IL_5NDK_350

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

UGUAG*CGAAG

Length

10 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_350 not in the Motif Atlas

Homologous match to IL_9DFE_026

Geometric discrepancy: 0.0993

The information below is about IL_9DFE_026

Detailed Annotation

5x5 Sarcin-Ricin with intercalated A; G-bulge

Broad Annotation

Sarcin-Ricin; G-bulge

Motif group

IL_38862.5

Basepair signature

cWW-cSH-R-tWH-tHS-cWW

Number of instances in this motif group

6

Unit IDs

5NDK|1|14|U|907
5NDK|1|14|G|908
5NDK|1|14|U|909
5NDK|1|14|A|910
5NDK|1|14|G|911
*
5NDK|1|14|C|963
5NDK|1|14|G|964
5NDK|1|14|A|965
5NDK|1|14|A|966
5NDK|1|14|G|967

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 1J

5S ribosomal RNA; 5S rRNA

Chain 45

50S ribosomal protein L16

Chain E5

50S ribosomal protein L27