IL_3UD4_005

3D structure

PDB id

3UD4 (explore in PDB, NAKB, or RNA 3D Hub)

Description

The C92U mutant c-di-GMP-I riboswitch bound to GpA

Experimental method

X-RAY DIFFRACTION

Resolution

2.7 Å

Loop

Sequence

CAC*GAUGG

Length

8 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_3UD4_005 not in the Motif Atlas

Geometric match to IL_3MXH_001

Geometric discrepancy: 0.3303

The information below is about IL_3MXH_001

Detailed Annotation

Minor groove platform with extra cWW

Broad Annotation

Minor groove platform

Motif group

IL_82096.1

Basepair signature

cWW-L-R-L-cWW

Number of instances in this motif group

6

Unit IDs

3UD4|1|R|C|11
3UD4|1|R|A|12
3UD4|1|R|C|13
*
3UD4|1|R|G|94
3UD4|1|R|A|95
3UD4|1|R|U|96
3UD4|1|R|G|97
3UD4|1|R|G|98

Current chains

Chain R

RNA (92-MER)

Nearby chains

Chain B

RNA (5'-R(*GP*A)-3')