data_8AYP
#
_model_server_result.job_id            H5UIJQjwzTiIYMC17Ul2GQ 
_model_server_result.datetime_utc      '2025-09-04 15:23:55' 
_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          8ayp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":206}' 
#
_entry.id    8AYP 
#
_exptl.entry_id    8AYP 
_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    29 
_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            8AYP 
_cell.length_a            68.171 
_cell.length_b            177.495 
_cell.length_c            68.042 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8AYP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    'C 2c 2' 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
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,D,E,F,G,H,I,J,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,SA 1 1,2 
B,C,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,QA,RA 2 1,3 
#
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_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -34.021 
3 'crystal symmetry operation' 3_455 -x-1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 -68.171 0 34.021 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 F N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 Q N N 
? 2 R N N 
? 2 S N N 
? 2 V N N 
? 2 W N N 
? 2 X N N 
? 2 Y N N 
? 2 Z N N 
? 2 AA N N 
? 2 BA N N 
? 2 CA N N 
? 2 FA N N 
? 2 GA N N 
? 2 HA N N 
? 2 IA N N 
? 2 JA N N 
? 2 KA N N 
? 2 LA N N 
? 2 MA N N 
? 2 NA N N 
? 2 OA 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 O THR 46 A THR 63 1_555 G RB RB . A RB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? 
metalc ? metalc2 A OG1 THR 46 A THR 63 1_555 G RB RB . A RB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.739 ? 
metalc ? metalc3 A O THR 46 A THR 63 1_555 G RB RB . A RB 203 3_554 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? 
metalc ? metalc4 A OG1 THR 46 A THR 63 1_555 G RB RB . A RB 203 3_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.738 ? 
metalc ? metalc5 A O THR 46 A THR 63 1_555 H RB RB . A RB 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? 
metalc ? metalc6 A O THR 46 A THR 63 1_555 H RB RB . A RB 204 3_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? 
metalc ? metalc7 A O VAL 47 A VAL 64 1_555 H RB RB . A RB 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.886 ? 
metalc ? metalc8 A O VAL 47 A VAL 64 1_555 H RB RB . A RB 204 3_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.883 ? 
metalc ? metalc9 G RB RB . A RB 203 1_555 D OG1 THR 46 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? 
metalc ? metalc10 G RB RB . A RB 203 3_554 D OG1 THR 46 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? 
metalc ? metalc11 H RB RB . A RB 204 1_555 D O THR 46 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.792 ? 
metalc ? metalc12 H RB RB . A RB 204 3_554 D O THR 46 B THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? 
metalc ? metalc13 H RB RB . A RB 204 1_555 D O VAL 47 B VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? 
metalc ? metalc14 H RB RB . A RB 204 3_554 D O VAL 47 B VAL 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.852 ? 
metalc ? metalc15 I BA BA . A BA 205 1_555 SA O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? 
metalc ? metalc16 I BA BA . A BA 205 1_555 SA O HOH . B HOH 302 3_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? 
metalc ? metalc17 J BA BA . A BA 206 1_555 PA O HOH . A HOH 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? 
metalc ? metalc18 J BA BA . A BA 206 1_555 PA O HOH . A HOH 320 3_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? 
metalc ? metalc19 B O THR 46 C THR 63 1_555 T RB RB . C RB 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.081 ? 
metalc ? metalc20 B OG1 THR 46 C THR 63 1_555 T RB RB . C RB 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? 
metalc ? metalc21 B O THR 46 C THR 63 1_555 T RB RB . C RB 210 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 3.081 ? 
metalc ? metalc22 B OG1 THR 46 C THR 63 1_555 T RB RB . C RB 210 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? 
metalc ? metalc23 B O THR 46 C THR 63 1_555 DA RB RB . D RB 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.113 ? 
metalc ? metalc24 B O THR 46 C THR 63 1_555 DA RB RB . D RB 209 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? 
metalc ? metalc25 B O VAL 47 C VAL 64 1_555 DA RB RB . D RB 209 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? 
metalc ? metalc26 T RB RB . C RB 210 1_555 C O THR 46 D THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? 
metalc ? metalc27 T RB RB . C RB 210 1_555 C OG1 THR 46 D THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? 
metalc ? metalc28 T RB RB . C RB 210 3_455 C O THR 46 D THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? 
metalc ? metalc29 T RB RB . C RB 210 3_455 C OG1 THR 46 D THR 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.815 ? 
