0.021337
0.012319
0.000000
0.000000
0.024638
0.000000
0.000000
0.000000
0.004672
0.00000
0.00000
0.00000
Kiliszek, A.
Blaszczyk, L.
Rypniewski, W.
Micura, R.
Nakatani, K.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
24
90.00
90.00
120.00
46.866
46.866
214.028
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H16 N3 O7 P Se
400.184
n
(D)-2'-METHYLSELENYL-2'-DEOXYCYTIDINE-5'-PHOSPHATE
(D)-2'-DEOXY-2'-SE-METHYLCYTIDINE-5'-PHOSPHATE
DNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
H2 O
18.015
WATER
non-polymer
C26 H26 N7 O4 1
500.529
CMBL3a
non-polymer
UK
Nucleic Acids Res.
NARHAD
0389
1362-4962
47
10906
10913
10.1093/nar/gkz832
31566242
Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats.
2019
100
1
N
PIXEL
2018-01-13
DECTRIS PILATUS3 S 6M
SINGLE WAVELENGTH
M
x-ray
1
0.9756
1.0
P13 (MX1)
PETRA III, EMBL c/o DESY
0.9756
SYNCHROTRON
PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)
2641.604
RNA (5'-R(*GP*CP*AP*G)-D(P*(CSL))-R(P*AP*GP*C)-3')
2
syn
polymer
500.529
CMBL3a
2
syn
non-polymer
18.015
water
6
nat
water
no
yes
GCAG(CSL)AGC
GCAGCAGC
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
1
VAPOR DIFFUSION, SITTING DROP
7.5
5mM MgCl2 and 30% PEG 400
292
-0.906
1
19
A
1
B
8
-2.925
A_G1:C8_B
1
-7.267
0.050
0.110
-0.280
-1.363
1
19
A
2
B
7
4.739
A_C2:G7_B
2
-12.381
-0.387
0.429
0.060
-0.618
1
19
A
7
B
2
-1.231
A_G7:C2_B
3
-5.032
-0.075
0.112
-0.207
3.839
1
19
A
8
B
1
2.553
A_C8:G1_B
4
-6.340
0.207
-0.090
-0.150
-2.950
1
19
A
1
A
8
-19.397
A_G1:C8_A
5
2.827
26.600
-28.147
17.745
2.950
1
19
A
8
A
1
19.397
A_C8:G1_A
6
-2.827
-26.600
28.147
-17.745
-12.444
1
19
A
4
A
5
-4.748
A_G4:CSL5_A
7
14.885
0.528
-0.506
0.051
12.444
1
19
A
5
A
4
-4.748
A_CSL5:G4_A
8
14.885
-0.528
-0.506
0.051
-43.368
1
19
B
1
B
8
-5.136
B_G1:C8_B
9
-40.141
27.261
-24.321
14.911
43.368
1
19
B
8
B
1
5.136
B_C8:G1_B
10
40.141
-27.261
24.321
-14.911
-14.846
1
19
B
4
B
5
4.574
B_G4:CSL5_B
11
8.109
-0.062
-0.048
0.132
14.846
1
19
B
5
B
4
4.574
B_CSL5:G4_B
12
8.109
0.062
-0.048
0.132
2.887
27.846
A
A
1
2
8.562
B
B
8
7
3.208
4.084
-0.303
-2.010
AA_G1C2:G7C8_BB
1
-5.019
10.522
27.098
-5.101
-0.506
3.280
32.504
A
A
7
8
-2.217
B
B
2
1
3.202
-1.239
0.118
-2.171
AA_G7C8:G1C2_BB
2
2.644
-4.731
32.376
-3.664
0.248
0.000
-180.000
A
A
1
8
11.737
A
A
8
1
0.000
-23.457
-2.355
5.050
AA_G1C8:G1C8_AA
3
-12.984
-6.476
-180.000
