J4_5HD1_024

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

GGGC*GAC*GGAAG*CGC

Length

15 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

J4_5HD1_024 not in the Motif Atlas

Homologous match to J4_9DFE_010

Geometric discrepancy: 0.0776

The information below is about J4_9DFE_010

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_77044.4

Basepair signature

cWW-F-tHS-F-cWW-cWW-cWW-F-cWW

Number of instances in this motif group

3

Unit IDs

5HD1|1|2A|G|2654
5HD1|1|2A|G|2655
5HD1|1|2A|G|2656
5HD1|1|2A|C|2657
*
5HD1|1|2A|G|2685
5HD1|1|2A|A|2686
5HD1|1|2A|C|2687
*
5HD1|1|2A|G|2743
5HD1|1|2A|G|2744
5HD1|1|2A|A|2745
5HD1|1|2A|A|2746
5HD1|1|2A|G|2747
*
5HD1|1|2A|C|2781
5HD1|1|2A|G|2782
5HD1|1|2A|C|2783

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2E

50S ribosomal protein L3

Chain 2N

50S ribosomal protein L13

Chain 2O

50S ribosomal protein L14