HL_5NDK_088

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

CGCAAGGG

Length

8 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

HL_5NDK_088 not in the Motif Atlas

Homologous match to HL_7RQB_056

Geometric discrepancy: 0.0612

The information below is about HL_7RQB_056

Detailed Annotation

Pseudoknot geometry

Broad Annotation

No text annotation

Motif group

HL_12078.4

Basepair signature

cWW-F-F-F-F-F

Number of instances in this motif group

31

Unit IDs

5NDK|1|14|C|2339
5NDK|1|14|G|2340
5NDK|1|14|C|2341
5NDK|1|14|A|2342
5NDK|1|14|A|2343
5NDK|1|14|G|2344
5NDK|1|14|G|2345
5NDK|1|14|G|2346

Current chains

Chain 14

23S ribosomal RNA

Nearby chains

Chain 45

50S ribosomal protein L16

Chain 49

50S ribosomal protein L5

Chain E5

50S ribosomal protein L27

Chain X4

Transfer RNA; tRNA