data_6DK4
#
_model_server_result.job_id            u5bO_iLAzvz1wajidmeADQ 
_model_server_result.datetime_utc      '2024-10-20 03:24:02' 
_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          6dk4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":206}' 
#
_entry.id    6DK4 
#
_exptl.entry_id    6DK4 
_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            (4S)-2-METHYL-2,4-PENTANEDIOL 
_entity.pdbx_number_of_molecules    4 
_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            6DK4 
_cell.length_a            48.11 
_cell.length_b            70.186 
_cell.length_c            85.158 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6DK4 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
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,K 1 1 
B,I,J,L 1 2 
#
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_545 -x,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 -35.093 42.579 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 E N N 
? 4 F N N 
? 4 G N N 
? 4 H 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 NE2 HIS 30 A HIS 30 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc2 A OD2 ASP 78 A ASP 78 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc3 A NE2 HIS 84 A HIS 84 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc4 A NE2 HIS 86 A HIS 86 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? 
metalc ? metalc5 A SG CYS 89 A CYS 89 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? 
metalc ? metalc6 A SG CYS 92 A CYS 92 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc7 A OD1 ASP 97 A ASP 97 1_555 C MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc8 A SG CYS 132 A CYS 132 1_555 D ZN ZN . A ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.835 ? 
metalc ? metalc9 B NE2 HIS 30 B HIS 30 1_555 I MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc10 B OD2 ASP 78 B ASP 78 1_555 I MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? 
metalc ? metalc11 B NE2 HIS 84 B HIS 84 1_555 I MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc12 B NE2 HIS 86 B HIS 86 1_555 I MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? 
metalc ? metalc13 B SG CYS 89 B CYS 89 1_555 J ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? 
metalc ? metalc14 B SG CYS 92 B CYS 92 1_555 J ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? 
metalc ? metalc15 B OD1 ASP 97 B ASP 97 1_555 I MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
metalc ? metalc16 B SG CYS 132 B CYS 132 1_555 J ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc17 B SG CYS 135 B CYS 135 1_555 J ZN ZN . B ZN 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
#
_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                     6DK4 
_atom_sites.fract_transf_matrix[1][1]    0.020786 
_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]    0.014248 
_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]    0.011743 
_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 MN A 1 201 1 MN MN . 
D 3 ZN A 1 202 2 ZN ZN . 
E 4 MPD A 1 203 1 MPD MPD . 
F 4 MPD A 1 204 2 MPD MPD . 
G 4 MPD A 1 205 3 MPD MPD . 
H 4 MPD A 1 206 4 MPD MPD . 
I 2 MN B 1 201 2 MN MN . 
J 3 ZN B 1 202 1 ZN ZN . 
K 5 HOH A 1 301 4 HOH HOH . 
K 5 HOH A 2 302 40 HOH HOH . 
K 5 HOH A 3 303 31 HOH HOH . 
K 5 HOH A 4 304 35 HOH HOH . 
K 5 HOH A 5 305 11 HOH HOH . 
K 5 HOH A 6 306 7 HOH HOH . 
K 5 HOH A 7 307 6 HOH HOH . 
K 5 HOH A 8 308 5 HOH HOH . 
K 5 HOH A 9 309 36 HOH HOH . 
K 5 HOH A 10 310 10 HOH HOH . 
K 5 HOH A 11 311 23 HOH HOH . 
K 5 HOH A 12 312 12 HOH HOH . 
K 5 HOH A 13 313 30 HOH HOH . 
K 5 HOH A 14 314 38 HOH HOH . 
L 5 HOH B 1 301 20 HOH HOH . 
L 5 HOH B 2 302 22 HOH HOH . 
L 5 HOH B 3 303 9 HOH HOH . 
L 5 HOH B 4 304 27 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 . . . H 4 -12.202 -39.595 18.41 1 78.41 ? C1 MPD 206 A 1 
HETATM 2 C C2 MPD . . . H 4 -11.325 -38.827 19.398 1 77.36 ? C2 MPD 206 A 1 
HETATM 3 O O2 MPD . . . H 4 -12.186 -38.19 20.359 1 79.94 ? O2 MPD 206 A 1 
HETATM 4 C CM MPD . . . H 4 -10.448 -39.778 20.182 1 75.42 ? CM MPD 206 A 1 
HETATM 5 C C3 MPD . . . H 4 -10.393 -37.816 18.67 1 77.71 ? C3 MPD 206 A 1 
HETATM 6 C C4 MPD . . . H 4 -11.011 -36.44 18.299 1 78.1 ? C4 MPD 206 A 1 
HETATM 7 O O4 MPD . . . H 4 -10.405 -35.411 19.088 1 77.33 ? O4 MPD 206 A 1 
HETATM 8 C C5 MPD . . . H 4 -10.811 -36.131 16.834 1 78.55 ? C5 MPD 206 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           8 
#