data_8YFK
#
_model_server_result.job_id            BvS6Qe_ez1-mn2MAtDpvyA 
_model_server_result.datetime_utc      '2024-10-11 05:26:00' 
_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          8yfk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":1601}' 
#
_entry.id    8YFK 
#
_exptl.entry_id    8YFK 
_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         81.2 
_cell.angle_beta          89.67 
_cell.angle_gamma         88.74 
_cell.entry_id            8YFK 
_cell.length_a            37.812 
_cell.length_b            45.936 
_cell.length_c            72.951 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YFK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,J,N,O 1 1 
C,D,K,P,Q 2 1 
E,F,L,R,S 3 1 
G,H,M,T,U 4 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 I N N 
? 3 K N N 
? 3 M 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
covale ? covale1 B C SER 5 B SER 103 1_555 B N SEP 6 B SEP 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale2 B C SEP 6 B SEP 104 1_555 B N GLU 7 B GLU 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale3 D C SER 5 H SER 103 1_555 D N SEP 6 H SEP 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 D C SEP 6 H SEP 104 1_555 D N GLU 7 H GLU 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale5 F C SER 5 D SER 103 1_555 F N SEP 6 D SEP 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale6 F C SEP 6 D SEP 104 1_555 F N GLU 7 D GLU 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale7 H C SER 5 F SER 103 1_555 H N SEP 6 F SEP 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale8 H C SEP 6 F SEP 104 1_555 H N GLU 7 F GLU 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
metalc ? metalc1 E OG SER 43 C SER 1532 1_555 L MG MG . C MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.892 ? 
#
_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                     8YFK 
_atom_sites.fract_transf_matrix[1][1]    0.026447 
_atom_sites.fract_transf_matrix[1][2]    -0.000582 
_atom_sites.fract_transf_matrix[1][3]    -0.000062 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021775 
_atom_sites.fract_transf_matrix[2][3]    -0.003369 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.013871 
_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
I 3 MPD A 1 1601 1601 MPD MPD . 
J 4 MG A 1 1602 1 MG MG . 
K 3 MPD G 1 1601 1602 MPD MPD . 
L 4 MG C 1 1601 2 MG MG . 
M 3 MPD E 1 1601 1603 MPD MPD . 
N 5 HOH A 1 1701 10 HOH HOH . 
N 5 HOH A 2 1702 15 HOH HOH . 
N 5 HOH A 3 1703 157 HOH HOH . 
N 5 HOH A 4 1704 50 HOH HOH . 
N 5 HOH A 5 1705 61 HOH HOH . 
N 5 HOH A 6 1706 121 HOH HOH . 
N 5 HOH A 7 1707 71 HOH HOH . 
N 5 HOH A 8 1708 91 HOH HOH . 
N 5 HOH A 9 1709 48 HOH HOH . 
N 5 HOH A 10 1710 154 HOH HOH . 
N 5 HOH A 11 1711 81 HOH HOH . 
N 5 HOH A 12 1712 106 HOH HOH . 
N 5 HOH A 13 1713 33 HOH HOH . 
N 5 HOH A 14 1714 28 HOH HOH . 
N 5 HOH A 15 1715 135 HOH HOH . 
N 5 HOH A 16 1716 24 HOH HOH . 
N 5 HOH A 17 1717 26 HOH HOH . 
N 5 HOH A 18 1718 22 HOH HOH . 
N 5 HOH A 19 1719 140 HOH HOH . 
N 5 HOH A 20 1720 85 HOH HOH . 
N 5 HOH A 21 1721 93 HOH HOH . 
N 5 HOH A 22 1722 17 HOH HOH . 
N 5 HOH A 23 1723 177 HOH HOH . 
N 5 HOH A 24 1724 172 HOH HOH . 
N 5 HOH A 25 1725 122 HOH HOH . 
N 5 HOH A 26 1726 54 HOH HOH . 
N 5 HOH A 27 1727 58 HOH HOH . 
N 5 HOH A 28 1728 51 HOH HOH . 
N 5 HOH A 29 1729 143 HOH HOH . 
N 5 HOH A 30 1730 188 HOH HOH . 
N 5 HOH A 31 1731 113 HOH HOH . 
N 5 HOH A 32 1732 180 HOH HOH . 
N 5 HOH A 33 1733 68 HOH HOH . 
N 5 HOH A 34 1734 88 HOH HOH . 
N 5 HOH A 35 1735 185 HOH HOH . 
N 5 HOH A 36 1736 168 HOH HOH . 
N 5 HOH A 37 1737 187 HOH HOH . 
O 5 HOH B 1 201 104 HOH HOH . 
P 5 HOH G 1 1701 79 HOH HOH . 
P 5 HOH G 2 1702 21 HOH HOH . 
P 5 HOH G 3 1703 16 HOH HOH . 
