IL_2YDH_007

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

CAAC*GUG

Length

7 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_2YDH_007 not in the Motif Atlas

Geometric match to IL_4OQU_001

Geometric discrepancy: 0.1025

The information below is about IL_4OQU_001

Detailed Annotation

Major groove platform with extra pair

Broad Annotation

Major groove platform

Motif group

IL_15698.4

Basepair signature

cWW-L-R-L-cWW

Number of instances in this motif group

10

Unit IDs

2YDH|1|A|C|44||||8_555
2YDH|1|A|A|45||||8_555
2YDH|1|A|A|46||||8_555
2YDH|1|A|C|47||||8_555
*
2YDH|1|A|G|56||||8_555
2YDH|1|A|U|57||||8_555
2YDH|1|A|G|58||||8_555

Current chains

Chain A

SAM-I RIBOSWITCH

Nearby chains