1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Horowitz, E.D.
Lilavivat, S.
Holladay, B.W.
Germann, M.W.
Hud, N.V.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C10 H14 N5 O8 P
363.221
y
GUANOSINE-5'-MONOPHOSPHATE
RNA linking
C13 H11 N3
209.247
PROFLAVIN
non-polymer
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
131
5831
5838
10.1021/ja810068e
19309071
Solution structure and thermodynamics of 2',5' RNA intercalation.
2009
10.2210/pdb2kd4/pdb
pdb_00002kd4
2556.593
5'-R(*GP*CP*CP*GP*CP*GP*GP*C)-2'
2
syn
polymer
209.247
PROFLAVIN
2
syn
non-polymer
no
no
GCCGCGGC
GCCGCGGC
A,B
polyribonucleotide
n
n
n
n
n
n
n
n
-23.280
1
19
A
1
B
8
3.603
A_G1:C8_B
1
-29.530
-0.240
-0.546
0.023
15.650
1
19
A
2
B
7
-6.304
A_C2:G7_B
2
-39.027
0.359
0.406
-0.210
15.018
1
19
A
3
B
6
2.153
A_C3:G6_B
3
-8.216
0.880
-0.198
-0.276
7.428
1
19
A
4
B
5
0.727
A_G4:C5_B
4
-13.834
-1.083
0.560
-0.463
-3.789
1
19
A
5
B
4
1.215
A_C5:G4_B
5
-13.446
1.049
0.501
-0.424
-13.600
1
19
A
6
B
3
-1.714
A_G6:C3_B
6
-12.364
-0.958
0.166
-0.413
-15.672
1
19
A
7
B
2
-1.036
A_G7:C2_B
7
-30.999
-0.206
-0.102
-0.074
12.867
1
19
A
8
B
1
1.480
A_C8:G1_B
8
-26.131
0.152
-0.262
-0.029
-0.195
-163.946
A
A
1
2
-87.043
B
B
8
7
-1.209
162.562
3.746
-0.499
AA_G1C2:G7C8_BB
1
13.000
6.961
-36.680
0.761
1.851
3.743
39.958
A
A
2
3
0.091
B
B
7
6
4.093
0.061
0.421
-1.821
AA_C2C3:G6G7_BB
2
-13.222
19.691
37.792
-2.674
-2.493
6.065
24.776
A
A
3
4
-29.639
B
B
6
5
6.681
-11.950
-0.083
-1.167
AA_C3G4:C5G6_BB
3
-7.874
19.528
20.278
5.069
-4.936
3.399
49.803
A
A
4
5
-0.671
B
B
5
4
3.397
-0.565
0.069
-0.188
AA_G4C5:G4C5_BB
4
0.222
-0.263
49.800
-0.180
-0.065
6.574
23.037
A
A
5
6
-17.545
B
B
4
3
6.619
-6.875
-0.135
-1.180
AA_C5G6:C3G4_BB
5
3.496
-8.922
21.724
2.057
2.887
2.887
43.478
A
A
6
7
17.677
B
B
3
2
3.686
12.693
0.164
-1.822
AA_G6G7:C2C3_BB
6
14.100
-19.636
39.303
-3.763
1.227
-0.154
-166.211
A
A
7
8
-86.610
B
B
2
1
-1.268
164.474
-3.411
-0.634
AA_G7C8:G1C2_BB
7
-10.038
-5.286
-49.960
0.773
-1.690
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
pdbx_validate_polymer_linkage
struct_conn
struct_site
repository
Initial release
Version format compliance
Advisory
Data collection
Database references
Derived calculations
1
0
2009-04-07
1
1
2011-07-13
1
2
2022-03-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BMRB
Y
RCSB
2009-01-02
REL
REL
PRL
PROFLAVIN
Synthetic 2',5' RNA
sample
14
14
378
258
378
258
structures with the lowest energy
10
1
1H-1H NOESY
31P-1H HETCOR
1H-1H TOCSY
31P-decoupled 1H-1H COSY
1H-1H NOESY with WATERGATE water suppression
2
mM
4
mM
60
mM
200
mM
260
