J4_5D8B_001

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

GUGG*CGU*AAGGUCG*CC

Length

16 nucleotides

Bulged bases

5D8B|1|BD|U|8, 5D8B|1|BD|U|47, 5D8B|1|BD|C|48

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_001 not in the Motif Atlas

Homologous match to J4_6UFG_001

Geometric discrepancy: 0.2003

The information below is about J4_6UFG_001

Detailed Annotation

tRNA junction

Broad Annotation

No text annotation

Motif group

J4_95067.1

Basepair signature

cWW-F-cWW-cWW-cHS-F-cWW-cWW

Number of instances in this motif group

48

Unit IDs

5D8B|1|BD|G|7
5D8B|1|BD|U|8
5D8B|1|BD|G|9
5D8B|1|BD|G|10
*
5D8B|1|BD|C|25
5D8B|1|BD|G|26
5D8B|1|BD|U|27
*
5D8B|1|BD|A|43
5D8B|1|BD|A|44
5D8B|1|BD|G|45
5D8B|1|BD|G|46
5D8B|1|BD|U|47
5D8B|1|BD|C|48
5D8B|1|BD|G|49
*
5D8B|1|BD|C|65
5D8B|1|BD|C|66

Current chains

Chain BD

tRNA

Nearby chains

Chain DC

30S ribosomal protein S7

Chain HC

30S ribosomal protein S11

Chain VB

50S ribosomal protein L33