J3_5NDK_070

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

CGAAG*CGCCAGAGAG*CGUAG

Length

20 nucleotides

Bulged bases

5NDK|1|1H|G|346

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_5NDK_070 not in the Motif Atlas

Homologous match to J3_9DFE_006

Geometric discrepancy: 0.0628

The information below is about J3_9DFE_006

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_77124.1

Basepair signature

cWW-tSH-cHH-cSW-F-tHS-cWW-cWW-F-F-cWW-F

Number of instances in this motif group

4

Unit IDs

5NDK|1|1H|C|322
5NDK|1|1H|G|323
5NDK|1|1H|A|324
5NDK|1|1H|A|325
5NDK|1|1H|G|326
*
5NDK|1|1H|C|341
5NDK|1|1H|G|342
5NDK|1|1H|C|343
5NDK|1|1H|C|344
5NDK|1|1H|A|345
5NDK|1|1H|G|346
5NDK|1|1H|A|347
5NDK|1|1H|G|348
5NDK|1|1H|A|349
5NDK|1|1H|G|350
*
5NDK|1|1H|C|362
5NDK|1|1H|G|363
5NDK|1|1H|U|364
5NDK|1|1H|A|365
5NDK|1|1H|G|366

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 31

50S ribosomal protein L4

Chain G8

50S ribosomal protein L24