HL_5NDW_120

3D structure

PDB id

5NDW (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of aminoglycoside TC007 bound to the yeast 80S ribosome

Experimental method

X-RAY DIFFRACTION

Resolution

3.7 Å

Loop

Sequence

GUGAGAAUC

Length

9 nucleotides

Bulged bases

5NDW|1|5|G|218, 5NDW|1|5|A|219, 5NDW|1|5|G|220

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_5NDW_120 not in the Motif Atlas

Homologous match to HL_5TBW_007

Geometric discrepancy: 0.1059

The information below is about HL_5TBW_007

Detailed Annotation

T-loop with unstacked turn

Broad Annotation

T-loop

Motif group

HL_08002.12

Basepair signature

cWW-cWW-F-tWH

Number of instances in this motif group

16

Unit IDs

5NDW|1|5|G|216
5NDW|1|5|U|217
5NDW|1|5|G|218
5NDW|1|5|A|219
5NDW|1|5|G|220
5NDW|1|5|A|221
5NDW|1|5|A|222
5NDW|1|5|U|223
5NDW|1|5|C|224

Current chains

Chain 5

25S ribosomal RNA

Nearby chains

Chain 8

5.8S ribosomal RNA; 5.8S rRNA

Chain l4

60S ribosomal protein L4-A

Chain n6

60S ribosomal protein L26-A