J4_5VP2_001

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

CU*GAGUAC*GGAAUCUG*UAAG

Length

20 nucleotides

Bulged bases

5VP2|1|1A|U|432

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_5VP2_001 not in the Motif Atlas

Homologous match to J4_9DFE_001

Geometric discrepancy: 0.0684

The information below is about J4_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_94698.1

Basepair signature

cWW-cWW-cSS-F-tHH-cWW-cSH-tWH-F-tHS-cWW

Number of instances in this motif group

10

Unit IDs

5VP2|1|1A|C|257
5VP2|1|1A|U|258
*
5VP2|1|1A|G|397
5VP2|1|1A|A|398
5VP2|1|1A|G|399
5VP2|1|1A|U|400
5VP2|1|1A|A|401
5VP2|1|1A|C|402
*
5VP2|1|1A|G|426
5VP2|1|1A|G|427
5VP2|1|1A|A|428
5VP2|1|1A|A|429
5VP2|1|1A|U|430
5VP2|1|1A|C|431
5VP2|1|1A|U|432
5VP2|1|1A|G|433
*
5VP2|1|1A|U|448
5VP2|1|1A|A|449
5VP2|1|1A|A|450
5VP2|1|1A|G|451

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 11

50S ribosomal protein L28

Chain 1I

50S ribosomal protein L9