J4_5D8B_015

3D structure

PDB id

5D8B (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of T. thermophilus ribosome containing a P-site wobble mismatch

Experimental method

X-RAY DIFFRACTION

Resolution

3.63 Å

Loop

Sequence

UUG*CG*CCUAAGGUAG*CGAAAA

Length

21 nucleotides

Bulged bases

5D8B|1|VC|A|1971

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

J4_5D8B_015 not in the Motif Atlas

Homologous match to J4_9DFE_008

Geometric discrepancy: 0.0996

The information below is about J4_9DFE_008

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_42306.1

Basepair signature

cWW-tSS-cSS-cWH-cWW-tWH-tHS-cWW-cWW-tWW-F-cSH-F-F

Number of instances in this motif group

5

Unit IDs

5D8B|1|VC|U|1833
5D8B|1|VC|U|1834
5D8B|1|VC|G|1835
*
5D8B|1|VC|C|1905
5D8B|1|VC|G|1906
*
5D8B|1|VC|C|1924
5D8B|1|VC|C|1925
5D8B|1|VC|U|1926
5D8B|1|VC|A|1927
5D8B|1|VC|A|1928
5D8B|1|VC|G|1929
5D8B|1|VC|G|1930
5D8B|1|VC|U|1931
5D8B|1|VC|A|1932
5D8B|1|VC|G|1933
*
5D8B|1|VC|C|1967
5D8B|1|VC|G|1968
5D8B|1|VC|A|1969
5D8B|1|VC|A|1970
5D8B|1|VC|A|1971
5D8B|1|VC|A|1972

Current chains

Chain VC

23S ribosomal RNA

Nearby chains

Chain A

50S ribosomal protein L2

Chain ED

Transfer RNA; tRNA

Chain UC

Small subunit ribosomal RNA; SSU rRNA