HL_5NDJ_220

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

GUUCGAUUC

Length

9 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_220 not in the Motif Atlas

Homologous match to HL_4YYE_003

Geometric discrepancy: 0.1119

The information below is about HL_4YYE_003

Detailed Annotation

T-loop with 2 stacked bulged bases

Broad Annotation

T-loop

Motif group

HL_28252.9

Basepair signature

cWW-tWH-F-F-F-F-F

Number of instances in this motif group

141

Unit IDs

5NDJ|1|X1|G|53
5NDJ|1|X1|U|54
5NDJ|1|X1|U|55
5NDJ|1|X1|C|56
5NDJ|1|X1|G|57
5NDJ|1|X1|A|58
5NDJ|1|X1|U|59
5NDJ|1|X1|U|60
5NDJ|1|X1|C|61

Current chains

Chain X1

tRNA-Phe

Nearby chains

Chain 1H

Large subunit ribosomal RNA; LSU rRNA

Chain 41

50S ribosomal protein L5

Chain 88

50S ribosomal protein L16