HL_5NDW_118

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

UUGGAACA

Length

8 nucleotides

Bulged bases

5NDW|1|5|C|200

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_118 not in the Motif Atlas

Homologous match to HL_8C3A_005

Geometric discrepancy: 0.0981

The information below is about HL_8C3A_005

Detailed Annotation

T-loop with 2 stacked bulged bases

Broad Annotation

T-loop

Motif group

HL_58705.1

Basepair signature

cWW-tWH-F-F-F

Number of instances in this motif group

23

Unit IDs

5NDW|1|5|U|194
5NDW|1|5|U|195
5NDW|1|5|G|196
5NDW|1|5|G|197
5NDW|1|5|A|198
5NDW|1|5|A|199
5NDW|1|5|C|200
5NDW|1|5|A|201

Current chains

Chain 5

25S ribosomal RNA

Nearby chains

Chain l4

60S ribosomal protein L4-A

Chain n6

60S ribosomal protein L26-A

Chain o2

60S ribosomal protein L32