HL_5D8B_100

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

CGCAAGGG

Length

8 nucleotides

Bulged bases

None detected

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

HL_5D8B_100 not in the Motif Atlas

Homologous match to HL_7RQB_056

Geometric discrepancy: 0.108

The information below is about HL_7RQB_056

Detailed Annotation

Pseudoknot geometry

Broad Annotation

No text annotation

Motif group

HL_12078.4

Basepair signature

cWW-F-F-F-F-F

Number of instances in this motif group

31

Unit IDs

5D8B|1|VC|C|2324
5D8B|1|VC|G|2325
5D8B|1|VC|C|2326
5D8B|1|VC|A|2327
5D8B|1|VC|A|2328
5D8B|1|VC|G|2329
5D8B|1|VC|G|2330
5D8B|1|VC|G|2331

Current chains

Chain VC

23S ribosomal RNA

Nearby chains

Chain D

50S ribosomal protein L5

Chain ED

Transfer RNA; tRNA

Chain U

50S ribosomal protein L27