data_6S53
#
_model_server_result.job_id            SaEyDxwwpWQZE2daVKJxOw 
_model_server_result.datetime_utc      '2024-12-21 16:22:10' 
_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          6s53 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":103}' 
#
_entry.id    6S53 
#
_exptl.entry_id    6S53 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         89.9 
_cell.angle_beta          89.05 
_cell.angle_gamma         88.7 
_cell.entry_id            6S53 
_cell.length_a            49.75 
_cell.length_b            83.31 
_cell.length_c            86.75 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6S53 
_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
? hexameric 6 author_defined_assembly 1 
? hexameric 6 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,M,N,O,P,Q,V,W,X 1 1 
G,H,I,J,K,L,R,S,T,U,Y 2 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             Q 
_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 E SG CYS 16 B CYS 16 1_555 M ZN ZN . B ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? 
metalc ? metalc2 E SG CYS 19 B CYS 19 1_555 M ZN ZN . B ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
metalc ? metalc3 E SG CYS 31 B CYS 31 1_555 N ZN ZN . B ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? 
metalc ? metalc4 E ND1 HIS 33 B HIS 33 1_555 N ZN ZN . B ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? 
metalc ? metalc5 E SG CYS 36 B CYS 36 1_555 M ZN ZN . B ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
metalc ? metalc6 E SG CYS 39 B CYS 39 1_555 M ZN ZN . B ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc7 E SG CYS 51 B CYS 51 1_555 N ZN ZN . B ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc8 E SG CYS 54 B CYS 54 1_555 N ZN ZN . B ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc9 F SG CYS 16 A CYS 16 1_555 O ZN ZN . A ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? 
metalc ? metalc10 F SG CYS 19 A CYS 19 1_555 O ZN ZN . A ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc11 F SG CYS 31 A CYS 31 1_555 P ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc12 F ND1 HIS 33 A HIS 33 1_555 P ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? 
metalc ? metalc13 F SG CYS 36 A CYS 36 1_555 O ZN ZN . A ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc14 F SG CYS 39 A CYS 39 1_555 O ZN ZN . A ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc15 F SG CYS 51 A CYS 51 1_555 P ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? 
metalc ? metalc16 F SG CYS 54 A CYS 54 1_555 P ZN ZN . A ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc17 K SG CYS 16 H CYS 16 1_555 S ZN ZN . H ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? 
metalc ? metalc18 K SG CYS 19 H CYS 19 1_555 S ZN ZN . H ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? 
metalc ? metalc19 K SG CYS 31 H CYS 31 1_555 R ZN ZN . H ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? 
metalc ? metalc20 K ND1 HIS 33 H HIS 33 1_555 R ZN ZN . H ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc21 K SG CYS 36 H CYS 36 1_555 S ZN ZN . H ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc22 K SG CYS 39 H CYS 39 1_555 S ZN ZN . H ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc23 K SG CYS 51 H CYS 51 1_555 R ZN ZN . H ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc24 K SG CYS 54 H CYS 54 1_555 R ZN ZN . H ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? 
metalc ? metalc25 L SG CYS 16 G CYS 16 1_555 U ZN ZN . G ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? 
metalc ? metalc26 L SG CYS 19 G CYS 19 1_555 U ZN ZN . G ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? 
metalc ? metalc27 L SG CYS 31 G CYS 31 1_555 T ZN ZN . G ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc28 L ND1 HIS 33 G HIS 33 1_555 T ZN ZN . G ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
metalc ? metalc29 L SG CYS 36 G CYS 36 1_555 U ZN ZN . G ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc30 L SG CYS 39 G CYS 39 1_555 U ZN ZN . G ZN 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc31 L SG CYS 51 G CYS 51 1_555 T ZN ZN . G ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc32 L SG CYS 54 G CYS 54 1_555 T ZN ZN . G ZN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? 
#
_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                     6S53 
_atom_sites.fract_transf_matrix[1][1]    0.020101 
_atom_sites.fract_transf_matrix[1][2]    -0.000455 
_atom_sites.fract_transf_matrix[1][3]    -0.000332 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012006 
_atom_sites.fract_transf_matrix[2][3]    -0.000017 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.011529 
_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
M 4 ZN B 1 101 86 ZN ZN . 
N 4 ZN B 1 102 87 ZN ZN . 
O 4 ZN A 1 101 86 ZN ZN . 
P 4 ZN A 1 102 87 ZN ZN . 
Q 5 MPD A 1 103 161 MPD MPD . 
R 4 ZN H 1 101 86 ZN ZN . 
S 4 ZN H 1 102 87 ZN ZN . 
T 4 ZN G 1 101 86 ZN ZN . 
U 4 ZN G 1 102 87 ZN ZN . 
V 6 HOH E 1 201 12 HOH HOH . 
V 6 HOH E 2 202 10 HOH HOH . 
W 6 HOH C 1 201 3 HOH HOH . 
W 6 HOH C 2 202 4 HOH HOH . 
X 6 HOH A 1 201 17 HOH HOH . 
Y 6 HOH K 1 201 16 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 . . . Q 5 0.297 -28.3 -54.034 1 103.72 ? C1 MPD 103 A 1 
HETATM 2 C C2 MPD . . . Q 5 -0.491 -28.173 -55.324 1 104.52 ? C2 MPD 103 A 1 
HETATM 3 O O2 MPD . . . Q 5 -0.755 -26.79 -55.47 1 118.46 ? O2 MPD 103 A 1 
HETATM 4 C CM MPD . . . Q 5 0.387 -28.541 -56.514 1 97.22 ? CM MPD 103 A 1 
HETATM 5 C C3 MPD . . . Q 5 -1.828 -28.963 -55.317 1 101.72 ? C3 MPD 103 A 1 
HETATM 6 C C4 MPD . . . Q 5 -2.874 -28.673 -54.204 1 97.26 ? C4 MPD 103 A 1 
HETATM 7 O O4 MPD . . . Q 5 -3.132 -27.282 -53.913 1 92.18 ? O4 MPD 103 A 1 
HETATM 8 C C5 MPD . . . Q 5 -4.234 -29.25 -54.585 1 93.64 ? C5 MPD 103 A 1 
#
_model_server_stats.io_time_ms              43 
_model_server_stats.parse_time_ms           55 
_model_server_stats.create_model_time_ms    43 
_model_server_stats.query_time_ms           1373 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           8 
#