IL_5NDK_319

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

AG*CCU

Length

5 nucleotides

Bulged bases

None detected

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_319 not in the Motif Atlas

Geometric match to IL_7RQB_091

Geometric discrepancy: 0.0607

The information below is about IL_7RQB_091

Detailed Annotation

Single stack bend

Broad Annotation

No text annotation

Motif group

IL_76488.4

Basepair signature

cWW-L-cWW

Number of instances in this motif group

36

Unit IDs

5NDK|1|1H|A|2468
5NDK|1|1H|G|2469
*
5NDK|1|1H|C|2513
5NDK|1|1H|C|2514
5NDK|1|1H|U|2515

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 21

50S ribosomal protein L3

Chain I8

50S ribosomal protein L27

Chain W1

Transfer RNA; tRNA