J5_5D8B_003

3D structure

PDB id

5D8B (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of T. thermophilus ribosome containing a P-site wobble mismatch

Experimental method

X-RAY DIFFRACTION

Resolution

3.63 Å

Loop

Sequence

CGAUGAAG*CGAAUG*CG*CAC*GGG

Length

22 nucleotides

Bulged bases

5D8B|1|VC|U|50

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_5D8B_003 not in the Motif Atlas

Homologous match to J5_5J7L_013

Geometric discrepancy: 0.0794

The information below is about J5_5J7L_013

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

5D8B|1|VC|C|47
5D8B|1|VC|G|48
5D8B|1|VC|A|49
5D8B|1|VC|U|50
5D8B|1|VC|G|51
5D8B|1|VC|A|52
5D8B|1|VC|A|53
5D8B|1|VC|G|54
*
5D8B|1|VC|C|116
5D8B|1|VC|G|117
5D8B|1|VC|A|118
5D8B|1|VC|A|119
5D8B|1|VC|U|120
5D8B|1|VC|G|121
*
5D8B|1|VC|C|130
5D8B|1|VC|G|131
*
5D8B|1|VC|C|148
5D8B|1|VC|A|149
5D8B|1|VC|C|150
*
5D8B|1|VC|G|176
5D8B|1|VC|G|177
5D8B|1|VC|G|178

Current chains

Chain VC

23S ribosomal RNA

Nearby chains

Chain AA

50S ribosomal protein L34

Chain R

50S ribosomal protein L23