HL_5NDK_215

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

CAGUCGGUAG

Length

10 nucleotides

Bulged bases

5NDK|1|W4|U|16, 5NDK|1|W4|C|17, 5NDK|1|W4|G|18, 5NDK|1|W4|G|19, 5NDK|1|W4|U|20

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_215 not in the Motif Atlas

Homologous match to HL_6JXM_001

Geometric discrepancy: 0.202

The information below is about HL_6JXM_001

Detailed Annotation

tRNA D-loop

Broad Annotation

No text annotation

Motif group

HL_20811.4

Basepair signature

cWW-cWS-F

Number of instances in this motif group

14

Unit IDs

5NDK|1|W4|C|13
5NDK|1|W4|A|14
5NDK|1|W4|G|15
5NDK|1|W4|U|16
5NDK|1|W4|C|17
5NDK|1|W4|G|18
5NDK|1|W4|G|19
5NDK|1|W4|U|20
5NDK|1|W4|A|21
5NDK|1|W4|G|22

Current chains

Chain W4

tRNA-Phe

Nearby chains

Chain 14

Large subunit ribosomal RNA; LSU rRNA

Chain X4

Transfer RNA; tRNA