IL_5FDU_202

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

UGUAG*CGAAG

Length

10 nucleotides

Bulged bases

None detected

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

IL_5FDU_202 not in the Motif Atlas

Geometric match to IL_7RQB_027

Geometric discrepancy: 0.047

The information below is about IL_7RQB_027

Detailed Annotation

5x5 Sarcin-Ricin with intercalated A; G-bulge

Broad Annotation

Sarcin-Ricin; G-bulge

Motif group

IL_38862.1

Basepair signature

cWW-L-R-tWH-tHS-cWW

Number of instances in this motif group

4

Unit IDs

5FDU|1|2A|U|858
5FDU|1|2A|G|859
5FDU|1|2A|U|860
5FDU|1|2A|A|861
5FDU|1|2A|G|862
*
5FDU|1|2A|C|915
5FDU|1|2A|G|916
5FDU|1|2A|A|917
5FDU|1|2A|A|918
5FDU|1|2A|G|919

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 20

50S ribosomal protein L27

Chain 23

50S ribosomal protein L30

Chain 2B

5S ribosomal RNA; 5S rRNA

Chain 2Q

50S ribosomal protein L16