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

Coloring options:


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