IL_5FDU_325

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

GGAGUACG*UGAAAC

Length

14 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_325 not in the Motif Atlas

Homologous match to IL_4LFB_034

Geometric discrepancy: 0.0808

The information below is about IL_4LFB_034

Detailed Annotation

8x6 Sarcin-Ricin with inserted Y; G-bulge

Broad Annotation

Sarcin-Ricin; G-bulge

Motif group

IL_41756.4

Basepair signature

cWW-tSH-tHH-cSH-tWH-tHS-cWW-L

Number of instances in this motif group

4

Unit IDs

5FDU|1|2a|G|887
5FDU|1|2a|G|888
5FDU|1|2a|A|889
5FDU|1|2a|G|890
5FDU|1|2a|U|891
5FDU|1|2a|A|892
5FDU|1|2a|C|893
5FDU|1|2a|G|894
*
5FDU|1|2a|U|905
5FDU|1|2a|G|906
5FDU|1|2a|A|907
5FDU|1|2a|A|908
5FDU|1|2a|A|909
5FDU|1|2a|C|910

Current chains

Chain 2a

16S ribosomal RNA

Nearby chains

Chain 2l

30S ribosomal protein S12

Chain 2q

30S ribosomal protein S17