-2.525
-1.182
0.067
21.116
A
A
4
5
84.508
A
A
5
4
2.918
21.018
0.000
-0.218
AA_G4CSL5:G4CSL5_AA
4
0.000
0.000
2.044
-7.983
0.000
0.000
180.000
B
B
1
8
11.021
B
B
8
1
0.000
22.043
5.514
3.081
BB_G1C8:G1C8_BB
5
1.146
-0.573
180.000
1.541
-2.757
1.939
32.648
B
B
4
5
25.256
B
B
5
4
2.579
13.775
0.000
-0.996
BB_G4CSL5:G4CSL5_BB
6
0.000
0.000
29.671
-3.507
0.000
citation
citation
repository
Initial release
Data collection
Database references
Database references
1
0
2019-09-25
1
1
2019-10-09
1
2
2019-11-20
_citation.pdbx_database_id_DOI
_citation.pdbx_database_id_PubMed
_citation.title
_citation.journal_volume
_citation.page_first
_citation.page_last
Poland
NCN 2017/26/E/NZ1/00950
N
PDBE
Y
PDBE
2019-01-21
REL
REL
J48
CMBL3a
HOH
water
9606
Human
Homo sapiens
sample
1
8
MBL
2
2
J48
J48
101
A
MBL
1
2
J48
J48
101
B
HOH
1
3
HOH
HOH
201
A
HOH
4
3
HOH
HOH
202
A
HOH
6
3
HOH
HOH
201
B
HOH
3
3
HOH
HOH
202
B
HOH
2
3
HOH
HOH
203
B
HOH
5
3
HOH
HOH
204
B
G
1
n
1
G
1
A
C
2
n
2
C
2
A
A
3
n
3
A
3
A
G
4
n
4
G
4
A
CSL
5
n
5
CSL
5
A
A
6
n
6
A
6
A
G
7
n
7
G
7
A
C
8
n
8
C
8
A
G
1
n
1
G
1
B
C
2
n
2
C
2
B
A
3
n
3
A
3
B
G
4
n
4
G
4
B
CSL
5
n
5
CSL
5
B
A
6
n
6
A
6
B
G
7
n
7
G
7
B
C
8
n
8
C
8
B
1.9649
0.4141
-0.0931
1.5609
0.7684
0.9644
-0.3134
-0.9380
-0.1052
0.1990
0.4531
-0.0802
0.0728
0.7278
-0.0867
0.8666
0.0667
0.0699
1.1315
0.1185
1.1133
refined
-3.8444
12.4394
-1.3703
X-RAY DIFFRACTION
4.2559
-3.4050
0.4939
3.4158
-0.7447
5.2793
-0.5137
-0.5882
1.1596
0.6188
0.1795
-0.3494
-0.7577
0.3344
-0.9626
0.4811
0.0132
0.0519
0.6911
-0.0232
0.4280
refined
-8.9398
18.9758
-6.9403
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
chain 'A' and (resid 1 through 8 )
X-RAY DIFFRACTION
2
chain 'B' and (resid 1 through 8 )
author_and_software_defined_assembly
PISA
2
dimeric
none
2160
-2
3530
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
1
-2.50
0.40
120.30
117.80
A
A
A
C6
N1
C2
C
C
C
2
2
2
N
0.2271
0.2045
0.2057
2.519
40.587
449
8867
5.06
99.51
0.54
1
FREE R-VALUE
1.92
SAD
33.36
0.70
0.90
ML
FLAT BULK SOLVENT MODEL
2.519
40.587
6
422
74
342
0
0.012
460
1.988
702
13.280
280
0.096
76
0.006
106
0.4591
0.3809
2.8832
152
2819
100.00
0.2380
0.2339
3.6322
151
2783
99.00
0.2013
0.1765
40.5924
146
2816
100.00
2.519
40.587
6QIQ
8907
0.99
0.113
1
18.3
27.9
99.9
2.873
2.519
2.67
1.0
1420
0.65
1
28.5
99.9
refinement
PHENIX
(1.13_2998: ???)
