J3_5D8B_048

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

AC*GAUAAGC*GAUGU

Length

14 nucleotides

Bulged bases

5D8B|1|VC|U|72, 5D8B|1|VC|A|74

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

J3_5D8B_048 not in the Motif Atlas

Homologous match to J3_9DFE_004

Geometric discrepancy: 0.1261

The information below is about J3_9DFE_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_01004.1

Basepair signature

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

Number of instances in this motif group

10

Unit IDs

5D8B|1|VC|A|56
5D8B|1|VC|C|57
*
5D8B|1|VC|G|70
5D8B|1|VC|A|71
5D8B|1|VC|U|72
5D8B|1|VC|A|73
5D8B|1|VC|A|74
5D8B|1|VC|G|75
5D8B|1|VC|C|76
*
5D8B|1|VC|G|110
5D8B|1|VC|A|111
5D8B|1|VC|U|112
5D8B|1|VC|G|113
5D8B|1|VC|U|114

Current chains

Chain VC

23S ribosomal RNA

Nearby chains

Chain AA

50S ribosomal protein L34

Chain R

50S ribosomal protein L23

Chain W

50S ribosomal protein L29