J5_9D7S_015

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

GCAAGUUGG*UG*CC*GUGAACAGG*CGC

Length

25 nucleotides

Bulged bases

9D7S|1|2A|G|1758, 9D7S|1|2A|G|1763

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_9D7S_015 not in the Motif Atlas

Homologous match to J5_9DFE_005

Geometric discrepancy: 0.0633

The information below is about J5_9DFE_005

Detailed Annotation

No text annotation

Broad Annotation

No text annotation

Motif group

J5_62523.6

Basepair signature

cWW-F-F-F-cWW-F-F-F-F-F-F-F-F-F-cWW-F-cWW-cWW

Number of instances in this motif group

7

Unit IDs

9D7S|1|2A|G|1674
9D7S|1|2A|C|1675
9D7S|1|2A|A|1676
9D7S|1|2A|A|1677
9D7S|1|2A|G|1678
9D7S|1|2A|U|1679
9D7S|1|2A|U|1680
9D7S|1|2A|G|1681
9D7S|1|2A|G|1682
*
9D7S|1|2A|U|1706
9D7S|1|2A|G|1707
*
9D7S|1|2A|C|1751
9D7S|1|2A|C|1752
*
9D7S|1|2A|G|1756
9D7S|1|2A|U|1757
9D7S|1|2A|G|1758
9D7S|1|2A|A|1759
9D7S|1|2A|A|1760
9D7S|1|2A|C|1761
9D7S|1|2A|A|1762
9D7S|1|2A|G|1763
9D7S|1|2A|G|1764
*
9D7S|1|2A|C|1988
9D7S|1|2A|G|1989
9D7S|1|2A|C|1990

Current chains

Chain 2A

23S Ribosomal RNA

Nearby chains

Chain 2E

50S ribosomal protein L3

Chain 2O

50S ribosomal protein L14

Chain 2T

50S ribosomal protein L19

Chain 2a

Small subunit ribosomal RNA; SSU rRNA