J5_5FDU_017

3D structure

PDB id

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

Description

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

Experimental method

X-RAY DIFFRACTION

Resolution

2.9 Å

Loop

Sequence

UUUA*UUUG*CG*CG*CGGAUAAAA

Length

21 nucleotides

Bulged bases

5FDU|1|2A|U|2076, 5FDU|1|2A|G|2428, 5FDU|1|2A|G|2429, 5FDU|1|2A|A|2430, 5FDU|1|2A|U|2431

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

J5_5FDU_017 not in the Motif Atlas

Homologous match to J5_9DFE_007

Geometric discrepancy: 0.0477

The information below is about J5_9DFE_007

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_39529.1

Basepair signature

cWW-cWH-cWH-F-cWW-F-F-cWW-F-cWW-cWW

Number of instances in this motif group

3

Unit IDs

5FDU|1|2A|U|2074
5FDU|1|2A|U|2075
5FDU|1|2A|U|2076
5FDU|1|2A|A|2077
*
5FDU|1|2A|U|2243
5FDU|1|2A|U|2244
5FDU|1|2A|U|2245
5FDU|1|2A|G|2246
*
5FDU|1|2A|C|2258
5FDU|1|2A|G|2259
*
5FDU|1|2A|C|2281
5FDU|1|2A|G|2282
*
5FDU|1|2A|C|2427
5FDU|1|2A|G|2428
5FDU|1|2A|G|2429
5FDU|1|2A|A|2430
5FDU|1|2A|U|2431
5FDU|1|2A|A|2432
5FDU|1|2A|A|2433
5FDU|1|2A|A|2434
5FDU|1|2A|A|2435

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 20

50S ribosomal protein L27

Chain 21

50S ribosomal protein L28

Chain 26

50S ribosomal protein L33

Chain 2D

50S ribosomal protein L2

Chain 2P

50S ribosomal protein L15

Chain 2Z

50S ribosomal protein L25