J4_5D8B_008

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

CGAAG*CGCC*GAG*CGUAG

Length

17 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

J4_5D8B_008 not in the Motif Atlas

Homologous match to J4_4WF9_002

Geometric discrepancy: 0.0975

The information below is about J4_4WF9_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_16174.1

Basepair signature

cWW-tSH-cHH-F-F-tHS-cWW-cWW-F-F-cWW

Number of instances in this motif group

5

Unit IDs

5D8B|1|VC|C|297
5D8B|1|VC|G|298
5D8B|1|VC|A|299
5D8B|1|VC|A|300
5D8B|1|VC|G|301
*
5D8B|1|VC|C|316
5D8B|1|VC|G|317
5D8B|1|VC|C|318
5D8B|1|VC|C|319
*
5D8B|1|VC|G|323
5D8B|1|VC|A|324
5D8B|1|VC|G|325
*
5D8B|1|VC|C|337
5D8B|1|VC|G|338
5D8B|1|VC|U|339
5D8B|1|VC|A|340
5D8B|1|VC|G|341

Current chains

Chain VC

23S ribosomal RNA

Nearby chains

Chain C

50S ribosomal protein L4

Chain S

50S ribosomal protein L24