J4_9D7S_017

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

CGAUAAA*UC*GCGC*GG

Length

15 nucleotides

Bulged bases

9D7S|1|2A|G|1271, 9D7S|1|2A|A|1272, 9D7S|1|2A|U|1273, 9D7S|1|2A|G|1647

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

J4_9D7S_017 not in the Motif Atlas

Homologous match to J4_9DFE_003

Geometric discrepancy: 0.063

The information below is about J4_9DFE_003

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J4_64571.5

Basepair signature

cWW-F-cWW-tSS-cWW-F-cWW

Number of instances in this motif group

4

Unit IDs

9D7S|1|2A|C|1270
9D7S|1|2A|G|1271
9D7S|1|2A|A|1272
9D7S|1|2A|U|1273
9D7S|1|2A|A|1274
9D7S|1|2A|A|1275
9D7S|1|2A|A|1276
*
9D7S|1|2A|U|1294
9D7S|1|2A|C|1295
*
9D7S|1|2A|G|1645
9D7S|1|2A|C|1646
9D7S|1|2A|G|1647
9D7S|1|2A|C|1648
*
9D7S|1|2A|G|2009
9D7S|1|2A|G|2010

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 25

50S ribosomal protein L32

Chain 2R

50S ribosomal protein L17

Chain 2W

50S ribosomal protein L22