J3_5VP2_055

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

CGAAG*CGCCAGAGAG*CGUAG

Length

20 nucleotides

Bulged bases

5VP2|1|1A|G|345

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_055 not in the Motif Atlas

Homologous match to J3_9DFE_006

Geometric discrepancy: 0.0611

The information below is about J3_9DFE_006

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_77124.1

Basepair signature

cWW-tSH-cHH-cSW-F-tHS-cWW-cWW-F-F-cWW-F

Number of instances in this motif group

4

Unit IDs

5VP2|1|1A|C|321
5VP2|1|1A|G|322
5VP2|1|1A|A|323
5VP2|1|1A|A|324
5VP2|1|1A|G|325
*
5VP2|1|1A|C|340
5VP2|1|1A|G|341
5VP2|1|1A|C|342
5VP2|1|1A|C|343
5VP2|1|1A|A|344
5VP2|1|1A|G|345
5VP2|1|1A|A|346
5VP2|1|1A|G|347
5VP2|1|1A|A|348
5VP2|1|1A|G|349
*
5VP2|1|1A|C|361
5VP2|1|1A|G|362
5VP2|1|1A|U|363
5VP2|1|1A|A|364
5VP2|1|1A|G|365

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 1F

50S ribosomal protein L4

Chain 1Y

50S ribosomal protein L24