HL_5DM8_033

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

GGUCGUC

Length

7 nucleotides

Bulged bases

5DM8|1|X|G|1325, 5DM8|1|X|U|1329

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

HL_5DM8_033 not in the Motif Atlas

Geometric match to HL_7A0S_033

Geometric discrepancy: 0.1048

The information below is about HL_7A0S_033

Detailed Annotation

Pseudoknot geometry with 3' bulge

Broad Annotation

No text annotation

Motif group

HL_49081.1

Basepair signature

cWW-F-F-F

Number of instances in this motif group

17

Unit IDs

5DM8|1|X|G|1324
5DM8|1|X|G|1325
5DM8|1|X|U|1326
5DM8|1|X|C|1327
5DM8|1|X|G|1328
5DM8|1|X|U|1329
5DM8|1|X|C|1330

Current chains

Chain X

Deinococcus radiodurans R1 chromosome 1, complete sequence

Nearby chains

Chain K

50S ribosomal protein L17

Chain P

50S ribosomal protein L22