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
GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC
Length
28 nucleotides
Bulged bases
5HD1|1|1A|U|528, 5HD1|1|1A|G|532
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
J3_5HD1_033 not in the Motif Atlas
Homologous match to J3_9DFE_002
Geometric discrepancy: 0.0422
The information below is about J3_9DFE_002
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
J3_92134.2
Basepair signature
cWW-cWW-cWW-F-tWH-cSS-tSS-tSH-tSH-tWW-tHH-tWH-tWW-F-F-cSS-cSW-F-tHS-cWW
Number of instances in this motif group
6

Unit IDs

5HD1|1|1A|G|29
5HD1|1|1A|C|30
*
5HD1|1|1A|G|499
5HD1|1|1A|U|500
5HD1|1|1A|G|501
5HD1|1|1A|A|502
5HD1|1|1A|A|503
5HD1|1|1A|A|504
5HD1|1|1A|A|505
5HD1|1|1A|G|506
5HD1|1|1A|A|507
5HD1|1|1A|A|508
5HD1|1|1A|C|509
*
5HD1|1|1A|G|520
5HD1|1|1A|A|521
5HD1|1|1A|G|522
5HD1|1|1A|U|523
5HD1|1|1A|G|524
5HD1|1|1A|A|525
5HD1|1|1A|A|526
5HD1|1|1A|A|527
5HD1|1|1A|U|528
5HD1|1|1A|A|529
5HD1|1|1A|G|530
5HD1|1|1A|A|531
5HD1|1|1A|G|532
5HD1|1|1A|C|533
5HD1|1|1A|C|534

Current chains

Chain 1A
23S Ribosomal RNA

Nearby chains

Chain 1U
50S ribosomal protein L20
Chain 1W
50S ribosomal protein L22
Chain 1Y
50S ribosomal protein L24

Coloring options:


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