data_6VYA
#
_model_server_result.job_id            koOPUjhQ4Gm0ziY9xV6iAw 
_model_server_result.datetime_utc      '2024-11-26 01:15:39' 
_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          6vya 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"HB","auth_seq_id":502}' 
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_entry.id    6VYA 
#
_exptl.entry_id    6VYA 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              262.158 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'DIMETHYLALLYL S-THIOLODIPHOSPHATE' 
_entity.pdbx_number_of_molecules    24 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         78.255 
_cell.angle_beta          65.051 
_cell.angle_gamma         66.396 
_cell.entry_id            6VYA 
_cell.length_a            157.893 
_cell.length_b            163.069 
_cell.length_c            167.857 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 6VYA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    'P 1' 
_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
? tetrameric 4 author_defined_assembly 1 
? tetrameric 4 author_defined_assembly 2 
? tetrameric 4 author_defined_assembly 3 
? tetrameric 4 author_defined_assembly 4 
? tetrameric 4 author_defined_assembly 5 
? tetrameric 4 author_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,D,E,Y,Z,AA,BA,EA,FA,GA,HA 1 1 
C,V,W,X,CA,DA,OB,PB,QB,RB,SB,TB 2 1 
F,G,H,I,IA,JA,KA,LA,MA,NA,OA,PA 3 1 
J,K,L,M,QA,RA,SA,TA,UA,VA,WA,XA 4 1 
N,O,P,Q,YA,ZA,AB,BB,CB,DB,EB,FB 5 1 
R,S,T,U,GB,HB,IB,JB,KB,LB,MB,NB 6 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 Z N N 
? 3 BA N N 
? 3 DA N N 
? 3 FA N N 
? 3 HA N N 
? 3 JA N N 
? 3 LA N N 
? 3 NA N N 
? 3 PA N N 
? 3 RA N N 
? 3 TA N N 
? 3 VA N N 
? 3 XA N N 
? 3 ZA N N 
? 3 BB N N 
? 3 DB N N 
? 3 FB N N 
? 3 HB N N 
? 3 JB N N 
? 3 LB N N 
? 3 NB N N 
? 3 PB N N 
? 3 RB N N 
? 3 TB N N 
#
_chem_comp.formula           'C5 H12 O6 P2 S' 
_chem_comp.formula_weight    262.158 
_chem_comp.id                DST 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'DIMETHYLALLYL S-THIOLODIPHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'DMASPP;DMAPP;DMADP;Dimethylallyl pyrophosphate;dimethylallyl diphosphate;isoprenyl pyrophosphate' 
#
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
O4 P1 DST sing 83 n n 
O4 HO4 DST sing 84 n n 
P1 O6 DST sing 85 n n 
P1 O5 DST doub 86 n n 
P1 O2 DST sing 87 n n 
O6 HO6 DST sing 88 n n 
O2 P3 DST sing 89 n n 
P3 O8 DST sing 90 n n 
P3 O7 DST doub 91 n n 
P3 S9 DST sing 92 n n 
O8 HO8 DST sing 93 n n 
S9 C10 DST sing 94 n n 
C10 C11 DST sing 95 n n 
C10 H101 DST sing 96 n n 
C10 H102 DST sing 97 n n 
C11 C12 DST doub 98 n n 
C11 H111 DST sing 99 n n 
C12 C13 DST sing 100 n n 
C12 C14 DST sing 101 n n 
C13 H131 DST sing 102 n n 
C13 H132 DST sing 103 n n 
C13 H133 DST sing 104 n n 
C14 H141 DST sing 105 n n 
C14 H142 DST sing 106 n n 
C14 H143 DST sing 107 n n 
#
_atom_sites.entry_id                     6VYA 
_atom_sites.fract_transf_matrix[1][1]    0.006333 
_atom_sites.fract_transf_matrix[1][2]    -0.002768 
_atom_sites.fract_transf_matrix[1][3]    -0.002833 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006692 
_atom_sites.fract_transf_matrix[2][3]    -0.000279 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.006576 
_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
Y 2 QRP C 1 501 501 QRP QRP . 
Z 3 DST C 1 502 601 DST DST . 
AA 2 QRP A 1 501 501 QRP QRP . 
BA 3 DST A 1 502 601 DST DST . 
CA 2 QRP V 1 501 501 QRP QRP . 
DA 3 DST V 1 502 601 DST DST . 
EA 2 QRP E 1 501 501 QRP QRP . 
FA 3 DST E 1 502 601 DST DST . 
GA 2 QRP G 1 501 501 QRP QRP . 
HA 3 DST G 1 502 601 DST DST . 
IA 2 QRP B 1 501 501 QRP QRP . 
JA 3 DST B 1 502 601 DST DST . 
KA 2 QRP D 1 501 501 QRP QRP . 
LA 3 DST D 1 502 601 DST DST . 
MA 2 QRP F 1 501 501 QRP QRP . 
NA 3 DST F 1 502 601 DST DST . 
OA 2 QRP H 1 501 501 QRP QRP . 
PA 3 DST H 1 502 601 DST DST . 
QA 2 QRP I 1 501 501 QRP QRP . 
RA 3 DST I 1 502 601 DST DST . 
