IL_5VP2_032

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

GG*CUAC

Length

6 nucleotides

Bulged bases

5VP2|1|1A|A|942

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_032 not in the Motif Atlas

Geometric match to IL_8DP3_001

Geometric discrepancy: 0.3597

The information below is about IL_8DP3_001

Detailed Annotation

Major groove platform

Broad Annotation

Major groove platform

Motif group

IL_15011.2

Basepair signature

cWW-L-cWW

Number of instances in this motif group

54

Unit IDs

5VP2|1|1A|G|928
5VP2|1|1A|G|929
*
5VP2|1|1A|C|940
5VP2|1|1A|U|941
5VP2|1|1A|A|942
5VP2|1|1A|C|943

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 1Z

50S ribosomal protein L25

Chain 1w

Transfer RNA; tRNA