J5_5J8B_006

3D structure

PDB id

5J8B (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of Elongation Factor 4 (EF-4/LepA) in complex with GDPCP bound to the Thermus thermophilus 70S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

2.6 Å

Loop

Sequence

GCAAGUUGG*UG*CC*GUGAACAGG*CGC

Length

25 nucleotides

Bulged bases

5J8B|1|A|G|1788, 5J8B|1|A|G|1793

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

J5_5J8B_006 not in the Motif Atlas

Homologous match to J5_9DFE_005

Geometric discrepancy: 0.0449

The information below is about J5_9DFE_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_62523.6

Basepair signature

cWW-F-F-F-cWW-F-F-F-F-F-F-F-F-F-cWW-F-cWW-cWW

Number of instances in this motif group

7

Unit IDs

5J8B|1|A|G|1720
5J8B|1|A|C|1721
5J8B|1|A|A|1722
5J8B|1|A|A|1723
5J8B|1|A|G|1724
5J8B|1|A|U|1725
5J8B|1|A|U|1726
5J8B|1|A|G|1727
5J8B|1|A|G|1728
*
5J8B|1|A|U|1752
5J8B|1|A|G|1753
*
5J8B|1|A|C|1781
5J8B|1|A|C|1782
*
5J8B|1|A|G|1786
5J8B|1|A|U|1787
5J8B|1|A|G|1788
5J8B|1|A|A|1789
5J8B|1|A|A|1790
5J8B|1|A|C|1791
5J8B|1|A|A|1792
5J8B|1|A|G|1793
5J8B|1|A|G|1794
*
5J8B|1|A|C|2009
5J8B|1|A|G|2010
5J8B|1|A|C|2011

Current chains

Chain A

23S Ribosomal RNA

Nearby chains

Chain E

50S ribosomal protein L3

Chain O

50S ribosomal protein L14

Chain T

50S ribosomal protein L19

Chain a

Small subunit ribosomal RNA; SSU rRNA