3D structure

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

Loop

Sequence
AAAAGACC*GGAUAACA*UCG(2MA)UGUC*GGUUCAG*CGGUCU
Length
37 nucleotides
Bulged bases
5FDU|1|2A|A|2062, 5FDU|1|2A|A|2448, 5FDU|1|2A|U|2449, 5FDU|1|2A|U|2585, 5FDU|1|2A|U|2609
QA status
Modified nucleotides: 2MA

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
Detailed Annotation
No text annotation
Broad Annotation
No text annotation
Motif group
Not in a motif group
Basepair signature
Not available
Number of instances in this motif group
0

Unit IDs

5FDU|1|2A|A|2057
5FDU|1|2A|A|2058
5FDU|1|2A|A|2059
5FDU|1|2A|A|2060
5FDU|1|2A|G|2061
5FDU|1|2A|A|2062
5FDU|1|2A|C|2063
5FDU|1|2A|C|2064
*
5FDU|1|2A|G|2446
5FDU|1|2A|G|2447
5FDU|1|2A|A|2448
5FDU|1|2A|U|2449
5FDU|1|2A|A|2450
5FDU|1|2A|A|2451
5FDU|1|2A|C|2452
5FDU|1|2A|A|2453
*
5FDU|1|2A|U|2500
5FDU|1|2A|C|2501
5FDU|1|2A|G|2502
5FDU|1|2A|2MA|2503
5FDU|1|2A|U|2504
5FDU|1|2A|G|2505
5FDU|1|2A|U|2506
5FDU|1|2A|C|2507
*
5FDU|1|2A|G|2582
5FDU|1|2A|G|2583
5FDU|1|2A|U|2584
5FDU|1|2A|U|2585
5FDU|1|2A|C|2586
5FDU|1|2A|A|2587
5FDU|1|2A|G|2588
*
5FDU|1|2A|C|2606
5FDU|1|2A|G|2607
5FDU|1|2A|G|2608
5FDU|1|2A|U|2609
5FDU|1|2A|C|2610
5FDU|1|2A|U|2611

Current chains

Chain 2A
23S ribosomal RNA

Nearby chains

Chain 25
50S ribosomal protein L32
Chain 2D
50S ribosomal protein L2
Chain 2E
50S ribosomal protein L3
Chain 2F
50S ribosomal protein L4
Chain 2P
50S ribosomal protein L15
Chain 2Q
50S ribosomal protein L16
Chain 2y
Metalnikowin I

Coloring options:

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