IL_5FDU_312

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

G(PSU)GCCAG*CGGUAAUAC

Length

16 nucleotides

Bulged bases

5FDU|1|2a|A|532, 5FDU|1|2a|U|534, 5FDU|1|2a|A|535

QA status

Modified nucleotides: PSU

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

IL_5FDU_312 not in the Motif Atlas

Homologous match to IL_4LFB_021

Geometric discrepancy: 0.0763

The information below is about IL_4LFB_021

Detailed Annotation

Kink-turn related

Broad Annotation

No text annotation

Motif group

IL_54177.4

Basepair signature

cWW-cSW-tWH-L-R-L-R-tHS-cWW

Number of instances in this motif group

4

Unit IDs

5FDU|1|2a|G|515
5FDU|1|2a|PSU|516
5FDU|1|2a|G|517
5FDU|1|2a|C|518
5FDU|1|2a|C|519
5FDU|1|2a|A|520
5FDU|1|2a|G|521
*
5FDU|1|2a|C|528
5FDU|1|2a|G|529
5FDU|1|2a|G|530
5FDU|1|2a|U|531
5FDU|1|2a|A|532
5FDU|1|2a|A|533
5FDU|1|2a|U|534
5FDU|1|2a|A|535
5FDU|1|2a|C|536

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2c

30S ribosomal protein S3

Chain 2d

30S ribosomal protein S4

Chain 2l

30S ribosomal protein S12

Chain 2x

Ribosome-associated inhibitor A