J4_5NDK_005

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*CGCC*GAG*CGUAG

Length

17 nucleotides

Bulged bases

None detected

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_005 not in the Motif Atlas

Homologous match to J4_9DFE_002

Geometric discrepancy: 0.0733

The information below is about J4_9DFE_002

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_16174.1

Basepair signature

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

Number of instances in this motif group

5

Unit IDs

5NDK|1|14|C|322
5NDK|1|14|G|323
5NDK|1|14|A|324
5NDK|1|14|A|325
5NDK|1|14|G|326
*
5NDK|1|14|C|341
5NDK|1|14|G|342
5NDK|1|14|C|343
5NDK|1|14|C|344
*
5NDK|1|14|G|348
5NDK|1|14|A|349
5NDK|1|14|G|350
*
5NDK|1|14|C|362
5NDK|1|14|G|363
5NDK|1|14|U|364
5NDK|1|14|A|365
5NDK|1|14|G|366

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 39

50S ribosomal protein L4

Chain C5

50S ribosomal protein L24