data_5WX2
#
_model_server_result.job_id            mQOBncqLgnwiHQwVtpiX1A 
_model_server_result.datetime_utc      '2024-11-14 07:17:54' 
_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          5wx2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"NA","auth_seq_id":404}' 
#
_entry.id    5WX2 
#
_exptl.entry_id    5WX2 
_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    22 
_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            5WX2 
_cell.length_a            168.402 
_cell.length_b            270.896 
_cell.length_c            135.429 
_cell.Z_PDB               64 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5WX2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_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 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,K,L,M,N,O,P,Q,R,S,SA,TA 1 1 
C,D,T,U,V,W,X,Y,Z,AA,UA,VA 2 1 
E,F,BA,CA,DA,EA,FA,GA,HA,IA,JA,WA,XA 3 1 
G,H,KA,LA,MA,NA,OA,PA,QA,RA,YA,ZA 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 J N N 
? 3 K N N 
? 3 L N N 
? 3 M N N 
? 3 P N N 
? 3 Q N N 
? 3 R N N 
? 3 S N N 
? 3 U N N 
? 3 X N N 
? 3 Y N N 
? 3 Z N N 
? 3 CA N N 
? 3 FA N N 
? 3 GA N N 
? 3 HA N N 
? 3 IA N N 
? 3 LA N N 
? 3 MA N N 
? 3 NA N N 
? 3 PA N N 
? 3 QA N N 
#
_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 328 n n 
C1 H11 MPD sing 329 n n 
C1 H12 MPD sing 330 n n 
C1 H13 MPD sing 331 n n 
C2 O2 MPD sing 332 n n 
C2 CM MPD sing 333 n n 
C2 C3 MPD sing 334 n n 
O2 HO2 MPD sing 335 n n 
CM HM1 MPD sing 336 n n 
CM HM2 MPD sing 337 n n 
CM HM3 MPD sing 338 n n 
C3 C4 MPD sing 339 n n 
C3 H31 MPD sing 340 n n 
C3 H32 MPD sing 341 n n 
C4 O4 MPD sing 342 n n 
C4 C5 MPD sing 343 n n 
C4 H4 MPD sing 344 n n 
O4 HO4 MPD sing 345 n n 
C5 H51 MPD sing 346 n n 
C5 H52 MPD sing 347 n n 
C5 H53 MPD sing 348 n n 
#
_atom_sites.entry_id                     5WX2 
_atom_sites.fract_transf_matrix[1][1]    0.005938 
_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]    0.003691 
_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]    0.007384 
_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 2 FAD A 1 401 401 FAD FAD . 
J 3 MPD A 1 402 402 MPD MPD . 
K 3 MPD A 1 403 411 MPD MPD . 
L 3 MPD A 1 404 412 MPD MPD . 
M 3 MPD A 1 405 417 MPD MPD . 
N 4 SO4 A 1 406 420 SO4 SO4 . 
O 2 FAD B 1 401 401 FAD FAD . 
P 3 MPD B 1 402 402 MPD MPD . 
Q 3 MPD B 1 403 412 MPD MPD . 
R 3 MPD B 1 404 413 MPD MPD . 
S 3 MPD B 1 405 414 MPD MPD . 
T 2 FAD C 1 401 401 FAD FAD . 
U 3 MPD C 1 402 412 MPD MPD . 
V 4 SO4 C 1 403 420 SO4 SO4 . 
W 2 FAD D 1 401 401 FAD FAD . 
X 3 MPD D 1 402 402 MPD MPD . 
Y 3 MPD D 1 403 411 MPD MPD . 
Z 3 MPD D 1 404 414 MPD MPD . 
AA 4 SO4 D 1 405 420 SO4 SO4 . 
BA 2 FAD E 1 401 401 FAD FAD . 
CA 3 MPD E 1 402 402 MPD MPD . 
DA 4 SO4 E 1 403 420 SO4 SO4 . 
EA 2 FAD F 1 401 401 FAD FAD . 
FA 3 MPD F 1 402 412 MPD MPD . 
GA 3 MPD F 1 403 411 MPD MPD . 
HA 3 MPD F 1 404 412 MPD MPD . 
IA 3 MPD F 1 405 413 MPD MPD . 
JA 4 SO4 F 1 406 420 SO4 SO4 . 
KA 2 FAD G 1 401 401 FAD FAD . 
LA 3 MPD G 1 402 402 MPD MPD . 
MA 3 MPD G 1 403 411 MPD MPD . 
NA 3 MPD G 1 404 412 MPD MPD . 
OA 2 FAD H 1 401 401 FAD FAD . 
PA 3 MPD H 1 402 411 MPD MPD . 
QA 3 MPD H 1 403 412 MPD MPD . 
RA 4 SO4 H 1 404 420 SO4 SO4 . 
SA 5 HOH A 1 501 514 HOH HOH . 
SA 5 HOH A 2 502 505 HOH HOH . 
SA 5 HOH A 3 503 513 HOH HOH . 
SA 5 HOH A 4 504 516 HOH HOH . 
SA 5 HOH A 5 505 503 HOH HOH . 
SA 5 HOH A 6 506 509 HOH HOH . 
