J4_5D8B_009

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

CGAG*CGUAG*CGAG*CGUCUAG

Length

20 nucleotides

Bulged bases

5D8B|1|VC|U|654

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_009 not in the Motif Atlas

Homologous match to J4_5J7L_020

Geometric discrepancy: 0.4862

The information below is about J4_5J7L_020

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_60168.1

Basepair signature

cWW-F-F-F-F-F-cWW-F-F-F-cWW-F-tSS-F-cWW

Number of instances in this motif group

2

Unit IDs

5D8B|1|VC|C|601
5D8B|1|VC|G|602
5D8B|1|VC|A|603
5D8B|1|VC|G|604
*
5D8B|1|VC|C|624
5D8B|1|VC|G|625
5D8B|1|VC|U|626
5D8B|1|VC|A|627
5D8B|1|VC|G|628
*
5D8B|1|VC|C|635
5D8B|1|VC|G|636
5D8B|1|VC|A|637
5D8B|1|VC|G|638
*
5D8B|1|VC|C|650
5D8B|1|VC|G|651
5D8B|1|VC|U|652
5D8B|1|VC|C|653
5D8B|1|VC|U|654
5D8B|1|VC|A|655
5D8B|1|VC|G|656

Current chains

Chain VC

23S ribosomal RNA

Nearby chains

Chain BA

50S ribosomal protein L35

Chain C

50S ribosomal protein L4

Chain J

50S ribosomal protein L15