J5_5VP2_011

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

CUAAAC*GGGUCGUG*CGAGUAC*GGAAUCUG*UAAG

Length

33 nucleotides

Bulged bases

5VP2|1|2A|C|271|||Z, 5VP2|1|2A|U|272|||A, 5VP2|1|2A|U|405

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

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

5VP2|1|2A|C|268
5VP2|1|2A|U|269
5VP2|1|2A|A|270
5VP2|1|2A|A|271
5VP2|1|2A|A|271|||A
5VP2|1|2A|C|271|||B
*
5VP2|1|2A|G|271|||V
5VP2|1|2A|G|271|||W
5VP2|1|2A|G|271|||X
5VP2|1|2A|U|271|||Y
5VP2|1|2A|C|271|||Z
5VP2|1|2A|G|272
5VP2|1|2A|U|272|||A
5VP2|1|2A|G|272|||B
*
5VP2|1|2A|C|366
5VP2|1|2A|G|370
5VP2|1|2A|A|371
5VP2|1|2A|G|372
5VP2|1|2A|U|373
5VP2|1|2A|A|374
5VP2|1|2A|C|375
*
5VP2|1|2A|G|399
5VP2|1|2A|G|400
5VP2|1|2A|A|401
5VP2|1|2A|A|402
5VP2|1|2A|U|403
5VP2|1|2A|C|404
5VP2|1|2A|U|405
5VP2|1|2A|G|406
*
5VP2|1|2A|U|421
5VP2|1|2A|A|422
5VP2|1|2A|A|423
5VP2|1|2A|G|424

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 21

50S ribosomal protein L28

Chain 2I

50S ribosomal protein L9