IL_5DM8_066

3D structure

PDB id

5DM8 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with orthoformimycin

Experimental method

X-RAY DIFFRACTION

Resolution

3.1 Å

Loop

Sequence

CCGG*CG

Length

6 nucleotides

Bulged bases

5DM8|1|X|C|1838

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_5DM8_066 not in the Motif Atlas

Geometric match to IL_7A0S_066

Geometric discrepancy: 0.1653

The information below is about IL_7A0S_066

Detailed Annotation

Minor groove platform, major groove intercalation

Broad Annotation

Minor groove platform, major groove intercalation

Motif group

IL_55206.2

Basepair signature

cWW-L-cWW

Number of instances in this motif group

11

Unit IDs

5DM8|1|X|C|1837
5DM8|1|X|C|1838
5DM8|1|X|G|1839
5DM8|1|X|G|1840
*
5DM8|1|X|C|1902
5DM8|1|X|G|1903

Current chains

Chain X

Deinococcus radiodurans R1 chromosome 1, complete sequence

Nearby chains

Chain A

50S ribosomal protein L2