6.5
1
atm
282
K
130
1
atm
282
K
300 random structures were generated and annealed. The lowest 10 energy structures were then re-annealed
simulated annealing
1
lowest energy
2 mM 2',5' RNA-1, 4 mM PROFLAVINE-2, 60 mM Sodium Phosphate-3, 200 mM sodium chloride-4, 99.9% D2O
99.9% D2O
Bruker Biospin
collection
XwinNMR
Bruker Biospin
data analysis
XwinNMR
Bruker Biospin
processing
XwinNMR
Goddard
chemical shift assignment
Sparky
Goddard
data analysis
Sparky
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
structure solution
Amber
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
refinement
Amber
600
Bruker
DRX
Bruker DRX
500
Bruker
DRX
Bruker DRX
PRL
17
2
PRL
PRL
17
A
PRL
17
2
PRL
PRL
17
B
G
1
n
1
G
1
A
C
2
n
2
C
2
A
C
3
n
3
C
3
A
G
4
n
4
G
4
A
C
5
n
5
C
5
A
G
6
n
6
G
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
C
3
n
3
C
3
B
G
4
n
4
G
4
B
C
5
n
5
C
5
B
G
6
n
6
G
6
B
G
7
n
7
G
7
B
C
8
n
8
C
8
B
author_defined_assembly
2
dimeric
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
A
G
1
0.077
SIDE CHAIN
1
A
C
2
0.120
SIDE CHAIN
1
A
G
4
0.127
SIDE CHAIN
1
A
G
6
0.149
SIDE CHAIN
1
A
G
7
0.089
SIDE CHAIN
1
B
G
1
0.065
SIDE CHAIN
1
B
C
2
0.117
SIDE CHAIN
1
B
G
4
0.115
SIDE CHAIN
1
B
G
6
0.115
SIDE CHAIN
1
B
G
7
0.129
SIDE CHAIN
1
7.28
0.80
106.10
113.38
A
A
A
O4'
C4'
C3'
G
G
G
1
1
1
N
1
5.49
0.90
109.80
115.29
A
A
A
C5'
C4'
O4'
G
G
G
1
1
1
N
1
3.19
0.50
113.10
116.29
A
A
A
N7
C8
N9
G
G
G
1
1
1
N
1
7.10
0.80
106.10
113.20
A
A
A
O4'
C4'
C3'
C
C
C
2
2
2
N
1
6.12
0.80
101.50
107.62
A
A
A
C3'
C2'
C1'
C
C
C
2
2
2
N
1
-5.40
0.80
108.20
102.80
A
A
A
O4'
C1'
N1
C
C
C
2
2
2
N
1
3.76
0.60
118.90
122.66
A
A
A
N1
C2
O2
C
C
C
2
2
2
N
1
-4.32
0.70
121.90
117.58
A
A
A
N3
C2
O2
C
C
C
5
5
5
N
1
-2.55
0.40
106.40
103.85
A
A
A
C8
N9
C4
G
G
G
6
6
6
N
1
13.65
1.90
111.70
125.35
A
A
A
O5'
C5'
C4'
G
G
G
7
7
7
N
1
-10.38
1.40
115.20
104.82
A
A
A
C5'
C4'
C3'
G
G
G
7
7
7
N
1
-5.68
0.80
108.20
102.52
A
A
A
O4'
C1'
N9
G
G
G
7
7
7
N
1
5.00
0.80
106.10
111.10
A
A
A
O4'
C4'
C3'
C
C
C
8
8
8
N
1
6.01
0.90
109.80
115.81
A
A
A
C5'
C4'
O4'
C
C
C
8
8
8
N
1
5.44
0.80
101.50
106.94
A
A
A
C3'
C2'
C1'
C
C
C
8
8
8
N
1
-7.59
1.20
120.80
113.21
A
A
A
C6
N1
C1'
C
C
C
8
8
8
N
1
8.06
1.10
118.80
126.86
A
A
A
C2
N1
C1'
C
C
C
8
8
8
N
1
6.88
0.80
106.10
112.98
B
B
B
O4'
C4'
C3'
G
G
G
1
1
1
N
1
5.97
0.90
109.80
115.77
B
B
B
C5'
C4'
O4'
G
G
G
1
1
1
N
1
6.88
0.80
106.10
112.98
B
B
B
O4'
C4'
C3'
C
C
C
2
2
2
N
1
5.41
0.80
101.50
106.91
B
B
B
C3'
C2'
C1'
C
C
C
2
2
2
N
1
-5.46
0.80
108.20
102.74
B
B
B
O4'
C1'
N1
C
C
C
2
2
2
N
1
-4.20
0.70
121.90
117.70
B
B
B
N3
C2
O2
C