P 5 HOH G 4 1704 92 HOH HOH . 
P 5 HOH G 5 1705 77 HOH HOH . 
P 5 HOH G 6 1706 137 HOH HOH . 
P 5 HOH G 7 1707 19 HOH HOH . 
P 5 HOH G 8 1708 11 HOH HOH . 
P 5 HOH G 9 1709 161 HOH HOH . 
P 5 HOH G 10 1710 86 HOH HOH . 
P 5 HOH G 11 1711 43 HOH HOH . 
P 5 HOH G 12 1712 142 HOH HOH . 
P 5 HOH G 13 1713 41 HOH HOH . 
P 5 HOH G 14 1714 116 HOH HOH . 
P 5 HOH G 15 1715 72 HOH HOH . 
P 5 HOH G 16 1716 84 HOH HOH . 
P 5 HOH G 17 1717 175 HOH HOH . 
P 5 HOH G 18 1718 73 HOH HOH . 
P 5 HOH G 19 1719 114 HOH HOH . 
P 5 HOH G 20 1720 70 HOH HOH . 
P 5 HOH G 21 1721 25 HOH HOH . 
P 5 HOH G 22 1722 5 HOH HOH . 
P 5 HOH G 23 1723 32 HOH HOH . 
P 5 HOH G 24 1724 49 HOH HOH . 
P 5 HOH G 25 1725 8 HOH HOH . 
P 5 HOH G 26 1726 166 HOH HOH . 
P 5 HOH G 27 1727 136 HOH HOH . 
P 5 HOH G 28 1728 181 HOH HOH . 
P 5 HOH G 29 1729 75 HOH HOH . 
P 5 HOH G 30 1730 63 HOH HOH . 
P 5 HOH G 31 1731 20 HOH HOH . 
P 5 HOH G 32 1732 133 HOH HOH . 
P 5 HOH G 33 1733 90 HOH HOH . 
P 5 HOH G 34 1734 74 HOH HOH . 
P 5 HOH G 35 1735 119 HOH HOH . 
P 5 HOH G 36 1736 36 HOH HOH . 
P 5 HOH G 37 1737 123 HOH HOH . 
P 5 HOH G 38 1738 62 HOH HOH . 
P 5 HOH G 39 1739 155 HOH HOH . 
P 5 HOH G 40 1740 29 HOH HOH . 
P 5 HOH G 41 1741 124 HOH HOH . 
P 5 HOH G 42 1742 1 HOH HOH . 
P 5 HOH G 43 1743 97 HOH HOH . 
P 5 HOH G 44 1744 69 HOH HOH . 
P 5 HOH G 45 1745 193 HOH HOH . 
P 5 HOH G 46 1746 64 HOH HOH . 
P 5 HOH G 47 1747 186 HOH HOH . 
P 5 HOH G 48 1748 141 HOH HOH . 
P 5 HOH G 49 1749 98 HOH HOH . 
P 5 HOH G 50 1750 184 HOH HOH . 
P 5 HOH G 51 1751 162 HOH HOH . 
P 5 HOH G 52 1752 152 HOH HOH . 
P 5 HOH G 53 1753 145 HOH HOH . 
P 5 HOH G 54 1754 158 HOH HOH . 
P 5 HOH G 55 1755 127 HOH HOH . 
P 5 HOH G 56 1756 99 HOH HOH . 
P 5 HOH G 57 1757 37 HOH HOH . 
P 5 HOH G 58 1758 134 HOH HOH . 
P 5 HOH G 59 1759 95 HOH HOH . 
P 5 HOH G 60 1760 170 HOH HOH . 
P 5 HOH G 61 1761 149 HOH HOH . 
P 5 HOH G 62 1762 153 HOH HOH . 
Q 5 HOH H 1 201 102 HOH HOH . 
Q 5 HOH H 2 202 189 HOH HOH . 
R 5 HOH C 1 1701 159 HOH HOH . 
R 5 HOH C 2 1702 89 HOH HOH . 
R 5 HOH C 3 1703 100 HOH HOH . 
R 5 HOH C 4 1704 78 HOH HOH . 
R 5 HOH C 5 1705 27 HOH HOH . 
R 5 HOH C 6 1706 13 HOH HOH . 
R 5 HOH C 7 1707 34 HOH HOH . 
R 5 HOH C 8 1708 46 HOH HOH . 
R 5 HOH C 9 1709 18 HOH HOH . 
R 5 HOH C 10 1710 118 HOH HOH . 
R 5 HOH C 11 1711 39 HOH HOH . 
R 5 HOH C 12 1712 52 HOH HOH . 
R 5 HOH C 13 1713 164 HOH HOH . 
R 5 HOH C 14 1714 53 HOH HOH . 
R 5 HOH C 15 1715 76 HOH HOH . 
R 5 HOH C 16 1716 47 HOH HOH . 
