IL_5HD1_253

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

CGAAAUUCCUUG*CCUG

Length

16 nucleotides

Bulged bases

5HD1|1|2A|A|1959, 5HD1|1|2A|U|1965, 5HD1|1|2A|U|1984

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_253 not in the Motif Atlas

Geometric match to IL_4WF9_077

Geometric discrepancy: 0.1214

The information below is about IL_4WF9_077

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

IL_42218.2

Basepair signature

cWW-L-R-cHW-cWW-L-L-L-R-L

Number of instances in this motif group

5

Unit IDs

5HD1|1|2A|C|1955
5HD1|1|2A|G|1956
5HD1|1|2A|A|1957
5HD1|1|2A|A|1958
5HD1|1|2A|A|1959
5HD1|1|2A|U|1960
5HD1|1|2A|U|1961
5HD1|1|2A|C|1962
5HD1|1|2A|C|1963
5HD1|1|2A|U|1964
5HD1|1|2A|U|1965
5HD1|1|2A|G|1966
*
5HD1|1|2A|C|1982
5HD1|1|2A|C|1983
5HD1|1|2A|U|1984
5HD1|1|2A|G|1985

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2D

50S ribosomal protein L2

Chain 2a

Small subunit ribosomal RNA; SSU rRNA