J3_5D8B_046

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

GC*GUGAAAAGAAC*GAGUGAAAUAGAGCC

Length

28 nucleotides

Bulged bases

5D8B|1|VC|U|504, 5D8B|1|VC|G|508

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

J3_5D8B_046 not in the Motif Atlas

Homologous match to J3_4WF9_011

Geometric discrepancy: 0.2479

The information below is about J3_4WF9_011

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_17917.1

Basepair signature

cWW-tWH-cSS-cWW-tSH-tHH-cWW-F-F-tWW-tSS-cSS-tWW-tSH-tWH-cSW-F-tHS-cWW-F

Number of instances in this motif group

9

Unit IDs

5D8B|1|VC|G|30
5D8B|1|VC|C|31
*
5D8B|1|VC|G|474
5D8B|1|VC|U|475
5D8B|1|VC|G|476
5D8B|1|VC|A|477
5D8B|1|VC|A|478
5D8B|1|VC|A|479
5D8B|1|VC|A|480
5D8B|1|VC|G|481
5D8B|1|VC|A|482
5D8B|1|VC|A|483
5D8B|1|VC|C|484
*
5D8B|1|VC|G|496
5D8B|1|VC|A|497
5D8B|1|VC|G|498
5D8B|1|VC|U|499
5D8B|1|VC|G|500
5D8B|1|VC|A|501
5D8B|1|VC|A|502
5D8B|1|VC|A|503
5D8B|1|VC|U|504
5D8B|1|VC|A|505
5D8B|1|VC|G|506
5D8B|1|VC|A|507
5D8B|1|VC|G|508
5D8B|1|VC|C|509
5D8B|1|VC|C|510

Current chains

Chain VC

23S ribosomal RNA

Nearby chains

Chain O

50S ribosomal protein L20

Chain Q

50S ribosomal protein L22

Chain S

50S ribosomal protein L24