J4_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

CGAUAAA*UC*GCGC*GG

Length

15 nucleotides

Bulged bases

1VY6|1|BA|G|1271, 1VY6|1|BA|A|1272, 1VY6|1|BA|U|1273, 1VY6|1|BA|G|1647

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_1VY6_007 not in the Motif Atlas

Homologous match to J4_9DFE_003

Geometric discrepancy: 0.0757

The information below is about J4_9DFE_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_64571.6

Basepair signature

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

Number of instances in this motif group

4

Unit IDs

1VY6|1|BA|C|1270
1VY6|1|BA|G|1271
1VY6|1|BA|A|1272
1VY6|1|BA|U|1273
1VY6|1|BA|A|1274
1VY6|1|BA|A|1275
1VY6|1|BA|A|1276
*
1VY6|1|BA|U|1294
1VY6|1|BA|C|1295
*
1VY6|1|BA|G|1645
1VY6|1|BA|C|1646
1VY6|1|BA|G|1647
1VY6|1|BA|C|1648
*
1VY6|1|BA|G|2009
1VY6|1|BA|G|2010

Current chains

Chain BA

23S Ribosomal RNA

Nearby chains

Chain B5

50S ribosomal protein L32

Chain BR

50S ribosomal protein L17

Chain BW

50S ribosomal protein L22