IL_5NDK_192

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

GGACG*CGGUAC

Length

11 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_192 not in the Motif Atlas

Geometric match to IL_4LFB_018

Geometric discrepancy: 0.1433

The information below is about IL_4LFB_018

Detailed Annotation

6x5 Sarcin-Ricin; G-bulge

Broad Annotation

Sarcin-Ricin; G-bulge

Motif group

IL_82100.1

Basepair signature

cWW-tWW-cSH-tWH-tHS-cWW

Number of instances in this motif group

3

Unit IDs

5NDK|1|1G|G|1086
5NDK|1|1G|G|1087
5NDK|1|1G|A|1088
5NDK|1|1G|C|1089
5NDK|1|1G|G|1090
*
5NDK|1|1G|C|1113
5NDK|1|1G|G|1114
5NDK|1|1G|G|1115
5NDK|1|1G|U|1116
5NDK|1|1G|A|1117
5NDK|1|1G|C|1118

Current chains

Chain 1G

16S ribosomal RNA

Nearby chains

Chain 32

30S ribosomal protein S4

Chain 7A

30S ribosomal protein S16