IL_1YKV_004

3D structure

PDB id

1YKV (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Diels-Alder ribozyme complexed with the product of the reaction between N-pentylmaleimide and covalently attached 9-hydroxymethylanthracene

Experimental method

X-RAY DIFFRACTION

Resolution

3.3 Å

Loop

Sequence

GUGCCAG*CAAUACUC

Length

15 nucleotides

Bulged bases

None detected

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

IL_1YKV_004 not in the Motif Atlas

Geometric match to IL_1YLS_011

Geometric discrepancy: 0.1196

The information below is about IL_1YLS_011

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_49867.1

Basepair signature

cWW-cWW-L-R-L-R-tHW-R-L-L-cWW

Number of instances in this motif group

1

Unit IDs

1YKV|1|D|G|211
1YKV|1|D|U|212
1YKV|1|D|G|213
1YKV|1|D|C|214
1YKV|1|D|C|215
1YKV|1|D|A|216
1YKV|1|D|G|217
*
1YKV|1|D|C|228
1YKV|1|D|A|229
1YKV|1|D|A|230
1YKV|1|D|U|231
1YKV|1|D|A|232
1YKV|1|D|C|233
1YKV|1|D|U|234
1YKV|1|D|C|235

Current chains

Chain D

Diels-Alder ribozyme

Nearby chains

Chain B

Diels-Alder ribozyme

Chain C

Diels-Alder ribozyme