J5_1VY7_006

3D structure

PDB id

1VY7 (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-Cytidine-Puromycin in the A site and acylated tRNA in the P site.

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

CGACUC*GGAC*GUUC*GC*GCGAAUG

Length

23 nucleotides

Bulged bases

1VY7|1|BA|U|1255

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

J5_1VY7_006 not in the Motif Atlas

Homologous match to J5_9DFE_004

Geometric discrepancy: 0.0373

The information below is about J5_9DFE_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_74302.6

Basepair signature

cWW-tSH-tSS-tHW-F-cHS-F-tWS-cWW-cWW-F-cWW-cWW-F

Number of instances in this motif group

4

Unit IDs

1VY7|1|BA|C|584
1VY7|1|BA|G|585
1VY7|1|BA|A|586
1VY7|1|BA|C|587
1VY7|1|BA|U|588
1VY7|1|BA|C|589
*
1VY7|1|BA|G|668
1VY7|1|BA|G|669
1VY7|1|BA|A|670
1VY7|1|BA|C|671
*
1VY7|1|BA|G|809
1VY7|1|BA|U|810
1VY7|1|BA|U|811
1VY7|1|BA|C|812
*
1VY7|1|BA|G|1195
1VY7|1|BA|C|1196
*
1VY7|1|BA|G|1250
1VY7|1|BA|C|1251
1VY7|1|BA|G|1252
1VY7|1|BA|A|1253
1VY7|1|BA|A|1254
1VY7|1|BA|U|1255
1VY7|1|BA|G|1256

Current chains

Chain BA

23S Ribosomal RNA

Nearby chains

Chain B8

50S ribosomal protein L35

Chain BF

50S ribosomal protein L4

Chain BP

50S ribosomal protein L15

Chain BU

50S ribosomal protein L20

Chain BV

50S ribosomal protein L21