J3_9D7S_056

3D structure

PDB id

9D7S (explore in PDB, NAKB, or RNA 3D Hub)

Description

Crystal structure of the wild-type Thermus thermophilus 70S ribosome in complex with Api antimicrobial peptide, mRNA, A-site release factor 1, and deacylated P-site and E-site tRNAphe at 2.85A resolution

Experimental method

X-RAY DIFFRACTION

Resolution

2.85 Å

Loop

Sequence

GCCUAAG*UAGGAAUCU*AGC

Length

19 nucleotides

Bulged bases

9D7S|1|2a|C|48, 9D7S|1|2a|A|50, 9D7S|1|2a|A|51

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_9D7S_056 not in the Motif Atlas

Homologous match to J3_4LFB_014

Geometric discrepancy: 0.0609

The information below is about J3_4LFB_014

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J3_46317.4

Basepair signature

cWW-cWW-cSW-F-cWW-F-F-F-F-cWW-F-F-F-F

Number of instances in this motif group

4

Unit IDs

9D7S|1|2a|G|46
9D7S|1|2a|C|47
9D7S|1|2a|C|48
9D7S|1|2a|U|49
9D7S|1|2a|A|50
9D7S|1|2a|A|51
9D7S|1|2a|G|52
*
9D7S|1|2a|U|359
9D7S|1|2a|A|360
9D7S|1|2a|G|361
9D7S|1|2a|G|362
9D7S|1|2a|A|363
9D7S|1|2a|A|364
9D7S|1|2a|U|365
9D7S|1|2a|C|366
9D7S|1|2a|U|367
*
9D7S|1|2a|A|393
9D7S|1|2a|G|394
9D7S|1|2a|C|395

Current chains

Chain 2a

16S Ribosomal RNA

Nearby chains

Chain 2l

30S ribosomal protein S12

Chain 2p

30S ribosomal protein S16