HL_5NDK_162

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

CGAUAACG

Length

8 nucleotides

Bulged bases

5NDK|1|1H|U|1005, 5NDK|1|1H|C|1008

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

HL_5NDK_162 not in the Motif Atlas

Homologous match to HL_7RQB_027

Geometric discrepancy: 0.0624

The information below is about HL_7RQB_027

Detailed Annotation

GNRA

Broad Annotation

No text annotation

Motif group

HL_35490.2

Basepair signature

cWW-tSH-F-F

Number of instances in this motif group

299

Unit IDs

5NDK|1|1H|C|1002
5NDK|1|1H|G|1003
5NDK|1|1H|A|1004
5NDK|1|1H|U|1005
5NDK|1|1H|A|1006
5NDK|1|1H|A|1007
5NDK|1|1H|C|1008
5NDK|1|1H|G|1009

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 16

5S ribosomal RNA; 5S rRNA

Chain 88

50S ribosomal protein L16