C
C
2
2
2
N
1
5.00
0.80
101.50
106.50
B
B
B
C3'
C2'
C1'
G
G
G
6
6
6
N
1
-6.03
0.80
108.20
102.17
B
B
B
O4'
C1'
N9
G
G
G
7
7
7
N
1
6.53
0.90
109.80
116.33
B
B
B
C5'
C4'
O4'
C
C
C
8
8
8
N
1
4.85
0.80
101.50
106.35
B
B
B
C3'
C2'
C1'
C
C
C
8
8
8
N
1
-7.79
1.20
120.80
113.01
B
B
B
C6
N1
C1'
C
C
C
8
8
8
N
1
8.03
1.10
118.80
126.83
B
B
B
C2
N1
C1'
C
C
C
8
8
8
N
lowest energy, model 1
Solution structure and thermodynamics of 2',5' RNA intercalation
1
N
N
1
N
N
2
N
N
2
N
N
covale
1.609
one
A
G
1
A
O2'
G
1
1_555
A
C
2
A
P
C
2
1_555
covale
1.595
one
A
C
2
A
O2'
C
2
1_555
A
C
3
A
P
C
3
1_555
covale
1.625
one
A
C
3
A
O2'
C
3
1_555
A
G
4
A
P
G
4
1_555
covale
1.600
one
A
G
4
A
O2'
G
4
1_555
A
C
5
A
P
C
5
1_555
covale
1.611
one
A
C
5
A
O2'
C
5
1_555
A
G
6
A
P
G
6
1_555
covale
1.619
one
A
G
6
A
O2'
G
6
1_555
A
G
7
A
P
G
7
1_555
covale
1.595
one
A
G
7
A
O2'
G
7
1_555
A
C
8
A
P
C
8
1_555
covale
1.608
one
B
G
1
B
O2'
G
1
1_555
B
C
2
B
P
C
2
1_555
covale
1.609
one
B
C
2
B
O2'
C
2
1_555
B
C
3
B
P
C
3
1_555
covale
1.613
one
B
C
3
B
O2'
C
3
1_555
B
G
4
B
P
G
4
1_555
covale
1.595
one
B
G
4
B
O2'
G
4
1_555
B
C
5
B
P
C
5
1_555
covale
1.605
one
B
C
5
B
O2'
C
5
1_555
B
G
6
B
P
G
6
1_555
covale
1.600
one
B
G
6
B
O2'
G
6
1_555
B
G
7
B
P
G
7
1_555
covale
1.601
one
B
G
7
B
O2'
G
7
1_555
B
C
8
B
P
C
8
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
C
3
A
N3
C
3
1_555
B
G
6
B
N1
G
6
1_555
hydrog
WATSON-CRICK
A
C
3
A
N4
C
3
1_555
B
G
6
B
O6
G
6
1_555
hydrog
WATSON-CRICK
A
C
3
A
O2
C
3
1_555
B
G
6
B
N2
G
6
1_555
hydrog
WATSON-CRICK
A
G
4
A
N1
G
4
1_555
B
C
5
B
N3
C
5
1_555
hydrog
WATSON-CRICK
A
G
4
A
N2
G
4
1_555
B
C
5
B
O2
C
5
1_555
hydrog
WATSON-CRICK
A
G
4
A
O6
G
4
1_555
B
C
5
B
N4
C
5
1_555
hydrog
WATSON-CRICK
A
C
5
A
N3
C
5
1_555
B
G
4
B
N1
G
4
1_555
hydrog
WATSON-CRICK
A
C
5
A
N4
C
5
1_555
B
G
4
B
O6
G
4
1_555
hydrog
WATSON-CRICK
A
C
5
A
O2
C
5
1_555
B
G
4
B
N2
G
4
1_555
hydrog
WATSON-CRICK
A
G
6
A
N1
G
6
1_555
B
C
3
B
N3
C
3
1_555
hydrog
WATSON-CRICK
A
G
6
A
N2
G
6
1_555
B
C
3
B
O2
C
3
1_555
hydrog
WATSON-CRICK
A
G
6
A
O6
G
6
1_555
B
C
3
B
N4
C
3
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
proflavine, intercalation, 2', 5' RNA, RNA, nearest-neighbor exclusion
2KD4
PDB
1
1
2KD4
GCCGCGGC
1
8
2KD4
1
8
2KD4
A
1
1
8
1
8
2KD4
1
8
2KD4
B
1
1
8
BINDING SITE FOR RESIDUE PRL B 17
B
PRL
17
Software
5
BINDING SITE FOR RESIDUE PRL A 17
A
PRL
17
Software
5
A
G
4
A
G
4
5
1_555
A
C
5
A
C
5
5
1_555
A
G
6
A
G
6
5
1_555
B
C
3
B
C
3
5
1_555
B
G
4
B
G
4
5
1_555
A
C
2
A
C
2
5
1_555
A
C
3
A
C
3
5
1_555
A
G
4
A
G
4
5
1_555
B
C
5
B
C
5
5
1_555
B
G
6
B
G
6
5
1_555