J4_2YDH_001

3D structure

PDB id

2YDH (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the SAM-I riboswitch A94G U34 G18U G19U variant in complex with SAM

Experimental method

X-RAY DIFFRACTION

Resolution

2.9 Å

Loop

Sequence

CAAGAG*CG*CAAUU*AG

Length

15 nucleotides

Bulged bases

2YDH|1|A|A|9, 2YDH|1|A|U|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

J4_2YDH_001 not in the Motif Atlas

Homologous match to J4_5FJC_001

Geometric discrepancy: 0.2105

The information below is about J4_5FJC_001

Detailed Annotation

SAM-I riboswitch junction

Broad Annotation

No text annotation

Motif group

J4_40439.2

Basepair signature

cWW-F-cWW-F-F-F-F-F-cWW-F-cWW

Number of instances in this motif group

3

Unit IDs

2YDH|1|A|C|8
2YDH|1|A|A|9
2YDH|1|A|A|10
2YDH|1|A|G|11
2YDH|1|A|A|12
2YDH|1|A|G|13
*
2YDH|1|A|C|41
2YDH|1|A|G|42
*
2YDH|1|A|C|60
2YDH|1|A|A|61
2YDH|1|A|A|62
2YDH|1|A|U|63
2YDH|1|A|U|64
*
2YDH|1|A|A|85
2YDH|1|A|G|86

Current chains

Chain A

SAM-I RIBOSWITCH

Nearby chains