IL_5NDK_099

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

CUAAGUG*CUUAAG

Length

13 nucleotides

Bulged bases

5NDK|1|14|U|1190, 5NDK|1|14|A|1192

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_099 not in the Motif Atlas

Geometric match to IL_4WF9_039

Geometric discrepancy: 0.1093

The information below is about IL_4WF9_039

Detailed Annotation

Kink-turn related

Broad Annotation

No text annotation

Motif group

IL_57188.6

Basepair signature

cWW-tWW-L-tWW-cWW-cSH

Number of instances in this motif group

6

Unit IDs

5NDK|1|14|C|1066
5NDK|1|14|U|1067
5NDK|1|14|A|1068
5NDK|1|14|A|1069
5NDK|1|14|G|1070
5NDK|1|14|U|1071
5NDK|1|14|G|1072
*
5NDK|1|14|C|1188
5NDK|1|14|U|1189
5NDK|1|14|U|1190
5NDK|1|14|A|1191
5NDK|1|14|A|1192
5NDK|1|14|G|1193

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 15

50S ribosomal protein L13

Chain 59

50S ribosomal protein L6