J5_5VP2_001

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*CGAAUG*CG*CAC*GGG

Length

22 nucleotides

Bulged bases

5VP2|1|1A|U|49

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

J5_5VP2_001 not in the Motif Atlas

Homologous match to J5_9DFE_001

Geometric discrepancy: 0.063

The information below is about J5_9DFE_001

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_01737.2

Basepair signature

cWW-F-cWW-F-cWW-tSH-tHH-tHS-cWW-cWW-cWW-F

Number of instances in this motif group

5

Unit IDs

5VP2|1|1A|C|46
5VP2|1|1A|G|47
5VP2|1|1A|A|48
5VP2|1|1A|U|49
5VP2|1|1A|G|50
5VP2|1|1A|A|51
5VP2|1|1A|A|52
5VP2|1|1A|G|53
*
5VP2|1|1A|C|114
5VP2|1|1A|G|115
5VP2|1|1A|A|116
5VP2|1|1A|A|117
5VP2|1|1A|U|118
5VP2|1|1A|G|119
*
5VP2|1|1A|C|128
5VP2|1|1A|G|129
*
5VP2|1|1A|C|148
5VP2|1|1A|A|149
5VP2|1|1A|C|150
*
5VP2|1|1A|G|165
5VP2|1|1A|G|166
5VP2|1|1A|G|167

Current chains

Chain 1A

23S Ribosomal RNA

Nearby chains

Chain 17

50S ribosomal protein L34

Chain 1X

50S ribosomal protein L23