HL_5NDJ_102

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

GGCGAC

Length

6 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_5NDJ_102 not in the Motif Atlas

Homologous match to HL_4V9F_072

Geometric discrepancy: 0.1082

The information below is about HL_4V9F_072

Detailed Annotation

GNRA

Broad Annotation

No text annotation

Motif group

HL_37824.8

Basepair signature

cWW-F-F-F-F

Number of instances in this motif group

352

Unit IDs

5NDJ|1|16|G|88
5NDJ|1|16|G|89
5NDJ|1|16|C|90
5NDJ|1|16|G|91
5NDJ|1|16|A|92
5NDJ|1|16|C|93

Current chains

Chain 16

5S ribosomal RNA

Nearby chains

Chain 1H

Large subunit ribosomal RNA; LSU rRNA

Chain 88

50S ribosomal protein L16

Chain H8

50S ribosomal protein L25