HL_5DM8_011

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

GUGAGAGUC

Length

9 nucleotides

Bulged bases

5DM8|1|X|G|329, 5DM8|1|X|A|330, 5DM8|1|X|G|331

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_011 not in the Motif Atlas

Geometric match to HL_5J7L_144

Geometric discrepancy: 0.1788

The information below is about HL_5J7L_144

Detailed Annotation

T-loop with unstacked turn

Broad Annotation

T-loop

Motif group

HL_27670.2

Basepair signature

cWW-tWH-F-F

Number of instances in this motif group

13

Unit IDs

5DM8|1|X|G|327
5DM8|1|X|U|328
5DM8|1|X|G|329
5DM8|1|X|A|330
5DM8|1|X|G|331
5DM8|1|X|A|332
5DM8|1|X|G|333
5DM8|1|X|U|334
5DM8|1|X|C|335

Current chains

Chain X

Deinococcus radiodurans R1 chromosome 1, complete sequence

Nearby chains

Chain C

50S ribosomal protein L4

Chain P

50S ribosomal protein L22

Chain R

50S ribosomal protein L24