data reduction
XDS
data scaling
XDS
phasing
Auto-Rickshaw
N
RNA (5'-R(*GP*CP*AP*G)-D(P*(CSL))-R(P*AP*GP*C)-3')
Crystal structure of seleno-derivative CAG repeats with synthetic CMBL3a compound
1
N
N
1
N
N
2
N
N
2
N
N
3
N
N
3
N
N
covale
1.591
both
A
G
4
A
O3'
G
4
1_555
A
CSL
5
A
P
CSL
5
1_555
covale
1.570
both
A
CSL
5
A
O3'
CSL
5
1_555
A
A
6
A
P
A
6
1_555
covale
1.547
both
B
G
4
B
O3'
G
4
1_555
B
CSL
5
B
P
CSL
5
1_555
covale
1.592
both
B
CSL
5
B
O3'
CSL
5
1_555
B
A
6
B
P
A
6
1_555
hydrog
WATSON-CRICK
A
G
1
A
N1
G
1
1_555
B
C
8
B
N3
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
N2
G
1
1_555
B
C
8
B
O2
C
8
1_555
hydrog
WATSON-CRICK
A
G
1
A
O6
G
1
1_555
B
C
8
B
N4
C
8
1_555
hydrog
WATSON-CRICK
A
C
2
A
N3
C
2
1_555
B
G
7
B
N1
G
7
1_555
hydrog
WATSON-CRICK
A
C
2
A
N4
C
2
1_555
B
G
7
B
O6
G
7
1_555
hydrog
WATSON-CRICK
A
C
2
A
O2
C
2
1_555
B
G
7
B
N2
G
7
1_555
hydrog
WATSON-CRICK
A
G
7
A
N1
G
7
1_555
B
C
2
B
N3
C
2
1_555
hydrog
WATSON-CRICK
A
G
7
A
N2
G
7
1_555
B
C
2
B
O2
C
2
1_555
hydrog
WATSON-CRICK
A
G
7
A
O6
G
7
1_555
B
C
2
B
N4
C
2
1_555
hydrog
WATSON-CRICK
A
C
8
A
N3
C
8
1_555
B
G
1
B
N1
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
N4
C
8
1_555
B
G
1
B
O6
G
1
1_555
hydrog
WATSON-CRICK
A
C
8
A
O2
C
8
1_555
B
G
1
B
N2
G
1
1_555
RNA
CAG repeats, CMBL, RNA complex with ligand, RNA
6QIQ
PDB
1
1
6QIQ
1
8
6QIQ
1
8
6QIQ
A
1
1
8
1
8
6QIQ
1
8
6QIQ
B
1
1
8
binding site for residue J48 A 101
A
J48
101
Software
7
binding site for residue J48 B 101
B
J48
101
Software
7
binding site for Di-nucleotide G B 4 and CSL B 5
B
G
4
Software
3
binding site for Di-nucleotide CSL B 5 and A B 6
B
CSL
5
Software
5
A
A
3
A
A
3
7
1_555
A
CSL
5
A
CSL
5
7
1_555
A
A
6
A
A
6
7
1_555
A
G
7
A
G
7
7
1_555
B
C
2
B
C
2
7
1_555
B
A
3
B
A
3
7
1_555
B
J48
101
D
J48
7
1_555
A
C
2
A
C
2
7
1_555
A
A
3
A
A
3
7
1_555
A
J48
101
C
J48
7
1_555
B
A
3
B
A
3
7
1_555
B
CSL
5
B
CSL
5
7
1_555
B
A
6
B
A
6
7
1_555
B
G
7
B
G
7
7
1_555
B
A
3
B
A
3
3
1_555
B
A
6
B
A
6
3
1_555
B
J48
101
D
J48
3
1_555
B
A
3
B
A
3
5
1_555
B
G
4
B
G
4
5
1_555
B
G
4
B
G
4
5
12_564
B
G
7
B
G
7
5
1_555
B
J48
101
D
J48
5
1_555
179
P 65 2 2