J4_5HD1_001

3D structure

PDB id

5HD1 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of antimicrobial peptide Pyrrhocoricin bound to the Thermus thermophilus 70S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

2.7 Å

Loop

Sequence

CU*GAGUAC*GGAAUCUG*UAAG

Length

20 nucleotides

Bulged bases

5HD1|1|1A|U|431

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_5HD1_001 not in the Motif Atlas

Homologous match to J4_9DFE_001

Geometric discrepancy: 0.0699

The information below is about J4_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_45801.6

Basepair signature

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

Number of instances in this motif group

7

Unit IDs

5HD1|1|1A|C|256
5HD1|1|1A|U|257
*
5HD1|1|1A|G|396
5HD1|1|1A|A|397
5HD1|1|1A|G|398
5HD1|1|1A|U|399
5HD1|1|1A|A|400
5HD1|1|1A|C|401
*
5HD1|1|1A|G|425
5HD1|1|1A|G|426
5HD1|1|1A|A|427
5HD1|1|1A|A|428
5HD1|1|1A|U|429
5HD1|1|1A|C|430
5HD1|1|1A|U|431
5HD1|1|1A|G|432
*
5HD1|1|1A|U|447
5HD1|1|1A|A|448
5HD1|1|1A|A|449
5HD1|1|1A|G|450

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 11

50S ribosomal protein L28