IL_5NDK_226

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

GUC*GUC

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

IL_5NDK_226 not in the Motif Atlas

Geometric match to IL_4ZC7_004

Geometric discrepancy: 0.1495

The information below is about IL_4ZC7_004

Detailed Annotation

Isolated non-canonical cWW pair

Broad Annotation

Isolated non-canonical cWW pair

Motif group

IL_87907.2

Basepair signature

cWW-cWW-cWW

Number of instances in this motif group

179

Unit IDs

5NDK|1|1G|G|2033
5NDK|1|1G|U|2034
5NDK|1|1G|C|2035
*
5NDK|1|1G|G|2117
5NDK|1|1G|U|2118
5NDK|1|1G|C|2119

Current chains

Chain 1G

16S ribosomal RNA

Nearby chains

Chain 14

Large subunit ribosomal RNA; LSU rRNA

Chain W4

Transfer RNA; tRNA

Chain Y4

mRNA