IL_5NDK_070

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

GC*GUC

Length

5 nucleotides

Bulged bases

5NDK|1|14|U|275

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_070 not in the Motif Atlas

Geometric match to IL_5TBW_125

Geometric discrepancy: 0.3645

The information below is about IL_5TBW_125

Detailed Annotation

Single bulged U

Broad Annotation

No text annotation

Motif group

IL_83039.19

Basepair signature

cWW-L-cWW

Number of instances in this motif group

123

Unit IDs

5NDK|1|14|G|270
5NDK|1|14|C|271
*
5NDK|1|14|G|274
5NDK|1|14|U|275
5NDK|1|14|C|276

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 69

50S ribosomal protein L9

Chain F5

50S ribosomal protein L28