J4_5VP2_026

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

GGGC*GAC*GGAAG*CGC

Length

15 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

J4_5VP2_026 not in the Motif Atlas

Homologous match to J4_9DFE_010

Geometric discrepancy: 0.0759

The information below is about J4_9DFE_010

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_77044.5

Basepair signature

cWW-F-tHS-F-cWW-cWW-cWW-F-cWW

Number of instances in this motif group

3

Unit IDs

5VP2|1|2A|G|2643
5VP2|1|2A|G|2644
5VP2|1|2A|G|2645
5VP2|1|2A|C|2646
*
5VP2|1|2A|G|2674
5VP2|1|2A|A|2675
5VP2|1|2A|C|2676
*
5VP2|1|2A|G|2731
5VP2|1|2A|G|2732
5VP2|1|2A|A|2733
5VP2|1|2A|A|2734
5VP2|1|2A|G|2735
*
5VP2|1|2A|C|2769
5VP2|1|2A|G|2770
5VP2|1|2A|C|2771

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2E

50S ribosomal protein L3

Chain 2N

50S ribosomal protein L13

Chain 2O

50S ribosomal protein L14