IL_5NDK_264

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

UAG*CA

Length

5 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

IL_5NDK_264 not in the Motif Atlas

Homologous match to IL_7RQB_032

Geometric discrepancy: 0.3349

The information below is about IL_7RQB_032

Detailed Annotation

Minor groove platform

Broad Annotation

No text annotation

Motif group

IL_80097.1

Basepair signature

cWW-tHS-cWW

Number of instances in this motif group

17

Unit IDs

5NDK|1|1H|U|926
5NDK|1|1H|A|927
5NDK|1|1H|G|928
*
5NDK|1|1H|C|946
5NDK|1|1H|A|947

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 88

50S ribosomal protein L16

Chain H8

50S ribosomal protein L25

Chain W1

Transfer RNA; tRNA