HL_5VP2_121

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

UUGGGAAG

Length

8 nucleotides

Bulged bases

5VP2|1|2A|A|311

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_5VP2_121 not in the Motif Atlas

Homologous match to HL_9DFE_009

Geometric discrepancy: 0.1334

The information below is about HL_9DFE_009

Detailed Annotation

T-loop with 1 bulged base

Broad Annotation

T-loop

Motif group

HL_01609.3

Basepair signature

cWW-tWH-F-F-F

Number of instances in this motif group

18

Unit IDs

5VP2|1|2A|U|305
5VP2|1|2A|U|306
5VP2|1|2A|G|307
5VP2|1|2A|G|308
5VP2|1|2A|G|309
5VP2|1|2A|A|310
5VP2|1|2A|A|311
5VP2|1|2A|G|312

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2Y

50S ribosomal protein L24