J3_1VY6_007

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

UUUAAUUC*GAAGAACCUUAC*GGCGA

Length

25 nucleotides

Bulged bases

1VY6|1|AA|A|975, 1VY6|1|AA|G|976, 1VY6|1|AA|A|978

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_007 not in the Motif Atlas

Homologous match to J3_4LFB_004

Geometric discrepancy: 0.0626

The information below is about J3_4LFB_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_88451.1

Basepair signature

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

Number of instances in this motif group

5

Unit IDs

1VY6|1|AA|U|955
1VY6|1|AA|U|956
1VY6|1|AA|U|957
1VY6|1|AA|A|958
1VY6|1|AA|A|959
1VY6|1|AA|U|960
1VY6|1|AA|U|961
1VY6|1|AA|C|962
*
1VY6|1|AA|G|973
1VY6|1|AA|A|974
1VY6|1|AA|A|975
1VY6|1|AA|G|976
1VY6|1|AA|A|977
1VY6|1|AA|A|978
1VY6|1|AA|C|979
1VY6|1|AA|C|980
1VY6|1|AA|U|981
1VY6|1|AA|U|982
1VY6|1|AA|A|983
1VY6|1|AA|C|984
*
1VY6|1|AA|G|1221
1VY6|1|AA|G|1222
1VY6|1|AA|C|1223
1VY6|1|AA|G|1224
1VY6|1|AA|A|1225

Current chains

Chain AA

16S Ribosomal RNA

Nearby chains

Chain AJ

30S ribosomal protein S10

Chain AM

30S ribosomal protein S13

Chain AN

30S ribosomal protein S14 type Z

Chain AS

30S ribosomal protein S19