J3_3NKB_001

3D structure

PDB id

3NKB (explore in PDB, NAKB, or RNA 3D Hub)

Description

A 1.9A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage

Experimental method

X-RAY DIFFRACTION

Resolution

1.92 Å

Loop

Sequence

AG*CGCAAGCUGGGCAAC*GGCGAAU

Length

24 nucleotides

Bulged bases

3NKB|1|B|G|63

QA status

Valid loop

Sequence variability

If this chain is mapped to an Rfam alignment, the link below will give its sequence variability.

R3DSVS

Structural variability across Equivalence Class

The link below will give the loop's structural variability across the equivalence class for this chain.

R3DMCS EC

Structural variability across Rfam

If this chain is mapped to an Rfam alignment, the link below will give the loop's structural variability between chains mapped to the same Rfam family.

R3DMCS Rfam

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_01596.1

Basepair signature

cWW-cWW-F-F-F-F-F-cWW-F-cWW-tWH-F-F-F-F-F-F-F-F

Number of instances in this motif group

1

Unit IDs

3NKB|1|B|A|17
3NKB|1|B|G|18
*
3NKB|1|B|C|30
3NKB|1|B|G|31
3NKB|1|B|C|32
3NKB|1|B|A|33
3NKB|1|B|A|34
3NKB|1|B|G|35
3NKB|1|B|C|36
3NKB|1|B|U|37
3NKB|1|B|G|38
3NKB|1|B|G|39
3NKB|1|B|G|40
3NKB|1|B|C|41
3NKB|1|B|A|42
3NKB|1|B|A|43
3NKB|1|B|C|44
*
3NKB|1|B|G|60
3NKB|1|B|G|61
3NKB|1|B|C|62
3NKB|1|B|G|63
3NKB|1|B|A|64
3NKB|1|B|A|65
3NKB|1|B|U|66

Current chains

Chain B

The hepatitis delta virus ribozyme

Nearby chains

Chain A

DNA/RNA (5'-D(*(DUR))-D(*GP*G)-R(P*CP*UP*UP*GP*CP*A)-3')