 NA NA . 
R 3 NA B 1 10 10 NA NA . 
S 4 HOH A 1 1 1 HOH HOH . 
S 4 HOH A 2 10 10 HOH HOH . 
S 4 HOH A 3 11 11 HOH HOH . 
S 4 HOH A 4 13 13 HOH HOH . 
S 4 HOH A 5 14 14 HOH HOH . 
S 4 HOH A 6 114 2 HOH HOH . 
S 4 HOH A 7 115 115 HOH HOH . 
S 4 HOH A 8 116 116 HOH HOH . 
S 4 HOH A 9 117 117 HOH HOH . 
S 4 HOH A 10 118 4 HOH HOH . 
S 4 HOH A 11 119 5 HOH HOH . 
S 4 HOH A 12 120 120 HOH HOH . 
S 4 HOH A 13 121 7 HOH HOH . 
S 4 HOH A 14 122 8 HOH HOH . 
S 4 HOH A 15 123 19 HOH HOH . 
S 4 HOH A 16 124 124 HOH HOH . 
S 4 HOH A 17 125 20 HOH HOH . 
S 4 HOH A 18 126 126 HOH HOH . 
S 4 HOH A 19 127 22 HOH HOH . 
S 4 HOH A 20 128 128 HOH HOH . 
S 4 HOH A 21 129 129 HOH HOH . 
S 4 HOH A 22 130 24 HOH HOH . 
S 4 HOH A 23 131 131 HOH HOH . 
S 4 HOH A 24 132 25 HOH HOH . 
S 4 HOH A 25 133 133 HOH HOH . 
S 4 HOH A 26 134 26 HOH HOH . 
S 4 HOH A 27 135 135 HOH HOH . 
S 4 HOH A 28 136 27 HOH HOH . 
S 4 HOH A 29 137 29 HOH HOH . 
S 4 HOH A 30 138 31 HOH HOH . 
S 4 HOH A 31 139 32 HOH HOH . 
S 4 HOH A 32 140 33 HOH HOH . 
S 4 HOH A 33 141 35 HOH HOH . 
S 4 HOH A 34 142 37 HOH HOH . 
S 4 HOH A 35 143 40 HOH HOH . 
S 4 HOH A 36 144 41 HOH HOH . 
S 4 HOH A 37 145 42 HOH HOH . 
S 4 HOH A 38 146 43 HOH HOH . 
S 4 HOH A 39 147 48 HOH HOH . 
S 4 HOH A 40 148 49 HOH HOH . 
S 4 HOH A 41 149 51 HOH HOH . 
S 4 HOH A 42 150 52 HOH HOH . 
S 4 HOH A 43 151 53 HOH HOH . 
S 4 HOH A 44 152 55 HOH HOH . 
S 4 HOH A 45 153 56 HOH HOH . 
S 4 HOH A 46 154 60 HOH HOH . 
S 4 HOH A 47 155 62 HOH HOH . 
S 4 HOH A 48 157 64 HOH HOH . 
S 4 HOH A 49 158 65 HOH HOH . 
S 4 HOH A 50 159 67 HOH HOH . 
S 4 HOH A 51 160 69 HOH HOH . 
S 4 HOH A 52 161 70 HOH HOH . 
S 4 HOH A 53 162 74 HOH HOH . 
S 4 HOH A 54 163 79 HOH HOH . 
S 4 HOH A 55 164 82 HOH HOH . 
S 4 HOH A 56 165 84 HOH HOH . 
S 4 HOH A 57 166 86 HOH HOH . 
S 4 HOH A 58 167 87 HOH HOH . 
S 4 HOH A 59 168 89 HOH HOH . 
S 4 HOH A 60 169 91 HOH HOH . 
S 4 HOH A 61 170 93 HOH HOH . 
S 4 HOH A 62 171 94 HOH HOH . 
S 4 HOH A 63 172 95 HOH HOH . 
S 4 HOH A 64 173 96 HOH HOH . 
S 4 HOH A 65 175 104 HOH HOH . 
S 4 HOH A 66 176 107 HOH HOH . 
S 4 HOH A 67 177 108 HOH HOH . 
S 4 HOH A 68 178 109 HOH HOH . 
S 4 HOH A 69 179 111 HOH HOH . 
T 4 HOH B 1 6 6 HOH HOH . 
T 4 HOH B 2 12 12 HOH HOH . 
T 4 HOH B 3 15 15 HOH HOH . 
T 4 HOH B 4 16 16 HOH HOH . 
T 4 HOH B 5 17 17 HOH HOH . 
T 4 HOH B 6 114 114 HOH HOH . 
T 4 HOH B 7 115 3 HOH HOH . 
