3D structure

PDB id
5HCQ (explore in PDB, NAKB, or RNA 3D Hub)
Description
Crystal structure of antimicrobial peptide Oncocin d15-19 bound to the Thermus thermophilus 70S ribosome
Experimental method
X-RAY DIFFRACTION
Resolution
2.8 Å

Loop

Sequence
GGG*CGAAAG*CCCUAAACGAUG*CC
Length
23 nucleotides
Bulged bases
5HCQ|1|1a|A|799
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_5HCQ_013 not in the Motif Atlas
Homologous match to J4_4LFB_003
Geometric discrepancy: 0.0457
The information below is about J4_4LFB_003
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
J4_61885.6
Basepair signature
cWW-cWW-cWW-F-F-tHW-F-F-F-F-F-cWW-F-F
Number of instances in this motif group
4

Unit IDs

5HCQ|1|1a|G|559
5HCQ|1|1a|G|560
5HCQ|1|1a|G|561
*
5HCQ|1|1a|C|748
5HCQ|1|1a|G|749
5HCQ|1|1a|A|750
5HCQ|1|1a|A|751
5HCQ|1|1a|A|752
5HCQ|1|1a|G|753
*
5HCQ|1|1a|C|794
5HCQ|1|1a|C|795
5HCQ|1|1a|C|796
5HCQ|1|1a|U|797
5HCQ|1|1a|A|798
5HCQ|1|1a|A|799
5HCQ|1|1a|A|800
5HCQ|1|1a|C|801
5HCQ|1|1a|G|802
5HCQ|1|1a|A|803
5HCQ|1|1a|U|804
5HCQ|1|1a|G|805
*
5HCQ|1|1a|C|857
5HCQ|1|1a|C|858

Current chains

Chain 1a
16S Ribosomal RNA

Nearby chains

Chain 1A
Large subunit ribosomal RNA; LSU rRNA
Chain 1h
30S ribosomal protein S8
Chain 1l
30S ribosomal protein S12
Chain 1o
30S ribosomal protein S15
Chain 1q
30S ribosomal protein S17

Coloring options:


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