R 5 HOH C 17 1717 111 HOH HOH . 
R 5 HOH C 18 1718 148 HOH HOH . 
R 5 HOH C 19 1719 115 HOH HOH . 
R 5 HOH C 20 1720 131 HOH HOH . 
R 5 HOH C 21 1721 67 HOH HOH . 
R 5 HOH C 22 1722 9 HOH HOH . 
R 5 HOH C 23 1723 83 HOH HOH . 
R 5 HOH C 24 1724 109 HOH HOH . 
R 5 HOH C 25 1725 190 HOH HOH . 
R 5 HOH C 26 1726 163 HOH HOH . 
S 5 HOH D 1 201 138 HOH HOH . 
T 5 HOH E 1 1701 96 HOH HOH . 
T 5 HOH E 2 1702 23 HOH HOH . 
T 5 HOH E 3 1703 108 HOH HOH . 
T 5 HOH E 4 1704 151 HOH HOH . 
T 5 HOH E 5 1705 107 HOH HOH . 
T 5 HOH E 6 1706 12 HOH HOH . 
T 5 HOH E 7 1707 38 HOH HOH . 
T 5 HOH E 8 1708 129 HOH HOH . 
T 5 HOH E 9 1709 57 HOH HOH . 
T 5 HOH E 10 1710 31 HOH HOH . 
T 5 HOH E 11 1711 14 HOH HOH . 
T 5 HOH E 12 1712 112 HOH HOH . 
T 5 HOH E 13 1713 56 HOH HOH . 
T 5 HOH E 14 1714 42 HOH HOH . 
T 5 HOH E 15 1715 65 HOH HOH . 
T 5 HOH E 16 1716 126 HOH HOH . 
T 5 HOH E 17 1717 87 HOH HOH . 
T 5 HOH E 18 1718 60 HOH HOH . 
T 5 HOH E 19 1719 45 HOH HOH . 
T 5 HOH E 20 1720 30 HOH HOH . 
T 5 HOH E 21 1721 167 HOH HOH . 
T 5 HOH E 22 1722 128 HOH HOH . 
T 5 HOH E 23 1723 146 HOH HOH . 
T 5 HOH E 24 1724 66 HOH HOH . 
T 5 HOH E 25 1725 59 HOH HOH . 
T 5 HOH E 26 1726 174 HOH HOH . 
T 5 HOH E 27 1727 144 HOH HOH . 
T 5 HOH E 28 1728 160 HOH HOH . 
T 5 HOH E 29 1729 40 HOH HOH . 
T 5 HOH E 30 1730 7 HOH HOH . 
T 5 HOH E 31 1731 105 HOH HOH . 
T 5 HOH E 32 1732 103 HOH HOH . 
T 5 HOH E 33 1733 44 HOH HOH . 
T 5 HOH E 34 1734 156 HOH HOH . 
T 5 HOH E 35 1735 82 HOH HOH . 
T 5 HOH E 36 1736 147 HOH HOH . 
T 5 HOH E 37 1737 2 HOH HOH . 
T 5 HOH E 38 1738 192 HOH HOH . 
T 5 HOH E 39 1739 80 HOH HOH . 
T 5 HOH E 40 1740 101 HOH HOH . 
T 5 HOH E 41 1741 182 HOH HOH . 
T 5 HOH E 42 1742 117 HOH HOH . 
T 5 HOH E 43 1743 169 HOH HOH . 
T 5 HOH E 44 1744 94 HOH HOH . 
T 5 HOH E 45 1745 35 HOH HOH . 
T 5 HOH E 46 1746 55 HOH HOH . 
T 5 HOH E 47 1747 191 HOH HOH . 
U 5 HOH F 1 201 194 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 3 -9.53 15.22 -24.17 1 34.74 ? C1 MPD 1601 E 1 
HETATM 2 C C2 MPD . . . M 3 -8.937 16.526 -24.643 1 46.78 ? C2 MPD 1601 E 1 
HETATM 3 O O2 MPD . . . M 3 -9.527 17.586 -23.849 1 49.35 ? O2 MPD 1601 E 1 
HETATM 4 C CM MPD . . . M 3 -7.435 16.475 -24.379 1 49.48 ? CM MPD 1601 E 1 
HETATM 5 C C3 MPD . . . M 3 -9.268 16.793 -26.114 1 49.01 ? C3 MPD 1601 E 1 
HETATM 6 C C4 MPD . . . M 3 -8.634 15.809 -27.091 1 46.04 ? C4 MPD 1601 E 1 
HETATM 7 O O4 MPD . . . M 3 -9.364 14.604 -27.105 1 41.71 ? O4 MPD 1601 E 1 
HETATM 8 C C5 MPD . . . M 3 -8.636 16.394 -28.499 1 38.3 ? C5 MPD 1601 E 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           8 
#