HL_4V4J_111

3D structure

PDB id

4V4J (explore in PDB, NAKB, or RNA 3D Hub)

Description

Interactions and Dynamics of the Shine-Dalgarno Helix in the 70S Ribosome.

Experimental method

X-RAY DIFFRACTION

Resolution

3.83 Å

Loop

Sequence

GUUCAAAUC

Length

9 nucleotides

Bulged bases

4V4J|1|z|C|56

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_4V4J_111 not in the Motif Atlas

Homologous match to HL_5HR6_003

Geometric discrepancy: 0.2314

The information below is about HL_5HR6_003

Detailed Annotation

T-loop with 2 stacked bulged bases

Broad Annotation

T-loop

Motif group

HL_28252.8

Basepair signature

cWW-tWH-F-F-F-F-F

Number of instances in this motif group

140

Unit IDs

4V4J|1|z|G|53
4V4J|1|z|U|54
4V4J|1|z|U|55
4V4J|1|z|C|56
4V4J|1|z|A|57
4V4J|1|z|A|58
4V4J|1|z|A|59
4V4J|1|z|U|60
4V4J|1|z|C|61

Current chains

Chain z

P-site tRNAfMET

Nearby chains

Chain E

50S ribosomal protein L5

Chain K

50S ribosomal protein L16

Chain w

Large subunit ribosomal RNA; LSU rRNA