J3_5NDK_071

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

GGGACG*CC*GAAAAGC

Length

15 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

J3_5NDK_071 not in the Motif Atlas

Homologous match to J3_9DFE_013

Geometric discrepancy: 0.0601

The information below is about J3_9DFE_013

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_34864.3

Basepair signature

cWW-tSH-tSH-tHH-F-F-cWW-F-cWW

Number of instances in this motif group

4

Unit IDs

5NDK|1|1H|G|1473
5NDK|1|1H|G|1474
5NDK|1|1H|G|1475
5NDK|1|1H|A|1476
5NDK|1|1H|C|1477
5NDK|1|1H|G|1478
*
5NDK|1|1H|C|1614
5NDK|1|1H|C|1615
*
5NDK|1|1H|G|1618
5NDK|1|1H|A|1619
5NDK|1|1H|A|1620
5NDK|1|1H|A|1621
5NDK|1|1H|A|1622
5NDK|1|1H|G|1623
5NDK|1|1H|C|1624

Current chains

Chain 1H

23S ribosomal RNA

Nearby chains

Chain 11

50S ribosomal protein L2