J3_5FDU_013

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

UUUAAUUC*GAAGAACCUUAC*GGCGA

Length

25 nucleotides

Bulged bases

5FDU|1|1a|A|975, 5FDU|1|1a|G|976, 5FDU|1|1a|A|978

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_013 not in the Motif Atlas

Homologous match to J3_4LFB_004

Geometric discrepancy: 0.0549

The information below is about J3_4LFB_004

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_83516.4

Basepair signature

cWW-tWW-F-F-F-F-F-tSS-cWW-F-F-cWW-F-F-F-F-F-F

Number of instances in this motif group

4

Unit IDs

5FDU|1|1a|U|955
5FDU|1|1a|U|956
5FDU|1|1a|U|957
5FDU|1|1a|A|958
5FDU|1|1a|A|959
5FDU|1|1a|U|960
5FDU|1|1a|U|961
5FDU|1|1a|C|962
*
5FDU|1|1a|G|973
5FDU|1|1a|A|974
5FDU|1|1a|A|975
5FDU|1|1a|G|976
5FDU|1|1a|A|977
5FDU|1|1a|A|978
5FDU|1|1a|C|979
5FDU|1|1a|C|980
5FDU|1|1a|U|981
5FDU|1|1a|U|982
5FDU|1|1a|A|983
5FDU|1|1a|C|984
*
5FDU|1|1a|G|1221
5FDU|1|1a|G|1222
5FDU|1|1a|C|1223
5FDU|1|1a|G|1224
5FDU|1|1a|A|1225

Current chains

Chain 1a

16S ribosomal RNA

Nearby chains

Chain 1j

30S ribosomal protein S10

Chain 1m

30S ribosomal protein S13

Chain 1n

30S ribosomal protein S14 type Z

Chain 1s

30S ribosomal protein S19

Chain 1x

Ribosome-associated inhibitor A