J4_5NDK_026

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

CAAAG*CUGAC*GGG*CGG

Length

16 nucleotides

Bulged bases

5NDK|1|1H|A|2303, 5NDK|1|1H|G|2397

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

J4_5NDK_026 not in the Motif Atlas

Homologous match to J4_9DFE_009

Geometric discrepancy: 0.1608

The information below is about J4_9DFE_009

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_04930.6

Basepair signature

cWW-F-F-tWW-tHH-cWW-cWW-cHW-cWW

Number of instances in this motif group

7

Unit IDs

5NDK|1|1H|C|2300
5NDK|1|1H|A|2301
5NDK|1|1H|A|2302
5NDK|1|1H|A|2303
5NDK|1|1H|G|2304
*
5NDK|1|1H|C|2358
5NDK|1|1H|U|2359
5NDK|1|1H|G|2360
5NDK|1|1H|A|2361
5NDK|1|1H|C|2362
*
5NDK|1|1H|G|2385
5NDK|1|1H|G|2386
5NDK|1|1H|G|2387
*
5NDK|1|1H|C|2396
5NDK|1|1H|G|2397
5NDK|1|1H|G|2398

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain A8

50S ribosomal protein L18

Chain I8

50S ribosomal protein L27

Chain Q8

50S ribosomal protein L35