metalc ? metalc30 QA O HOH . C HOH 302 1_555 EA BA BA . D BA 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? 
metalc ? metalc31 QA O HOH . C HOH 302 3_455 EA BA BA . D BA 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? 
metalc ? metalc32 C O THR 46 D THR 63 1_555 DA RB RB . D RB 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc33 C O VAL 47 D VAL 64 1_555 DA RB RB . D RB 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
metalc ? metalc34 C O VAL 47 D VAL 64 1_555 DA RB RB . D RB 209 3_455 ? ? ? ? ? ? ? ? ? ? ? ? 3.128 ? 
#
_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                     8AYP 
_atom_sites.fract_transf_matrix[1][1]    0.014669 
_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]    0.005634 
_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]    0.014697 
_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
E 2 MPD A 1 201 1 MPD MPD . 
F 2 MPD A 1 202 2 MPD MPD . 
G 3 RB A 1 203 1 RB RB . 
H 3 RB A 1 204 2 RB RB . 
I 4 BA A 1 205 1 BA BA . 
J 4 BA A 1 206 2 BA BA . 
K 2 MPD C 1 201 3 MPD MPD . 
L 2 MPD C 1 202 7 MPD MPD . 
M 2 MPD C 1 203 8 MPD MPD . 
N 2 MPD C 1 204 14 MPD MPD . 
O 2 MPD C 1 205 17 MPD MPD . 
P 2 MPD C 1 206 19 MPD MPD . 
Q 2 MPD C 1 207 20 MPD MPD . 
R 2 MPD C 1 208 23 MPD MPD . 
S 2 MPD C 1 209 28 MPD MPD . 
T 3 RB C 1 210 3 RB RB . 
U 4 BA C 1 211 4 BA BA . 
V 2 MPD D 1 201 9 MPD MPD . 
W 2 MPD D 1 202 10 MPD MPD . 
X 2 MPD D 1 203 11 MPD MPD . 
Y 2 MPD D 1 204 12 MPD MPD . 
Z 2 MPD D 1 205 13 MPD MPD . 
AA 2 MPD D 1 206 16 MPD MPD . 
BA 2 MPD D 1 207 18 MPD MPD . 
CA 2 MPD D 1 208 25 MPD MPD . 
DA 3 RB D 1 209 4 RB RB . 
EA 4 BA D 1 210 3 BA BA . 
FA 2 MPD B 1 201 4 MPD MPD . 
GA 2 MPD B 1 202 5 MPD MPD . 
HA 2 MPD B 1 203 6 MPD MPD . 
IA 2 MPD B 1 204 15 MPD MPD . 
JA 2 MPD B 1 205 22 MPD MPD . 
KA 2 MPD B 1 206 24 MPD MPD . 
LA 2 MPD B 1 207 26 MPD MPD . 
MA 2 MPD B 1 208 27 MPD MPD . 
NA 2 MPD B 1 209 29 MPD MPD . 
OA 2 MPD B 1 210 30 MPD MPD . 
PA 5 HOH A 1 301 11 HOH HOH . 
PA 5 HOH A 2 302 12 HOH HOH . 
PA 5 HOH A 3 303 6 HOH HOH . 
PA 5 HOH A 4 304 14 HOH HOH . 
PA 5 HOH A 5 305 13 HOH HOH . 
PA 5 HOH A 6 306 9 HOH HOH . 
PA 5 HOH A 7 307 41 HOH HOH . 
PA 5 HOH A 8 308 2 HOH HOH . 
PA 5 HOH A 9 309 39 HOH HOH . 
PA 5 HOH A 10 310 16 HOH HOH . 
PA 5 HOH A 11 311 36 HOH HOH . 
PA 5 HOH A 12 312 10 HOH HOH . 
PA 5 HOH A 13 313 21 HOH HOH . 
PA 5 HOH A 14 314 30 HOH HOH . 
PA 5 HOH A 15 315 27 HOH HOH . 
PA 5 HOH A 16 316 68 HOH HOH . 
PA 5 HOH A 17 317 69 HOH HOH . 
PA 5 HOH A 18 318 75 HOH HOH . 
PA 5 HOH A 19 319 31 HOH HOH . 
PA 5 HOH A 20 320 59 HOH HOH . 
QA 5 HOH C 1 301 79 HOH HOH . 
