IL_5HD1_312

3D structure

PDB id

5HD1 (explore in PDB, NAKB, or RNA 3D Hub)

Description

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

Experimental method

X-RAY DIFFRACTION

Resolution

2.7 Å

Loop

Sequence

GUGCCAG*CGGUAAUAC

Length

16 nucleotides

Bulged bases

5HD1|1|2a|A|516, 5HD1|1|2a|U|518, 5HD1|1|2a|A|519

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_5HD1_312 not in the Motif Atlas

Geometric match to IL_4V88_415

Geometric discrepancy: 0.141

The information below is about IL_4V88_415

Detailed Annotation

Kink-turn related

Broad Annotation

No text annotation

Motif group

IL_54177.1

Basepair signature

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

Number of instances in this motif group

5

Unit IDs

5HD1|1|2a|G|499
5HD1|1|2a|U|500
5HD1|1|2a|G|501
5HD1|1|2a|C|502
5HD1|1|2a|C|503
5HD1|1|2a|A|504
5HD1|1|2a|G|505
*
5HD1|1|2a|C|512
5HD1|1|2a|G|513
5HD1|1|2a|G|514
5HD1|1|2a|U|515
5HD1|1|2a|A|516
5HD1|1|2a|A|517
5HD1|1|2a|U|518
5HD1|1|2a|A|519
5HD1|1|2a|C|520

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