IL_5NDK_281

3D structure

PDB id

5NDK (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of aminoglycoside TC007 co-crystallized with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA

Experimental method

X-RAY DIFFRACTION

Resolution

2.95 Å

Loop

Sequence

GCAAUG*CAGC

Length

10 nucleotides

Bulged bases

5NDK|1|1H|G|1381

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

IL_5NDK_281 not in the Motif Atlas

Geometric match to IL_4V88_408

Geometric discrepancy: 0.3657

The information below is about IL_4V88_408

Detailed Annotation

C-loop with extra cWW pair

Broad Annotation

C-loop

Motif group

IL_11347.2

Basepair signature

cWW-cWW-L-cWW-L

Number of instances in this motif group

3

Unit IDs

5NDK|1|1H|G|1368
5NDK|1|1H|C|1369
5NDK|1|1H|A|1370
5NDK|1|1H|A|1371
5NDK|1|1H|U|1372
5NDK|1|1H|G|1373
*
5NDK|1|1H|C|1379
5NDK|1|1H|A|1380
5NDK|1|1H|G|1381
5NDK|1|1H|C|1382

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain E8

50S ribosomal protein L22

Chain F8

50S ribosomal protein L23