J3_5VP2_003

3D structure

PDB id

5VP2 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in complex with madumycin II and bound to mRNA and A-, P- and E-site tRNAs at 2.8A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

UAAAC*GGGUCGUG*CG

Length

15 nucleotides

Bulged bases

5VP2|1|1A|U|288

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_5VP2_003 not in the Motif Atlas

Homologous match to J3_9DFE_005

Geometric discrepancy: 0.1538

The information below is about J3_9DFE_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_97971.2

Basepair signature

cWW-F-F-tSH-cSH-tWH-tWS-cWW-F-cWW

Number of instances in this motif group

3

Unit IDs

5VP2|1|1A|U|258
5VP2|1|1A|A|259
5VP2|1|1A|A|260
5VP2|1|1A|A|261
5VP2|1|1A|C|262
*
5VP2|1|1A|G|282
5VP2|1|1A|G|283
5VP2|1|1A|G|284
5VP2|1|1A|U|285
5VP2|1|1A|C|286
5VP2|1|1A|G|287
5VP2|1|1A|U|288
5VP2|1|1A|G|289
*
5VP2|1|1A|C|396
5VP2|1|1A|G|397

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 11

50S ribosomal protein L28

Chain 1I

50S ribosomal protein L9