J3_1VY6_013

3D structure

PDB id

1VY6 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing short substrate-mimic Cytidine-Puromycin in the A site and acylated tRNA in the P site.

Experimental method

X-RAY DIFFRACTION

Resolution

2.9 Å

Loop

Sequence

CAAUG*CCCAGUUC*GCCG

Length

17 nucleotides

Bulged bases

1VY6|1|AA|U|1240

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_1VY6_013 not in the Motif Atlas

Homologous match to J3_4LFB_009

Geometric discrepancy: 0.1131

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

1VY6|1|AA|C|1237
1VY6|1|AA|A|1238
1VY6|1|AA|A|1239
1VY6|1|AA|U|1240
1VY6|1|AA|G|1241
*
1VY6|1|AA|C|1296
1VY6|1|AA|C|1297
1VY6|1|AA|C|1298
1VY6|1|AA|A|1299
1VY6|1|AA|G|1300
1VY6|1|AA|U|1301
1VY6|1|AA|U|1302
1VY6|1|AA|C|1303
*
1VY6|1|AA|G|1334
1VY6|1|AA|C|1335
1VY6|1|AA|C|1336
1VY6|1|AA|G|1337

Current chains

Chain AA

16S Ribosomal RNA

Nearby chains

Chain AG

30S ribosomal protein S7

Chain AM

30S ribosomal protein S13

Chain AU

30S ribosomal protein Thx