J4_5VP2_030

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

A(4SU)AG*CAG*CGU(7MG)UCCU*AGU

Length

18 nucleotides

Bulged bases

5VP2|1|2w|4SU|8, 5VP2|1|2w|U|47, 5VP2|1|2w|C|48

QA status

Modified nucleotides: 4SU, 7MG

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

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

Not in a motif group

Basepair signature

Not available

Number of instances in this motif group

0

Unit IDs

5VP2|1|2w|A|7
5VP2|1|2w|4SU|8
5VP2|1|2w|A|9
5VP2|1|2w|G|10
*
5VP2|1|2w|C|25
5VP2|1|2w|A|26
5VP2|1|2w|G|27
*
5VP2|1|2w|C|43
5VP2|1|2w|G|44
5VP2|1|2w|U|45
5VP2|1|2w|7MG|46
5VP2|1|2w|U|47
5VP2|1|2w|C|48
5VP2|1|2w|C|49
5VP2|1|2w|U|50
*
5VP2|1|2w|A|64
5VP2|1|2w|G|65
5VP2|1|2w|U|66

Current chains

Chain 2w

A-site and E-site tRNAs

Nearby chains

Chain 2A

Large subunit ribosomal RNA; LSU rRNA

Chain 2Q

50S ribosomal protein L16