J4_5NDK_018

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

CU*GAGUAC*GGAAUCUG*UAAG

Length

20 nucleotides

Bulged bases

5NDK|1|1H|U|433

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_018 not in the Motif Atlas

Homologous match to J4_9DFE_001

Geometric discrepancy: 0.1351

The information below is about J4_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_94698.1

Basepair signature

cWW-cWW-cSS-F-tHH-cWW-cSH-tWH-F-tHS-cWW

Number of instances in this motif group

10

Unit IDs

5NDK|1|1H|C|258
5NDK|1|1H|U|259
*
5NDK|1|1H|G|398
5NDK|1|1H|A|399
5NDK|1|1H|G|400
5NDK|1|1H|U|401
5NDK|1|1H|A|402
5NDK|1|1H|C|403
*
5NDK|1|1H|G|427
5NDK|1|1H|G|428
5NDK|1|1H|A|429
5NDK|1|1H|A|430
5NDK|1|1H|U|431
5NDK|1|1H|C|432
5NDK|1|1H|U|433
5NDK|1|1H|G|434
*
5NDK|1|1H|U|450
5NDK|1|1H|A|451
5NDK|1|1H|A|452
5NDK|1|1H|G|453

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 61

50S ribosomal protein L9

Chain J8

50S ribosomal protein L28