IL_5NDK_043

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

GG*UCAGC

Length

7 nucleotides

Bulged bases

5NDK|1|13|C|1827, 5NDK|1|13|A|1828

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_043 not in the Motif Atlas

Homologous match to IL_5J7L_048

Geometric discrepancy: 0.1005

The information below is about IL_5J7L_048

Detailed Annotation

Minor groove platform

Broad Annotation

No text annotation

Motif group

IL_95583.2

Basepair signature

cWW-L-cWW

Number of instances in this motif group

11

Unit IDs

5NDK|1|13|G|1685
5NDK|1|13|G|1686
*
5NDK|1|13|U|1826
5NDK|1|13|C|1827
5NDK|1|13|A|1828
5NDK|1|13|G|1829
5NDK|1|13|C|1830

Current chains

Chain 13

16S ribosomal RNA

Nearby chains

Chain 1I

30S ribosomal protein S10

Chain 2E

30S ribosomal protein S3

Chain 5I

30S ribosomal protein S14 type Z