T 4 HOH B 8 116 9 HOH HOH . 
T 4 HOH B 9 117 18 HOH HOH . 
T 4 HOH B 10 118 118 HOH HOH . 
T 4 HOH B 11 119 119 HOH HOH . 
T 4 HOH B 12 120 21 HOH HOH . 
T 4 HOH B 13 121 121 HOH HOH . 
T 4 HOH B 14 122 122 HOH HOH . 
T 4 HOH B 15 123 123 HOH HOH . 
T 4 HOH B 16 124 23 HOH HOH . 
T 4 HOH B 17 125 125 HOH HOH . 
T 4 HOH B 18 126 28 HOH HOH . 
T 4 HOH B 19 127 127 HOH HOH . 
T 4 HOH B 20 128 30 HOH HOH . 
T 4 HOH B 21 129 34 HOH HOH . 
T 4 HOH B 22 130 130 HOH HOH . 
T 4 HOH B 23 131 36 HOH HOH . 
T 4 HOH B 24 132 132 HOH HOH . 
T 4 HOH B 25 133 38 HOH HOH . 
T 4 HOH B 26 134 134 HOH HOH . 
T 4 HOH B 27 135 39 HOH HOH . 
T 4 HOH B 28 136 44 HOH HOH . 
T 4 HOH B 29 137 45 HOH HOH . 
T 4 HOH B 30 138 46 HOH HOH . 
T 4 HOH B 31 139 47 HOH HOH . 
T 4 HOH B 32 140 50 HOH HOH . 
T 4 HOH B 33 141 54 HOH HOH . 
T 4 HOH B 34 142 57 HOH HOH . 
T 4 HOH B 35 143 58 HOH HOH . 
T 4 HOH B 36 144 59 HOH HOH . 
T 4 HOH B 37 145 61 HOH HOH . 
T 4 HOH B 38 146 66 HOH HOH . 
T 4 HOH B 39 147 68 HOH HOH . 
T 4 HOH B 40 148 71 HOH HOH . 
T 4 HOH B 41 149 72 HOH HOH . 
T 4 HOH B 42 150 73 HOH HOH . 
T 4 HOH B 43 151 75 HOH HOH . 
T 4 HOH B 44 152 76 HOH HOH . 
T 4 HOH B 45 153 77 HOH HOH . 
T 4 HOH B 46 154 78 HOH HOH . 
T 4 HOH B 47 155 80 HOH HOH . 
T 4 HOH B 48 156 63 HOH HOH . 
T 4 HOH B 49 157 83 HOH HOH . 
T 4 HOH B 50 158 85 HOH HOH . 
T 4 HOH B 51 159 88 HOH HOH . 
T 4 HOH B 52 160 90 HOH HOH . 
T 4 HOH B 53 161 92 HOH HOH . 
T 4 HOH B 54 162 97 HOH HOH . 
T 4 HOH B 55 163 99 HOH HOH . 
T 4 HOH B 56 164 100 HOH HOH . 
T 4 HOH B 57 165 101 HOH HOH . 
T 4 HOH B 58 166 102 HOH HOH . 
T 4 HOH B 59 167 103 HOH HOH . 
T 4 HOH B 60 168 105 HOH HOH . 
T 4 HOH B 61 169 106 HOH HOH . 
T 4 HOH B 62 170 110 HOH HOH . 
T 4 HOH B 63 171 113 HOH HOH . 
T 4 HOH B 64 172 81 HOH HOH . 
T 4 HOH B 65 174 98 HOH HOH . 
T 4 HOH B 66 180 112 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 . . . M 2 -18.384 -0.485 -24.006 1 51.75 ? C1 MPD 501 B 1 
HETATM 2 C C2 MPD . . . M 2 -18.617 -1.322 -25.267 1 53.99 ? C2 MPD 501 B 1 
HETATM 3 O O2 MPD . . . M 2 -20.008 -1.629 -25.387 1 51.6 ? O2 MPD 501 B 1 
HETATM 4 C CM MPD . . . M 2 -18.157 -0.537 -26.492 1 51.48 ? CM MPD 501 B 1 
HETATM 5 C C3 MPD . . . M 2 -17.82 -2.63 -25.17 1 55.15 ? C3 MPD 501 B 1 
HETATM 6 C C4 MPD . . . M 2 -17.73 -3.552 -23.957 1 56.4 ? C4 MPD 501 B 1 
HETATM 7 O O4 MPD . . . M 2 -19.011 -4.126 -23.69 1 56.99 ? O4 MPD 501 B 1 
HETATM 8 C C5 MPD . . . M 2 -16.707 -4.659 -24.223 1 51.68 ? C5 MPD 501 B 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           320 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           8 
#