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A Portal for Three-dimensional Structural Information about Nucleic Acids
As of 15-Mar-2023 number of released structures: 12686
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Structural Content
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DNA:
Y
N
Ignore
OR
AND
RNA:
Y
N
Ignore
OR
AND
Hybrid:
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N
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AND
Protein:
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N
Ignore
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AND
Ligand:
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N
Ignore
Search ligand by:
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Ligand ID:
Experimental Information
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Crystal Structure:
Y
N
Ignore
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AND
Structure Factors Available:
Y
N
Ignore
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AND
NMR:
Y
N
Ignore
OR
AND
NMR Restraints Available:
Y
N
Ignore
Experimental Details
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OR
Space Group:
select one
B 2 21 2
C 1 2 1
C 2 2 2
C 2 2 21
F 2 2 2
F 2 3
F 4 3 2
H 3
H 3 2
I 2 2 2
I 2 3
I 21 21 21
I 21 3
I 4
I 4 2 2
I 4 3 2
I 41
I 41 2 2
I 41 3 2
P -1
P 1
P 1 1 21
P 1 2 1
P 1 21 1
P 2 2 21
P 2 21 21
P 2 3
P 21 2 21
P 21 21 2
P 21 21 21
P 21 3
P 3
P 3 1 2
P 3 2 1
P 31
P 31 1 2
P 31 2 1
P 32
P 32 1 2
P 32 2 1
P 4
P 4 2 2
P 4 21 2
P 41
P 41 2 2
P 41 21 2
P 41 3 2
P 42
P 42 2 2
P 42 21 2
P 42 3 2
P 43
P 43 2 2
P 43 21 2
P 43 3 2
P 6
P 6 2 2
P 61
P 61 2 2
P 62
P 62 2 2
P 63
P 63 2 2
P 64
P 64 2 2
P 65
P 65 2 2
R 3 2
Unit Cell Dimensions:
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OR
Alpha
=
>=
<=
°
AND
OR
a
=
>=
<=
Å
AND
OR
Resolution better than:
Å
AND
OR
Beta
=
>=
<=
°
AND
OR
b
=
>=
<=
Å
AND
OR
R-factor better than:
10
15
20
25
30
35
AND
OR
Gamma
=
>=
<=
°
AND
OR
c
=
>=
<=
Å
Citation Information
NDB ID
PDB ID
AND
OR
Author
AND
OR
Publication Year:
AND
OR
Released Since:
RNA 3D Interactions
AND
OR
Base Pair Interaction:
select base pair
cWW (cis Watson-Crick/Watson-Crick)
tWW (trans Watson-Crick/Watson-Crick)
cWH (cis Watson-Crick/Hoogsteen)
tWH (trans Watson-Crick/Hoogsteen)
cWS (cis Watson-Crick/Sugar Edge)
tWS (trans Watson-Crick/Sugar Edge)
cHH (cis Hoogsteen/Hoogsteen)
tHH (trans Hoogsteen/Hoogsteen)
cHS (cis Hoogsteen/Sugar Edge)
tHS (trans Hoogsteen/Sugar Edge)
cSS (cis Sugar Edge/Sugar Edge)
tSS (trans Sugar Edge/Sugar Edge)
AND
OR
Base Phosphate Interaction:
select base phosphate
1BPh (base-phosphate position 1)
2BPh (base-phosphate position 2)
3BPh (base-phosphate position 3)
4BPh (base-phosphate position 4)
5BPh (base-phosphate position 5)
6BPh (base-phosphate position 6)
7BPh (base-phosphate position 7)
8BPh (base-phosphate position 8)
9BPh (base-phosphate position 9)
0BPh (base-phosphate position 10)
AND
OR
Base Stack Interaction:
select base stack
s33 (stack, 3′ face on 3′ face)
s35 (stack, 3′ face on 5′ face)
s55 (stack, 5′ face on 5′ face)
Relative Frequency of various RNA 3D Interactions:
AND
OR
Base Pair Interaction
select base pair
cWW (cis Watson-Crick/Watson-Crick)
tWW (trans Watson-Crick/Watson-Crick)
cWH (cis Watson-Crick/Hoogsteen)
tWH (trans Watson-Crick/Hoogsteen)
cWS (cis Watson-Crick/Sugar Edge)
tWS (trans Watson-Crick/Sugar Edge)
cHH (cis Hoogsteen/Hoogsteen)
tHH (trans Hoogsteen/Hoogsteen)
cHS (cis Hoogsteen/Sugar Edge)
tHS (trans Hoogsteen/Sugar Edge)
cSS (cis Sugar Edge/Sugar Edge)
tSS (trans Sugar Edge/Sugar Edge)
with relative frequency:
>=
<=
AND
OR
Base Phosphate Interaction
select base phosphate
1BPh (base-phosphate position 1)
2BPh (base-phosphate position 2)
3BPh (base-phosphate position 3)
4BPh (base-phosphate position 4)
5BPh (base-phosphate position 5)
6BPh (base-phosphate position 6)
7BPh (base-phosphate position 7)
8BPh (base-phosphate position 8)
9BPh (base-phosphate position 9)
0BPh (base-phosphate position 10)
with relative frequency:
>=
<=
AND
OR
Base Stack Interaction
select base stack
s33 (stack, 3′ face on 3′ face)
s35 (stack, 3′ face on 5′ face)
s55 (stack, 5′ face on 5′ face)
with relative frequency:
>=
<=
RNA 3D Motifs
AND
OR
Internal Loop Motif
All
Sarcin-ricin
Kink-turn
C-loop
Double-sheared
Triple-sheared
AND
OR
Hairpin Loop Motif
All
T-loop
GNRA
UNCG
Representative RNA 3D Structure Sets
AND
OR
Resolution cutoff:
select resolution cutoff
All (X-ray + NMR)
1.5 Å (X-ray)
2.0 Å (X-ray)
2.5 Å (X-ray)
3.0 Å (X-ray)
3.5 Å (X-ray)
4.0 Å (X-ray)
20.0 Å (X-ray)
Sequence
AND
OR
Nucleic Acid Sequence Pattern:
AND
OR
Oligonucleotide Sequence Length between
and
Protein Function Types
AND
OR
Enzyme:
All
Oxidoreductase
Transferase
Transferase/Kinase
Transferase/Polymerase
Transferase/Methylase
Hydrolase
Hydrolase/Nuclease
Hydrolase/Protease
Hydrolase/Helicase
Lyase
Isomerase
Ligase
Ligase/Synthetase
Ligase/Amidotransferase
Recombinase
Enzyme/Unspecified
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AND
OR
AND
OR
Regulatory:
All
DNA Replication/Repair
Cell Cycle
Cell Signaling
Transcription
Translation
Splicing
Gene Silencing
Immune System
CRISPR
Toxin
Post-transcriptional
Regulatory/Other
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AND
OR
AND
OR
Structural:
All
Antibody
Chromatin
Chromatin/Nucleosome
Chromatin/Centromere
Chromatin/Telomere
Ribosome
Ribonucleoprotein
Signal Recognition Particle
Spliceosome
Structural/Other
Virus
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AND
OR
Nucleic Acid Structural Conformation
AND
OR
Strand Description:
Double Helix
Triple Helix
Quadruple Helix
I-motif
AND
OR
NA Features:
All Loops
Hairpin Loop
Internal Loop
Bulge
Hammerhead
Three Way Junction
Four Way Junction
Non-Watson-Crick base pairing
Mismatch Base Pairing
Select a clause for the individual types:
AND
OR
AND
OR
Conformation Type:
All
A
B
RH
T
U
Z
