data_3K06
#
_model_server_result.job_id            I2cFFzlY-Plhf-g6Zz4Hlw 
_model_server_result.datetime_utc      '2025-07-13 19:41:41' 
_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          3k06 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":502}' 
#
_entry.id    3K06 
#
_exptl.entry_id    3K06 
_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    7 
_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            3K06 
_cell.length_a            67.74 
_cell.length_b            67.74 
_cell.length_c            89.789 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3K06 
_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 G 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 H K K . A K 2 1_555 A O THR 46 A THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? 
metalc ? metalc2 H K K . A K 2 1_555 A O VAL 47 A VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? 
metalc ? metalc3 I K K . A K 4 1_555 A O THR 46 A THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? 
metalc ? metalc4 I K K . A K 4 1_555 A OG1 THR 46 A THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? 
metalc ? metalc5 J K K . A K 5 1_555 S O HOH . A HOH 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? 
metalc ? metalc6 J K K . A K 5 1_555 A O GLY 48 A GLY 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? 
metalc ? metalc7 K K K . A K 6 1_555 A O VAL 47 A VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.062 ? 
metalc ? metalc8 K K K . A K 6 1_555 A O GLY 48 A GLY 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? 
metalc ? metalc9 L K K . A K 8 1_555 S O HOH . A HOH 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? 
metalc ? metalc10 L K K . A K 8 1_555 S O HOH . A HOH 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? 
metalc ? metalc11 O K K . B K 1 1_555 B O THR 46 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? 
metalc ? metalc12 O K K . B K 1 1_555 B O VAL 47 B VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.864 ? 
metalc ? metalc13 P K K . B K 3 1_555 B O THR 46 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? 
metalc ? metalc14 P K K . B K 3 1_555 B OG1 THR 46 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
metalc ? metalc15 Q K K . B K 7 1_555 B O VAL 47 B VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.22 ? 
metalc ? metalc16 Q K K . B K 7 1_555 B O GLY 48 B GLY 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? 
metalc ? metalc17 R K K . B K 9 1_555 T O HOH . B HOH 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? 
#
_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                     3K06 
_atom_sites.fract_transf_matrix[1][1]    0.014762 
_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]    0.014762 
_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]    0.011137 
_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 2 MPD A 1 507 507 MPD MPD . 
H 3 K A 1 2 2 K K . 
I 3 K A 1 4 4 K K . 
J 3 K A 1 5 5 K K . 
K 3 K A 1 6 6 K K . 
L 3 K A 1 8 8 K K . 
M 2 MPD B 1 501 501 MPD MPD . 
N 2 MPD B 1 503 503 MPD MPD . 
O 3 K B 1 1 1 K K . 
P 3 K B 1 3 3 K K . 
Q 3 K B 1 7 7 K K . 
R 3 K B 1 9 9 K K . 
S 4 HOH A 1 1 1 HOH HOH . 
S 4 HOH A 2 3 3 HOH HOH . 
S 4 HOH A 3 7 7 HOH HOH . 
S 4 HOH A 4 9 9 HOH HOH . 
S 4 HOH A 5 10 10 HOH HOH . 
S 4 HOH A 6 12 12 HOH HOH . 
S 4 HOH A 7 13 13 HOH HOH . 
S 4 HOH A 8 14 14 HOH HOH . 
S 4 HOH A 9 15 15 HOH HOH . 
S 4 HOH A 10 16 16 HOH HOH . 
S 4 HOH A 11 17 17 HOH HOH . 
S 4 HOH A 12 114 114 HOH HOH . 
S 4 HOH A 13 115 115 HOH HOH . 
S 4 HOH A 14 116 2 HOH HOH . 
S 4 HOH A 15 117 117 HOH HOH . 
S 4 HOH A 16 118 4 HOH HOH . 
S 4 HOH A 17 119 8 HOH HOH . 
S 4 HOH A 18 120 18 HOH HOH . 
S 4 HOH A 19 121 121 HOH HOH . 
S 4 HOH A 20 122 20 HOH HOH . 
S 4 HOH A 21 123 22 HOH HOH . 
S 4 HOH A 22 124 24 HOH HOH . 
S 4 HOH A 23 125 25 HOH HOH . 
S 4 HOH A 24 126 27 HOH HOH . 
S 4 HOH A 25 127 32 HOH HOH . 
S 4 HOH A 26 128 36 HOH HOH . 
S 4 HOH A 27 129 39 HOH HOH . 
S 4 HOH A 28 130 41 HOH HOH . 
S 4 HOH A 29 131 46 HOH HOH . 
S 4 HOH A 30 132 47 HOH HOH . 
S 4 HOH A 31 133 48 HOH HOH . 
S 4 HOH A 32 134 49 HOH HOH . 
S 4 HOH A 33 135 55 HOH HOH . 
S 4 HOH A 34 136 56 HOH HOH . 
S 4 HOH A 35 137 58 HOH HOH . 
S 4 HOH A 36 138 60 HOH HOH . 
S 4 HOH A 37 139 62 HOH HOH . 
S 4 HOH A 38 140 64 HOH HOH . 
S 4 HOH A 39 141 68 HOH HOH . 
S 4 HOH A 40 142 69 HOH HOH . 
S 4 HOH A 41 143 71 HOH HOH . 
S 4 HOH A 42 145 74 HOH HOH . 
S 4 HOH A 43 146 78 HOH HOH . 
S 4 HOH A 44 147 79 HOH HOH . 
S 4 HOH A 45 148 82 HOH HOH . 
S 4 HOH A 46 149 83 HOH HOH . 
