IL_5NDJ_354

3D structure

PDB id

5NDJ (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of aminoglycoside TC007 in complex with 70S ribosome from Thermus thermophilus, three tRNAs and mRNA (soaking)

Experimental method

X-RAY DIFFRACTION

Resolution

3.15 Å

Loop

Sequence

CGG*CCCG

Length

7 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_5NDJ_354 not in the Motif Atlas

Geometric match to IL_5TBW_056

Geometric discrepancy: 0.3105

The information below is about IL_5TBW_056

Detailed Annotation

Major groove platform with extra cWW

Broad Annotation

No text annotation

Motif group

IL_63959.1

Basepair signature

cWW-cSH-cWW-cWW

Number of instances in this motif group

18

Unit IDs

5NDJ|1|1G|C|1285
5NDJ|1|1G|G|1286
5NDJ|1|1G|G|1287
*
5NDJ|1|1G|C|1376
5NDJ|1|1G|C|1377
5NDJ|1|1G|C|1378
5NDJ|1|1G|G|1379

Current chains

Chain 1G

16S ribosomal RNA

Nearby chains

Chain 6A

30S ribosomal protein S15