QA 5 HOH C 2 302 50 HOH HOH . 
QA 5 HOH C 3 303 4 HOH HOH . 
QA 5 HOH C 4 304 17 HOH HOH . 
QA 5 HOH C 5 305 77 HOH HOH . 
QA 5 HOH C 6 306 3 HOH HOH . 
QA 5 HOH C 7 307 37 HOH HOH . 
QA 5 HOH C 8 308 67 HOH HOH . 
QA 5 HOH C 9 309 51 HOH HOH . 
QA 5 HOH C 10 310 58 HOH HOH . 
QA 5 HOH C 11 311 52 HOH HOH . 
QA 5 HOH C 12 312 33 HOH HOH . 
RA 5 HOH D 1 301 55 HOH HOH . 
RA 5 HOH D 2 302 1 HOH HOH . 
RA 5 HOH D 3 303 54 HOH HOH . 
RA 5 HOH D 4 304 8 HOH HOH . 
RA 5 HOH D 5 305 19 HOH HOH . 
RA 5 HOH D 6 306 48 HOH HOH . 
RA 5 HOH D 7 307 29 HOH HOH . 
RA 5 HOH D 8 308 70 HOH HOH . 
RA 5 HOH D 9 309 63 HOH HOH . 
RA 5 HOH D 10 310 46 HOH HOH . 
RA 5 HOH D 11 311 66 HOH HOH . 
RA 5 HOH D 12 312 60 HOH HOH . 
RA 5 HOH D 13 313 53 HOH HOH . 
RA 5 HOH D 14 314 34 HOH HOH . 
RA 5 HOH D 15 315 61 HOH HOH . 
RA 5 HOH D 16 316 56 HOH HOH . 
RA 5 HOH D 17 317 45 HOH HOH . 
RA 5 HOH D 18 318 64 HOH HOH . 
RA 5 HOH D 19 319 42 HOH HOH . 
RA 5 HOH D 20 320 65 HOH HOH . 
SA 5 HOH B 1 301 5 HOH HOH . 
SA 5 HOH B 2 302 76 HOH HOH . 
SA 5 HOH B 3 303 7 HOH HOH . 
SA 5 HOH B 4 304 20 HOH HOH . 
SA 5 HOH B 5 305 15 HOH HOH . 
SA 5 HOH B 6 306 22 HOH HOH . 
SA 5 HOH B 7 307 71 HOH HOH . 
SA 5 HOH B 8 308 74 HOH HOH . 
SA 5 HOH B 9 309 18 HOH HOH . 
SA 5 HOH B 10 310 28 HOH HOH . 
SA 5 HOH B 11 311 72 HOH HOH . 
SA 5 HOH B 12 312 32 HOH HOH . 
SA 5 HOH B 13 313 24 HOH HOH . 
SA 5 HOH B 14 314 73 HOH HOH . 
SA 5 HOH B 15 315 26 HOH HOH . 
SA 5 HOH B 16 316 47 HOH HOH . 
SA 5 HOH B 17 317 23 HOH HOH . 
SA 5 HOH B 18 318 57 HOH HOH . 
SA 5 HOH B 19 319 25 HOH HOH . 
SA 5 HOH B 20 320 78 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 . . . P 2 -20.625 -45.916 10.49 1 69.46 ? C1 MPD 206 C 1 
HETATM 2 C C2 MPD . . . P 2 -19.669 -45.218 9.513 1 75.97 ? C2 MPD 206 C 1 
HETATM 3 O O2 MPD . . . P 2 -20.058 -43.881 9.438 1 79.99 ? O2 MPD 206 C 1 
HETATM 4 C CM MPD . . . P 2 -19.752 -45.91 8.147 1 73.6 ? CM MPD 206 C 1 
HETATM 5 C C3 MPD . . . P 2 -18.241 -45.384 10.032 1 71.98 ? C3 MPD 206 C 1 
HETATM 6 C C4 MPD . . . P 2 -17.257 -44.675 9.098 1 74.55 ? C4 MPD 206 C 1 
HETATM 7 O O4 MPD . . . P 2 -17.308 -43.287 9.216 1 71.54 ? O4 MPD 206 C 1 
HETATM 8 C C5 MPD . . . P 2 -15.865 -45.225 9.387 1 76.5 ? C5 MPD 206 C 1 
#
_model_server_stats.io_time_ms              75 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           251 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           8 
#