S 4 HOH A 47 150 84 HOH HOH . 
S 4 HOH A 48 151 86 HOH HOH . 
S 4 HOH A 49 152 88 HOH HOH . 
S 4 HOH A 50 153 89 HOH HOH . 
S 4 HOH A 51 154 92 HOH HOH . 
S 4 HOH A 52 155 93 HOH HOH . 
S 4 HOH A 53 156 95 HOH HOH . 
S 4 HOH A 54 157 100 HOH HOH . 
S 4 HOH A 55 158 102 HOH HOH . 
S 4 HOH A 56 159 103 HOH HOH . 
S 4 HOH A 57 160 106 HOH HOH . 
S 4 HOH A 58 161 109 HOH HOH . 
S 4 HOH A 59 162 110 HOH HOH . 
S 4 HOH A 60 163 111 HOH HOH . 
S 4 HOH A 61 164 113 HOH HOH . 
T 4 HOH B 1 5 5 HOH HOH . 
T 4 HOH B 2 6 6 HOH HOH . 
T 4 HOH B 3 11 11 HOH HOH . 
T 4 HOH B 4 114 19 HOH HOH . 
T 4 HOH B 5 115 21 HOH HOH . 
T 4 HOH B 6 116 116 HOH HOH . 
T 4 HOH B 7 117 23 HOH HOH . 
T 4 HOH B 8 118 118 HOH HOH . 
T 4 HOH B 9 119 119 HOH HOH . 
T 4 HOH B 10 120 120 HOH HOH . 
T 4 HOH B 11 121 26 HOH HOH . 
T 4 HOH B 12 122 28 HOH HOH . 
T 4 HOH B 13 123 29 HOH HOH . 
T 4 HOH B 14 124 30 HOH HOH . 
T 4 HOH B 15 125 31 HOH HOH . 
T 4 HOH B 16 126 33 HOH HOH . 
T 4 HOH B 17 127 34 HOH HOH . 
T 4 HOH B 18 128 35 HOH HOH . 
T 4 HOH B 19 129 37 HOH HOH . 
T 4 HOH B 20 130 38 HOH HOH . 
T 4 HOH B 21 131 40 HOH HOH . 
T 4 HOH B 22 132 42 HOH HOH . 
T 4 HOH B 23 133 43 HOH HOH . 
T 4 HOH B 24 134 44 HOH HOH . 
T 4 HOH B 25 135 45 HOH HOH . 
T 4 HOH B 26 136 50 HOH HOH . 
T 4 HOH B 27 137 51 HOH HOH . 
T 4 HOH B 28 138 52 HOH HOH . 
T 4 HOH B 29 139 53 HOH HOH . 
T 4 HOH B 30 140 54 HOH HOH . 
T 4 HOH B 31 141 57 HOH HOH . 
T 4 HOH B 32 142 59 HOH HOH . 
T 4 HOH B 33 143 61 HOH HOH . 
T 4 HOH B 34 144 72 HOH HOH . 
T 4 HOH B 35 145 65 HOH HOH . 
T 4 HOH B 36 146 66 HOH HOH . 
T 4 HOH B 37 147 67 HOH HOH . 
T 4 HOH B 38 148 70 HOH HOH . 
T 4 HOH B 39 149 73 HOH HOH . 
T 4 HOH B 40 150 75 HOH HOH . 
T 4 HOH B 41 151 76 HOH HOH . 
T 4 HOH B 42 152 77 HOH HOH . 
T 4 HOH B 43 153 80 HOH HOH . 
T 4 HOH B 44 154 81 HOH HOH . 
T 4 HOH B 45 155 85 HOH HOH . 
T 4 HOH B 46 156 87 HOH HOH . 
T 4 HOH B 47 157 90 HOH HOH . 
T 4 HOH B 48 158 91 HOH HOH . 
T 4 HOH B 49 159 94 HOH HOH . 
T 4 HOH B 50 160 96 HOH HOH . 
T 4 HOH B 51 161 97 HOH HOH . 
T 4 HOH B 52 162 98 HOH HOH . 
T 4 HOH B 53 163 99 HOH HOH . 
T 4 HOH B 54 164 101 HOH HOH . 
T 4 HOH B 55 165 104 HOH HOH . 
T 4 HOH B 56 166 105 HOH HOH . 
T 4 HOH B 57 167 107 HOH HOH . 
T 4 HOH B 58 168 108 HOH HOH . 
T 4 HOH B 59 169 112 HOH HOH . 
T 4 HOH B 60 170 63 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 2 4.356 -19.29 27.502 1 68.01 ? C1 MPD 502 A 1 
HETATM 2 C C2 MPD . . . C 2 4.733 -18.297 26.4 1 69.92 ? C2 MPD 502 A 1 
HETATM 3 O O2 MPD . . . C 2 4.367 -16.974 26.796 1 69.12 ? O2 MPD 502 A 1 
HETATM 4 C CM MPD . . . C 2 6.237 -18.361 26.148 1 69.26 ? CM MPD 502 A 1 
HETATM 5 C C3 MPD . . . C 2 3.992 -18.654 25.106 1 69.7 ? C3 MPD 502 A 1 
HETATM 6 C C4 MPD . . . C 2 4.619 -18.892 23.728 1 70.71 ? C4 MPD 502 A 1 
HETATM 7 O O4 MPD . . . C 2 4.579 -20.286 23.417 1 71.35 ? O4 MPD 502 A 1 
HETATM 8 C C5 MPD . . . C 2 3.851 -18.1 22.671 1 69.43 ? C5 MPD 502 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           309 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           8 
#