J4_5VP2_024

3D structure

PDB id

5VP2 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in complex with madumycin II and bound to mRNA and A-, P- and E-site tRNAs at 2.8A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

UUG*CG*CCUAAGGUAG*CGAAAA

Length

21 nucleotides

Bulged bases

5VP2|1|2A|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_5VP2_024 not in the Motif Atlas

Homologous match to J4_9DFE_008

Geometric discrepancy: 0.0802

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

5VP2|1|2A|U|1833
5VP2|1|2A|U|1834
5VP2|1|2A|G|1835
*
5VP2|1|2A|C|1905
5VP2|1|2A|G|1906
*
5VP2|1|2A|C|1924
5VP2|1|2A|C|1925
5VP2|1|2A|U|1926
5VP2|1|2A|A|1927
5VP2|1|2A|A|1928
5VP2|1|2A|G|1929
5VP2|1|2A|G|1930
5VP2|1|2A|U|1931
5VP2|1|2A|A|1932
5VP2|1|2A|G|1933
*
5VP2|1|2A|C|1967
5VP2|1|2A|G|1968
5VP2|1|2A|A|1969
5VP2|1|2A|A|1970
5VP2|1|2A|A|1971
5VP2|1|2A|A|1972

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA

Chain 2x

Transfer RNA; tRNA