J4_5D8B_011

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

GGUUC*GGUUAG*CU*ACCCGUAC

Length

21 nucleotides

Bulged bases

5D8B|1|VC|U|1341

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_011 not in the Motif Atlas

Homologous match to J4_4WF9_005

Geometric discrepancy: 0.1009

The information below is about J4_4WF9_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_77353.1

Basepair signature

cWW-F-cWW-F-tHW-F-cWW-F-F-F-F-F-cWW-cWW

Number of instances in this motif group

8

Unit IDs

5D8B|1|VC|G|1310
5D8B|1|VC|G|1311
5D8B|1|VC|U|1312
5D8B|1|VC|U|1313
5D8B|1|VC|C|1314
*
5D8B|1|VC|G|1338
5D8B|1|VC|G|1339
5D8B|1|VC|U|1340
5D8B|1|VC|U|1341
5D8B|1|VC|A|1342
5D8B|1|VC|G|1343
*
5D8B|1|VC|C|1404
5D8B|1|VC|U|1405
*
5D8B|1|VC|A|1597
5D8B|1|VC|C|1598
5D8B|1|VC|C|1599
5D8B|1|VC|C|1600
5D8B|1|VC|G|1601
5D8B|1|VC|U|1602
5D8B|1|VC|A|1603
5D8B|1|VC|C|1604

Current chains

Chain VC

23S ribosomal RNA

Nearby chains

Chain AA

50S ribosomal protein L34

Chain R

50S ribosomal protein L23