SA 2 QRP J 1 501 501 QRP QRP . 
TA 3 DST J 1 502 601 DST DST . 
UA 2 QRP K 1 501 501 QRP QRP . 
VA 3 DST K 1 502 601 DST DST . 
WA 2 QRP L 1 501 501 QRP QRP . 
XA 3 DST L 1 502 601 DST DST . 
YA 2 QRP M 1 501 501 QRP QRP . 
ZA 3 DST M 1 502 601 DST DST . 
AB 2 QRP N 1 501 501 QRP QRP . 
BB 3 DST N 1 502 601 DST DST . 
CB 2 QRP O 1 501 501 QRP QRP . 
DB 3 DST O 1 502 601 DST DST . 
EB 2 QRP P 1 501 501 QRP QRP . 
FB 3 DST P 1 502 601 DST DST . 
GB 2 QRP Q 1 501 501 QRP QRP . 
HB 3 DST Q 1 502 601 DST DST . 
IB 2 QRP R 1 501 501 QRP QRP . 
JB 3 DST R 1 502 601 DST DST . 
KB 2 QRP S 1 501 501 QRP QRP . 
LB 3 DST S 1 502 601 DST DST . 
MB 2 QRP T 1 501 501 QRP QRP . 
NB 3 DST T 1 502 601 DST DST . 
OB 2 QRP U 1 501 501 QRP QRP . 
PB 3 DST U 1 502 601 DST DST . 
QB 2 QRP W 1 501 501 QRP QRP . 
RB 3 DST W 1 502 601 DST DST . 
SB 2 QRP X 1 501 501 QRP QRP . 
TB 3 DST X 1 502 601 DST DST . 
#
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 O O4 DST . . . HB 3 -24.016 56.24 -11.525 1 144.52 ? O4 DST 502 Q 1 
HETATM 2 P P1 DST . . . HB 3 -24.792 55.12 -10.968 1 156.96 ? P1 DST 502 Q 1 
HETATM 3 O O6 DST . . . HB 3 -25.719 55.716 -9.951 1 123.64 ? O6 DST 502 Q 1 
HETATM 4 O O5 DST . . . HB 3 -25.4 54.339 -12.065 1 153.88 ? O5 DST 502 Q 1 
HETATM 5 O O2 DST . . . HB 3 -23.698 54.153 -10.245 1 146.71 ? O2 DST 502 Q 1 
HETATM 6 P P3 DST . . . HB 3 -22.12 54.557 -9.971 1 157.07 ? P3 DST 502 Q 1 
HETATM 7 O O8 DST . . . HB 3 -21.96 55.522 -8.8 1 147.97 ? O8 DST 502 Q 1 
HETATM 8 O O7 DST . . . HB 3 -21.61 55.183 -11.232 1 144.79 ? O7 DST 502 Q 1 
HETATM 9 S S9 DST . . . HB 3 -20.86 52.894 -9.653 1 145.08 ? S9 DST 502 Q 1 
HETATM 10 C C10 DST . . . HB 3 -19.173 53.566 -9.796 1 133.12 ? C10 DST 502 Q 1 
HETATM 11 C C11 DST . . . HB 3 -18.427 52.641 -10.739 1 133.88 ? C11 DST 502 Q 1 
HETATM 12 C C12 DST . . . HB 3 -17.104 52.674 -10.798 1 129.6 ? C12 DST 502 Q 1 
HETATM 13 C C13 DST . . . HB 3 -16.426 51.681 -11.781 1 128.52 ? C13 DST 502 Q 1 
HETATM 14 C C14 DST . . . HB 3 -16.274 53.627 -9.88 1 106.83 ? C14 DST 502 Q 1 
HETATM 15 H H101 DST . . . HB 3 -18.691 53.581 -8.824 1 159.5 ? H101 DST 502 Q 1 
HETATM 16 H H102 DST . . . HB 3 -19.202 54.572 -10.201 1 159.5 ? H102 DST 502 Q 1 
HETATM 17 H H111 DST . . . HB 3 -18.978 51.951 -11.366 1 160.41 ? H111 DST 502 Q 1 
HETATM 18 H H131 DST . . . HB 3 -16.327 50.71 -11.305 1 153.98 ? H131 DST 502 Q 1 
HETATM 19 H H132 DST . . . HB 3 -15.442 52.053 -12.051 1 153.98 ? H132 DST 502 Q 1 
HETATM 20 H H133 DST . . . HB 3 -17.034 51.585 -12.676 1 153.98 ? H133 DST 502 Q 1 
HETATM 21 H H141 DST . . . HB 3 -16.656 54.639 -9.97 1 127.96 ? H141 DST 502 Q 1 
HETATM 22 H H142 DST . . . HB 3 -16.357 53.299 -8.848 1 127.96 ? H142 DST 502 Q 1 
HETATM 23 H H143 DST . . . HB 3 -15.232 53.605 -10.184 1 127.96 ? H143 DST 502 Q 1 
#
_model_server_stats.io_time_ms              87 
_model_server_stats.parse_time_ms           37 
_model_server_stats.create_model_time_ms    113 
_model_server_stats.query_time_ms           300 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           23 
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