IL_5VP2_045

3D structure

PDB id

5VP2 (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the Thermus thermophilus 70S ribosome in complex with madumycin II and bound to mRNA and A-, P- and E-site tRNAs at 2.8A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.8 Å

Loop

Sequence

CGAUGAAG*UGGAG

Length

13 nucleotides

Bulged bases

5VP2|1|1A|U|1256

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_5VP2_045 not in the Motif Atlas

Homologous match to IL_9DFE_046

Geometric discrepancy: 0.0712

The information below is about IL_9DFE_046

Detailed Annotation

Kink-turn

Broad Annotation

No text annotation

Motif group

IL_90775.2

Basepair signature

cWW-tSS-tSH-L-tHS-tHS-cWW

Number of instances in this motif group

30

Unit IDs

5VP2|1|1A|C|1253
5VP2|1|1A|G|1254
5VP2|1|1A|A|1255
5VP2|1|1A|U|1256
5VP2|1|1A|G|1257
5VP2|1|1A|A|1258
5VP2|1|1A|A|1259
5VP2|1|1A|G|1260
*
5VP2|1|1A|U|1280
5VP2|1|1A|G|1281
5VP2|1|1A|G|1282
5VP2|1|1A|A|1283
5VP2|1|1A|G|1284

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 1U

50S ribosomal protein L20