J3_5FDU_043

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

GCC*GCCUAGUGAACC*GAUCAAC

Length

22 nucleotides

Bulged bases

5FDU|1|1A|A|2400, 5FDU|1|1A|U|2402, 5FDU|1|1A|A|2438

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_5FDU_043 not in the Motif Atlas

Homologous match to J3_9DFE_015

Geometric discrepancy: 0.0441

The information below is about J3_9DFE_015

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_20992.1

Basepair signature

cWW-F-F-cWW-tHW-tHW-F-cWW-F-F-F-F-F

Number of instances in this motif group

5

Unit IDs

5FDU|1|1A|G|2294
5FDU|1|1A|C|2295
5FDU|1|1A|C|2296
*
5FDU|1|1A|G|2396
5FDU|1|1A|C|2397
5FDU|1|1A|C|2398
5FDU|1|1A|U|2399
5FDU|1|1A|A|2400
5FDU|1|1A|G|2401
5FDU|1|1A|U|2402
5FDU|1|1A|G|2403
5FDU|1|1A|A|2404
5FDU|1|1A|A|2405
5FDU|1|1A|C|2406
5FDU|1|1A|C|2407
*
5FDU|1|1A|G|2433
5FDU|1|1A|A|2434
5FDU|1|1A|U|2435
5FDU|1|1A|C|2436
5FDU|1|1A|A|2437
5FDU|1|1A|A|2438
5FDU|1|1A|C|2439

Current chains

Chain 1A

23S ribosomal RNA

Nearby chains

Chain 10

50S ribosomal protein L27

Chain 11

50S ribosomal protein L28

Chain 16

50S ribosomal protein L33

Chain 18

50S ribosomal protein L35

Chain 1P

50S ribosomal protein L15

Chain 1Z

50S ribosomal protein L25