SA 5 HOH A 7 507 502 HOH HOH . 
SA 5 HOH A 8 508 515 HOH HOH . 
SA 5 HOH A 9 509 508 HOH HOH . 
SA 5 HOH A 10 510 512 HOH HOH . 
SA 5 HOH A 11 511 501 HOH HOH . 
SA 5 HOH A 12 512 519 HOH HOH . 
SA 5 HOH A 13 513 506 HOH HOH . 
SA 5 HOH A 14 514 510 HOH HOH . 
SA 5 HOH A 15 515 520 HOH HOH . 
SA 5 HOH A 16 516 511 HOH HOH . 
SA 5 HOH A 17 517 517 HOH HOH . 
SA 5 HOH A 18 518 504 HOH HOH . 
TA 5 HOH B 1 501 504 HOH HOH . 
TA 5 HOH B 2 502 505 HOH HOH . 
TA 5 HOH B 3 503 518 HOH HOH . 
TA 5 HOH B 4 504 515 HOH HOH . 
TA 5 HOH B 5 505 511 HOH HOH . 
TA 5 HOH B 6 506 510 HOH HOH . 
TA 5 HOH B 7 507 513 HOH HOH . 
TA 5 HOH B 8 508 508 HOH HOH . 
TA 5 HOH B 9 509 501 HOH HOH . 
TA 5 HOH B 10 510 514 HOH HOH . 
TA 5 HOH B 11 511 512 HOH HOH . 
TA 5 HOH B 12 512 516 HOH HOH . 
TA 5 HOH B 13 513 506 HOH HOH . 
TA 5 HOH B 14 514 520 HOH HOH . 
TA 5 HOH B 15 515 509 HOH HOH . 
TA 5 HOH B 16 516 518 HOH HOH . 
TA 5 HOH B 17 517 517 HOH HOH . 
TA 5 HOH B 18 518 502 HOH HOH . 
TA 5 HOH B 19 519 507 HOH HOH . 
TA 5 HOH B 20 520 519 HOH HOH . 
TA 5 HOH B 21 521 507 HOH HOH . 
TA 5 HOH B 22 522 503 HOH HOH . 
UA 5 HOH C 1 501 504 HOH HOH . 
UA 5 HOH C 2 502 501 HOH HOH . 
UA 5 HOH C 3 503 503 HOH HOH . 
UA 5 HOH C 4 504 402 HOH HOH . 
UA 5 HOH C 5 505 502 HOH HOH . 
VA 5 HOH D 1 501 501 HOH HOH . 
VA 5 HOH D 2 502 505 HOH HOH . 
VA 5 HOH D 3 503 502 HOH HOH . 
VA 5 HOH D 4 504 504 HOH HOH . 
VA 5 HOH D 5 505 508 HOH HOH . 
VA 5 HOH D 6 506 506 HOH HOH . 
VA 5 HOH D 7 507 507 HOH HOH . 
VA 5 HOH D 8 508 510 HOH HOH . 
VA 5 HOH D 9 509 503 HOH HOH . 
VA 5 HOH D 10 510 509 HOH HOH . 
WA 5 HOH E 1 501 501 HOH HOH . 
WA 5 HOH E 2 502 504 HOH HOH . 
WA 5 HOH E 3 503 502 HOH HOH . 
WA 5 HOH E 4 504 503 HOH HOH . 
XA 5 HOH F 1 501 501 HOH HOH . 
XA 5 HOH F 2 502 402 HOH HOH . 
YA 5 HOH G 1 501 503 HOH HOH . 
YA 5 HOH G 2 502 504 HOH HOH . 
YA 5 HOH G 3 503 501 HOH HOH . 
YA 5 HOH G 4 504 502 HOH HOH . 
ZA 5 HOH H 1 501 501 HOH HOH . 
ZA 5 HOH H 2 502 502 HOH HOH . 
ZA 5 HOH H 3 503 504 HOH HOH . 
ZA 5 HOH H 4 504 503 HOH HOH . 
ZA 5 HOH H 5 505 402 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 . . . NA 3 90.663 -12.385 12.005 1 92.57 ? C1 MPD 404 G 1 
HETATM 2 C C2 MPD . . . NA 3 91.123 -13.564 11.143 1 91.35 ? C2 MPD 404 G 1 
HETATM 3 O O2 MPD . . . NA 3 89.976 -14.284 10.681 1 83.51 ? O2 MPD 404 G 1 
HETATM 4 C CM MPD . . . NA 3 91.916 -13.012 9.967 1 90.12 ? CM MPD 404 G 1 
HETATM 5 C C3 MPD . . . NA 3 91.984 -14.589 11.878 1 91.34 ? C3 MPD 404 G 1 
HETATM 6 C C4 MPD . . . NA 3 91.388 -15.035 13.223 1 93.71 ? C4 MPD 404 G 1 
HETATM 7 O O4 MPD . . . NA 3 91.596 -16.439 13.453 1 89.81 ? O4 MPD 404 G 1 
HETATM 8 C C5 MPD . . . NA 3 91.969 -14.233 14.388 1 93.88 ? C5 MPD 404 G 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    34 
_model_server_stats.query_time_ms           288 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           8 
#