J3_5FDU_055

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

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

5FDU|1|2A|U|504, 5FDU|1|2A|G|508

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_5FDU_055 not in the Motif Atlas

Homologous match to J3_9DFE_002

Geometric discrepancy: 0.0457

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

5FDU|1|2A|G|30
5FDU|1|2A|C|31
*
5FDU|1|2A|G|474
5FDU|1|2A|U|475
5FDU|1|2A|G|476
5FDU|1|2A|A|477
5FDU|1|2A|A|478
5FDU|1|2A|A|479
5FDU|1|2A|A|480
5FDU|1|2A|G|481
5FDU|1|2A|A|482
5FDU|1|2A|A|483
5FDU|1|2A|C|484
*
5FDU|1|2A|G|496
5FDU|1|2A|A|497
5FDU|1|2A|G|498
5FDU|1|2A|U|499
5FDU|1|2A|G|500
5FDU|1|2A|A|501
5FDU|1|2A|A|502
5FDU|1|2A|A|503
5FDU|1|2A|U|504
5FDU|1|2A|A|505
5FDU|1|2A|G|506
5FDU|1|2A|A|507
5FDU|1|2A|G|508
5FDU|1|2A|C|509
5FDU|1|2A|C|510

Current chains

Chain 2A

23S ribosomal RNA

Nearby chains

Chain 2U

50S ribosomal protein L20

Chain 2W

50S ribosomal protein L22

Chain 2Y

50S ribosomal protein L24