J3_5D8B_025

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

CAAUG*CCCAGUUC*GCCG

Length

17 nucleotides

Bulged bases

5D8B|1|YC|U|1240, 5D8B|1|YC|U|1302

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_025 not in the Motif Atlas

Homologous match to J3_4LFB_009

Geometric discrepancy: 0.1458

The information below is about J3_4LFB_009

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_03192.1

Basepair signature

cWW-cSS-tHW-F-F-F-cWW-cWW-cSH-cSH-F

Number of instances in this motif group

5

Unit IDs

5D8B|1|YC|C|1237
5D8B|1|YC|A|1238
5D8B|1|YC|A|1239
5D8B|1|YC|U|1240
5D8B|1|YC|G|1241
*
5D8B|1|YC|C|1296
5D8B|1|YC|C|1297
5D8B|1|YC|C|1298
5D8B|1|YC|A|1299
5D8B|1|YC|G|1300
5D8B|1|YC|U|1301
5D8B|1|YC|U|1302
5D8B|1|YC|C|1303
*
5D8B|1|YC|G|1334
5D8B|1|YC|C|1335
5D8B|1|YC|C|1336
5D8B|1|YC|G|1337

Current chains

Chain YC

16S ribosomal RNA

Nearby chains

Chain DC

30S ribosomal protein S7

Chain JC

30S ribosomal protein S13

Chain RC

30S ribosomal protein Thx